Starting phenix.real_space_refine on Thu Jun 12 17:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7p_41988/06_2025/8u7p_41988_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.094 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 3 5.49 5 S 64 5.16 5 C 9187 2.51 5 N 2272 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6851 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 876} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 6811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6811 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 876} Chain breaks: 3 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 238 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 186 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.86, per 1000 atoms: 0.70 Number of scatterers: 14086 At special positions: 0 Unit cell: (113.16, 118.68, 131.1, 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 64 16.00 P 3 15.00 O 2560 8.00 N 2272 7.00 C 9187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.0 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 72.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.628A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 4.346A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.847A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.913A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.929A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 254 removed outlier: 4.082A pdb=" N SER A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 3.583A pdb=" N VAL A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 298 through 319 Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.321A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.645A pdb=" N GLU A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.732A pdb=" N TYR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.635A pdb=" N TRP A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.618A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.199A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.686A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 572 through 600 removed outlier: 3.747A pdb=" N HIS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.922A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 639 through 652 removed outlier: 4.460A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 854 removed outlier: 4.624A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 4.246A pdb=" N LYS A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.913A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.922A pdb=" N ALA A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 932 " --> pdb=" O HIS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 962 removed outlier: 3.850A pdb=" N TRP A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 972 removed outlier: 3.788A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.646A pdb=" N THR A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1106 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1120 Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.714A pdb=" N LYS B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.510A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 4.321A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.788A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.665A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.952A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'B' and resid 180 through 189 removed outlier: 4.199A pdb=" N LEU B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 223 through 253 removed outlier: 4.055A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.836A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.562A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 336 removed outlier: 4.450A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 removed outlier: 3.640A pdb=" N GLU B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.719A pdb=" N TYR B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.595A pdb=" N GLY B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.680A pdb=" N TRP B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.697A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.249A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.779A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 572 through 600 removed outlier: 3.584A pdb=" N HIS B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.926A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 639 through 652 removed outlier: 4.364A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 854 removed outlier: 4.511A pdb=" N LYS B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 854 " --> pdb=" O VAL B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.524A pdb=" N LEU B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 882 " --> pdb=" O VAL B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.129A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.667A pdb=" N ALA B 927 " --> pdb=" O ASP B 923 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 929 " --> pdb=" O MET B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 962 removed outlier: 4.633A pdb=" N ASN B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.535A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1049 removed outlier: 3.928A pdb=" N VAL B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1081 removed outlier: 3.793A pdb=" N THR B1081 " --> pdb=" O ILE B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1106 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1120 Processing helix chain 'B' and resid 1121 through 1123 No H-bonds generated for 'chain 'B' and resid 1121 through 1123' Processing sheet with id=AA1, first strand: chain 'A' and resid 980 through 982 removed outlier: 6.393A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id=AA3, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 4.025A pdb=" N PHE A1136 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A1174 " --> pdb=" O PHE A1136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1142 through 1149 removed outlier: 6.211A pdb=" N VAL A1145 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A1189 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 980 through 982 removed outlier: 6.362A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 999 " --> pdb=" O ILE B1042 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id=AA7, first strand: chain 'B' and resid 1135 through 1137 removed outlier: 3.964A pdb=" N PHE B1136 " --> pdb=" O LEU B1174 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B1174 " --> pdb=" O PHE B1136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1142 through 1149 removed outlier: 6.289A pdb=" N VAL B1145 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL B1189 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2548 1.33 - 1.45: 3444 1.45 - 1.58: 8270 1.58 - 1.70: 6 1.70 - 1.82: 116 Bond restraints: 14384 Sorted by residual: bond pdb=" C35 AJP A1404 " pdb=" O34 AJP A1404 " ideal model delta sigma weight residual 1.380 1.421 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C45 AJP B1402 " pdb=" O44 AJP B1402 " ideal model delta sigma weight residual 1.375 1.414 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C65 AJP A1404 " pdb=" O64 AJP A1404 " ideal model delta sigma weight residual 1.373 1.412 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.413 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C45 AJP A1404 " pdb=" O44 AJP A1404 " ideal model delta sigma weight residual 1.375 1.411 -0.036 2.00e-02 2.50e+03 3.25e+00 ... (remaining 14379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18988 2.33 - 4.67: 521 4.67 - 7.00: 89 7.00 - 9.34: 37 9.34 - 11.67: 9 Bond angle restraints: 19644 Sorted by residual: angle pdb=" N LEU B 94 " pdb=" CA LEU B 94 " pdb=" C LEU B 94 " ideal model delta sigma weight residual 113.23 118.79 -5.56 1.24e+00 6.50e-01 2.01e+01 angle pdb=" C ALA A 274 " pdb=" N GLY A 275 " pdb=" CA GLY A 275 " ideal model delta sigma weight residual 121.87 115.48 6.39 1.57e+00 4.06e-01 1.65e+01 angle pdb=" CB LYS A 218 " pdb=" CG LYS A 218 " pdb=" CD LYS A 218 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CB MET B 154 " pdb=" CG MET B 154 " pdb=" SD MET B 154 " ideal model delta sigma weight residual 112.70 124.37 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C HIS A 502 " pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 121.14 115.08 6.06 1.75e+00 3.27e-01 1.20e+01 ... (remaining 19639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 8652 28.64 - 57.28: 332 57.28 - 85.93: 47 85.93 - 114.57: 58 114.57 - 143.21: 19 Dihedral angle restraints: 9108 sinusoidal: 3865 harmonic: 5243 Sorted by residual: dihedral pdb=" O31 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual 177.28 34.07 143.21 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C29 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual 299.04 157.15 141.89 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C45 AJP B1403 " pdb=" C49 AJP B1403 " pdb=" O50 AJP B1403 " pdb=" C48 AJP B1403 " ideal model delta sinusoidal sigma weight residual -62.82 67.42 -130.24 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 9105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1857 0.057 - 0.113: 508 0.113 - 0.170: 73 0.170 - 0.226: 9 0.226 - 0.283: 5 Chirality restraints: 2452 Sorted by residual: chirality pdb=" C35 AJP B1403 " pdb=" C36 AJP B1403 " pdb=" O34 AJP B1403 " pdb=" O40 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB THR B 466 " pdb=" CA THR B 466 " pdb=" OG1 THR B 466 " pdb=" CG2 THR B 466 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2449 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 392 " 0.012 2.00e-02 2.50e+03 1.86e-02 6.91e+00 pdb=" CG TYR B 392 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 392 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 392 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 392 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 392 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 392 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 392 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 837 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C TYR A 837 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR A 837 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 838 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 835 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C LEU A 835 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 835 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 836 " -0.014 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1736 2.75 - 3.29: 15053 3.29 - 3.83: 23849 3.83 - 4.36: 25379 4.36 - 4.90: 42171 Nonbonded interactions: 108188 Sorted by model distance: nonbonded pdb=" O VAL B 423 " pdb=" OG1 THR B 426 " model vdw 2.214 3.040 nonbonded pdb=" O VAL A 423 " pdb=" OG1 THR A 426 " model vdw 2.232 3.040 nonbonded pdb=" O ASN A 831 " pdb=" OG SER A 834 " model vdw 2.237 3.040 nonbonded pdb=" O VAL A 123 " pdb=" OG1 THR A 127 " model vdw 2.238 3.040 nonbonded pdb=" OD2 ASP A 129 " pdb=" O42 AJP A1404 " model vdw 2.238 3.040 ... (remaining 108183 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 955 or (resid 956 and (name N or name CA or nam \ e C or name O or name CB )) or resid 957 through 969 or (resid 970 through 977 a \ nd (name N or name CA or name C or name O or name CB )) or resid 978 through 982 \ or (resid 983 and (name N or name CA or name C or name O or name CB )) or resid \ 984 through 986 or (resid 987 and (name N or name CA or name C or name O or nam \ e CB )) or resid 988 through 992 or (resid 993 through 994 and (name N or name C \ A or name C or name O or name CB )) or resid 995 through 1066 or (resid 1067 and \ (name N or name CA or name C or name O or name CB )) or resid 1068 through 1097 \ or (resid 1098 through 1099 and (name N or name CA or name C or name O or name \ CB )) or resid 1100 through 1101 or (resid 1102 and (name N or name CA or name C \ or name O or name CB )) or resid 1103 through 1109 or (resid 1110 and (name N o \ r name CA or name C or name O or name CB )) or resid 1111 through 1114 or (resid \ 1115 through 1116 and (name N or name CA or name C or name O or name CB )) or r \ esid 1117 through 1128 or (resid 1129 through 1131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1132 through 1141 or (resid 1142 and (name \ N or name CA or name C or name O or name CB )) or resid 1143 through 1174 or (re \ sid 1175 through 1183 and (name N or name CA or name C or name O or name CB )) o \ r resid 1184 through 1185 or (resid 1186 through 1187 and (name N or name CA or \ name C or name O or name CB )) or resid 1188 through 1191 or (resid 1401 and (na \ me C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C3 or name C31 or name C32 or name 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 C310 or name C311 or name C312)) or resid 1403)) selection = (chain 'B' and (resid 76 through 970 or (resid 971 through 977 and (name N or na \ me CA or name C or name O or name CB )) or resid 978 through 1076 or (resid 1077 \ through 1079 and (name N or name CA or name C or name O or name CB )) or resid \ 1080 through 1087 or (resid 1088 through 1089 and (name N or name CA or name C o \ r name O or name CB )) or resid 1090 through 1136 or (resid 1137 and (name N or \ name CA or name C or name O or name CB )) or resid 1138 or (resid 1139 through 1 \ 142 and (name N or name CA or name C or name O or name CB )) or resid 1143 throu \ gh 1150 or (resid 1151 through 1152 and (name N or name CA or name C or name O o \ r name CB )) or resid 1153 through 1158 or (resid 1159 and (name N or name CA or \ name C or name O or name CB )) or resid 1160 through 1191 or (resid 1401 and (n \ ame C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C3 or name C31 or name C32 or name 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 C310 or name C311 or name C312)) or (resid 1403 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C32 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C41 or name C55 or name C56 or name C57 or name C58 or name C59 or na \ me C61 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 o \ r name O31 or name O33 or name O34 or name O40 or name O42 or name O43 or name O \ 44 or name O54 or name O60 or name O62 or name O63 or name O64 or name O76 or na \ me O77 or name O78 or name O79 or name O82 or name O84)))) } 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.500 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.004 0.041 14384 Z= 0.210 Angle : 0.952 11.674 19644 Z= 0.448 Chirality : 0.051 0.283 2452 Planarity : 0.005 0.051 2369 Dihedral : 19.294 143.208 5712 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1792 helix: 0.04 (0.14), residues: 1246 sheet: 1.01 (0.57), residues: 94 loop : -0.47 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 635 HIS 0.019 0.001 HIS A 458 PHE 0.040 0.002 PHE A 455 TYR 0.044 0.002 TYR B 392 ARG 0.005 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.12734 ( 965) hydrogen bonds : angle 5.86572 ( 2859) covalent geometry : bond 0.00433 (14384) covalent geometry : angle 0.95198 (19644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9080 (t80) cc_final: 0.8803 (t80) REVERT: A 401 MET cc_start: 0.8700 (tpt) cc_final: 0.8365 (tpp) REVERT: A 578 MET cc_start: 0.8946 (ppp) cc_final: 0.8718 (ppp) REVERT: A 608 LEU cc_start: 0.9404 (tt) cc_final: 0.9167 (tt) REVERT: A 872 GLU cc_start: 0.9273 (tt0) cc_final: 0.8944 (pt0) REVERT: A 911 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 925 MET cc_start: 0.9023 (mpp) cc_final: 0.8590 (mpp) REVERT: B 154 MET cc_start: 0.7789 (mmm) cc_final: 0.7496 (mmt) REVERT: B 167 CYS cc_start: 0.9417 (p) cc_final: 0.8965 (p) REVERT: B 201 PHE cc_start: 0.9116 (t80) cc_final: 0.8889 (t80) REVERT: B 386 PHE cc_start: 0.8660 (m-80) cc_final: 0.8323 (m-80) REVERT: B 438 LEU cc_start: 0.9719 (mm) cc_final: 0.9500 (mm) REVERT: B 588 LYS cc_start: 0.9259 (pttm) cc_final: 0.9008 (pttm) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2263 time to fit residues: 107.8087 Evaluate side-chains 244 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 50.0000 chunk 141 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 900 GLN B 831 ASN B 900 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.094034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063353 restraints weight = 55018.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065441 restraints weight = 30881.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066742 restraints weight = 21634.565| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14384 Z= 0.154 Angle : 0.729 10.813 19644 Z= 0.344 Chirality : 0.042 0.235 2452 Planarity : 0.004 0.040 2369 Dihedral : 13.931 133.427 2764 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1792 helix: 0.93 (0.15), residues: 1262 sheet: 1.05 (0.57), residues: 94 loop : -0.24 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.009 0.001 HIS A 458 PHE 0.024 0.001 PHE A 455 TYR 0.017 0.001 TYR A 309 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 965) hydrogen bonds : angle 4.34699 ( 2859) covalent geometry : bond 0.00324 (14384) covalent geometry : angle 0.72869 (19644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9506 (t) cc_final: 0.9167 (p) REVERT: A 167 CYS cc_start: 0.9390 (p) cc_final: 0.9135 (p) REVERT: A 390 ILE cc_start: 0.9574 (pt) cc_final: 0.9362 (pt) REVERT: A 401 MET cc_start: 0.8646 (tpt) cc_final: 0.8314 (tpp) REVERT: A 578 MET cc_start: 0.8975 (ppp) cc_final: 0.8737 (ppp) REVERT: A 588 LYS cc_start: 0.9363 (pttm) cc_final: 0.8918 (pttt) REVERT: A 591 LYS cc_start: 0.9396 (pttp) cc_final: 0.9062 (pttp) REVERT: A 911 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 201 PHE cc_start: 0.9132 (t80) cc_final: 0.8890 (t80) REVERT: B 367 MET cc_start: 0.8763 (tpt) cc_final: 0.8511 (tpp) REVERT: B 386 PHE cc_start: 0.8719 (m-80) cc_final: 0.8338 (m-80) REVERT: B 591 LYS cc_start: 0.9479 (pttm) cc_final: 0.9206 (pttp) REVERT: B 616 GLU cc_start: 0.9247 (tp30) cc_final: 0.9041 (tp30) REVERT: B 900 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8191 (tp40) REVERT: B 939 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8769 (mtmm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2376 time to fit residues: 102.5628 Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 50.0000 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 164 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 165 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 900 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.065624 restraints weight = 55059.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065800 restraints weight = 43913.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066609 restraints weight = 28185.813| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14384 Z= 0.142 Angle : 0.690 13.493 19644 Z= 0.327 Chirality : 0.040 0.204 2452 Planarity : 0.003 0.033 2369 Dihedral : 10.834 134.531 2764 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1792 helix: 1.19 (0.15), residues: 1264 sheet: 0.98 (0.55), residues: 104 loop : -0.21 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 635 HIS 0.007 0.001 HIS A 458 PHE 0.016 0.001 PHE A 455 TYR 0.016 0.001 TYR A 309 ARG 0.002 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 965) hydrogen bonds : angle 4.12807 ( 2859) covalent geometry : bond 0.00300 (14384) covalent geometry : angle 0.69019 (19644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9523 (t) cc_final: 0.9183 (p) REVERT: A 133 MET cc_start: 0.8915 (mpp) cc_final: 0.8636 (mpp) REVERT: A 159 PHE cc_start: 0.9212 (t80) cc_final: 0.9001 (t80) REVERT: A 167 CYS cc_start: 0.9362 (p) cc_final: 0.9120 (p) REVERT: A 201 PHE cc_start: 0.9132 (t80) cc_final: 0.8810 (t80) REVERT: A 591 LYS cc_start: 0.9398 (pttp) cc_final: 0.9046 (pttp) REVERT: A 911 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 939 LYS cc_start: 0.9210 (pttp) cc_final: 0.8882 (ptpp) REVERT: B 133 MET cc_start: 0.8820 (mpp) cc_final: 0.8556 (mpp) REVERT: B 159 PHE cc_start: 0.9206 (t80) cc_final: 0.8944 (t80) REVERT: B 167 CYS cc_start: 0.9407 (p) cc_final: 0.9110 (p) REVERT: B 201 PHE cc_start: 0.9148 (t80) cc_final: 0.8911 (t80) REVERT: B 386 PHE cc_start: 0.8789 (m-80) cc_final: 0.8392 (m-80) REVERT: B 427 TRP cc_start: 0.9216 (m100) cc_final: 0.8949 (m100) REVERT: B 588 LYS cc_start: 0.9361 (pttm) cc_final: 0.9056 (pttm) REVERT: B 591 LYS cc_start: 0.9485 (pttm) cc_final: 0.9063 (pttp) REVERT: B 616 GLU cc_start: 0.9294 (tp30) cc_final: 0.9061 (tp30) REVERT: B 911 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 939 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8580 (mtmm) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.2158 time to fit residues: 91.9980 Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 50.0000 chunk 154 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.093491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065647 restraints weight = 55302.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066318 restraints weight = 32828.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066970 restraints weight = 23764.840| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14384 Z= 0.164 Angle : 0.684 9.081 19644 Z= 0.331 Chirality : 0.041 0.205 2452 Planarity : 0.003 0.030 2369 Dihedral : 9.307 134.945 2764 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1792 helix: 1.28 (0.15), residues: 1264 sheet: 1.09 (0.59), residues: 86 loop : -0.20 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.005 0.001 HIS A 458 PHE 0.014 0.001 PHE B 95 TYR 0.018 0.001 TYR A 309 ARG 0.002 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 965) hydrogen bonds : angle 4.08805 ( 2859) covalent geometry : bond 0.00351 (14384) covalent geometry : angle 0.68361 (19644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9510 (t) cc_final: 0.9189 (p) REVERT: A 159 PHE cc_start: 0.9201 (t80) cc_final: 0.8992 (t80) REVERT: A 167 CYS cc_start: 0.9433 (p) cc_final: 0.9204 (p) REVERT: A 172 PHE cc_start: 0.8621 (m-10) cc_final: 0.8366 (m-10) REVERT: A 367 MET cc_start: 0.8762 (tpt) cc_final: 0.8429 (tpp) REVERT: A 524 ASP cc_start: 0.8870 (p0) cc_final: 0.8588 (p0) REVERT: A 578 MET cc_start: 0.9043 (ppp) cc_final: 0.8804 (ppp) REVERT: A 588 LYS cc_start: 0.9404 (pttm) cc_final: 0.9088 (pttm) REVERT: A 591 LYS cc_start: 0.9375 (pttp) cc_final: 0.9076 (pttp) REVERT: A 911 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8496 (tm-30) REVERT: B 133 MET cc_start: 0.8923 (mpp) cc_final: 0.8648 (mpp) REVERT: B 159 PHE cc_start: 0.9188 (t80) cc_final: 0.8959 (t80) REVERT: B 167 CYS cc_start: 0.9398 (p) cc_final: 0.9118 (p) REVERT: B 201 PHE cc_start: 0.9155 (t80) cc_final: 0.8873 (t80) REVERT: B 367 MET cc_start: 0.8705 (tpt) cc_final: 0.8329 (tpp) REVERT: B 386 PHE cc_start: 0.8774 (m-80) cc_final: 0.8370 (m-80) REVERT: B 427 TRP cc_start: 0.9215 (m100) cc_final: 0.8943 (m100) REVERT: B 591 LYS cc_start: 0.9525 (pttm) cc_final: 0.9175 (pttp) REVERT: B 594 TYR cc_start: 0.8446 (m-80) cc_final: 0.8064 (m-80) REVERT: B 616 GLU cc_start: 0.9138 (tp30) cc_final: 0.8810 (tp30) REVERT: B 911 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8480 (tm-30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2046 time to fit residues: 85.6454 Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 178 optimal weight: 0.3980 chunk 148 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.095453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064472 restraints weight = 54676.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066624 restraints weight = 30712.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067963 restraints weight = 21479.537| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14384 Z= 0.117 Angle : 0.653 7.656 19644 Z= 0.310 Chirality : 0.040 0.216 2452 Planarity : 0.003 0.032 2369 Dihedral : 8.581 134.615 2764 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1792 helix: 1.34 (0.15), residues: 1264 sheet: 1.21 (0.59), residues: 84 loop : -0.09 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.004 0.000 HIS A 458 PHE 0.014 0.001 PHE B 999 TYR 0.016 0.001 TYR A 309 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 965) hydrogen bonds : angle 3.90068 ( 2859) covalent geometry : bond 0.00237 (14384) covalent geometry : angle 0.65297 (19644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9489 (t) cc_final: 0.9097 (p) REVERT: A 133 MET cc_start: 0.8622 (mpp) cc_final: 0.8301 (mpp) REVERT: A 159 PHE cc_start: 0.9176 (t80) cc_final: 0.8975 (t80) REVERT: A 167 CYS cc_start: 0.9451 (p) cc_final: 0.9203 (p) REVERT: A 172 PHE cc_start: 0.8554 (m-10) cc_final: 0.8199 (m-10) REVERT: A 201 PHE cc_start: 0.9124 (t80) cc_final: 0.8856 (t80) REVERT: A 401 MET cc_start: 0.8602 (tpt) cc_final: 0.8375 (tpp) REVERT: A 524 ASP cc_start: 0.8811 (p0) cc_final: 0.8477 (p0) REVERT: A 578 MET cc_start: 0.8975 (ppp) cc_final: 0.8755 (ppp) REVERT: A 588 LYS cc_start: 0.9337 (pttm) cc_final: 0.8997 (pttm) REVERT: A 591 LYS cc_start: 0.9400 (pttp) cc_final: 0.9177 (pttp) REVERT: A 911 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 932 LEU cc_start: 0.9568 (mt) cc_final: 0.8488 (mt) REVERT: B 159 PHE cc_start: 0.9095 (t80) cc_final: 0.8889 (t80) REVERT: B 167 CYS cc_start: 0.9409 (p) cc_final: 0.9122 (p) REVERT: B 367 MET cc_start: 0.8767 (tpt) cc_final: 0.8382 (tpp) REVERT: B 386 PHE cc_start: 0.8711 (m-80) cc_final: 0.8332 (m-80) REVERT: B 427 TRP cc_start: 0.9158 (m100) cc_final: 0.8923 (m100) REVERT: B 591 LYS cc_start: 0.9514 (pttm) cc_final: 0.9135 (pttp) REVERT: B 594 TYR cc_start: 0.8466 (m-80) cc_final: 0.7847 (m-80) REVERT: B 616 GLU cc_start: 0.9135 (tp30) cc_final: 0.8823 (tp30) REVERT: B 911 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8402 (tm-30) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.2200 time to fit residues: 101.5066 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 135 optimal weight: 0.4980 chunk 83 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 900 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 = 0.3726 r_free = 0.3726 target = 0.095998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068173 restraints weight = 55122.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067581 restraints weight = 44851.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068410 restraints weight = 29389.193| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14384 Z= 0.120 Angle : 0.664 7.691 19644 Z= 0.319 Chirality : 0.040 0.213 2452 Planarity : 0.003 0.032 2369 Dihedral : 8.267 134.629 2764 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.14 % Allowed : 2.58 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1792 helix: 1.37 (0.15), residues: 1278 sheet: 1.07 (0.59), residues: 86 loop : -0.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.006 0.001 HIS A 126 PHE 0.014 0.001 PHE B 95 TYR 0.020 0.001 TYR B 392 ARG 0.002 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 965) hydrogen bonds : angle 3.86220 ( 2859) covalent geometry : bond 0.00244 (14384) covalent geometry : angle 0.66415 (19644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8624 (mpp) cc_final: 0.8408 (mpp) REVERT: A 159 PHE cc_start: 0.9216 (t80) cc_final: 0.9012 (t80) REVERT: A 167 CYS cc_start: 0.9462 (p) cc_final: 0.9218 (p) REVERT: A 172 PHE cc_start: 0.8550 (m-10) cc_final: 0.8205 (m-10) REVERT: A 201 PHE cc_start: 0.9092 (t80) cc_final: 0.8837 (t80) REVERT: A 401 MET cc_start: 0.8714 (tpt) cc_final: 0.8484 (tpp) REVERT: A 503 GLU cc_start: 0.8959 (pm20) cc_final: 0.8682 (pm20) REVERT: A 524 ASP cc_start: 0.8892 (p0) cc_final: 0.8555 (p0) REVERT: A 588 LYS cc_start: 0.9335 (pttm) cc_final: 0.8963 (pttm) REVERT: A 591 LYS cc_start: 0.9372 (pttp) cc_final: 0.9098 (pttp) REVERT: A 932 LEU cc_start: 0.9503 (mt) cc_final: 0.9118 (mt) REVERT: B 159 PHE cc_start: 0.9129 (t80) cc_final: 0.8896 (t80) REVERT: B 167 CYS cc_start: 0.9425 (p) cc_final: 0.9143 (p) REVERT: B 367 MET cc_start: 0.8565 (tpt) cc_final: 0.8267 (tpp) REVERT: B 386 PHE cc_start: 0.8739 (m-80) cc_final: 0.8357 (m-80) REVERT: B 591 LYS cc_start: 0.9493 (pttm) cc_final: 0.9047 (pttp) REVERT: B 594 TYR cc_start: 0.8376 (m-80) cc_final: 0.7730 (m-80) REVERT: B 616 GLU cc_start: 0.9128 (tp30) cc_final: 0.8822 (tp30) REVERT: B 911 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8303 (tm-30) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.2104 time to fit residues: 94.9894 Evaluate side-chains 236 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 1 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 108 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 160 optimal weight: 50.0000 chunk 143 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 65 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 GLN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067621 restraints weight = 54696.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067650 restraints weight = 44490.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068517 restraints weight = 28076.892| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14384 Z= 0.119 Angle : 0.665 7.744 19644 Z= 0.318 Chirality : 0.040 0.201 2452 Planarity : 0.003 0.030 2369 Dihedral : 8.113 134.675 2764 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1792 helix: 1.40 (0.15), residues: 1278 sheet: 1.03 (0.59), residues: 86 loop : -0.20 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 427 HIS 0.008 0.001 HIS A 458 PHE 0.015 0.001 PHE B 95 TYR 0.016 0.001 TYR B 392 ARG 0.004 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 965) hydrogen bonds : angle 3.80020 ( 2859) covalent geometry : bond 0.00244 (14384) covalent geometry : angle 0.66515 (19644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8685 (mpp) cc_final: 0.8451 (mpp) REVERT: A 159 PHE cc_start: 0.9246 (t80) cc_final: 0.9016 (t80) REVERT: A 167 CYS cc_start: 0.9475 (p) cc_final: 0.9225 (p) REVERT: A 172 PHE cc_start: 0.8538 (m-10) cc_final: 0.8215 (m-10) REVERT: A 201 PHE cc_start: 0.9129 (t80) cc_final: 0.8832 (t80) REVERT: A 296 ASP cc_start: 0.8850 (t0) cc_final: 0.8315 (t70) REVERT: A 401 MET cc_start: 0.8588 (tpt) cc_final: 0.8350 (tpp) REVERT: A 503 GLU cc_start: 0.8933 (pm20) cc_final: 0.8680 (pm20) REVERT: A 524 ASP cc_start: 0.8890 (p0) cc_final: 0.8510 (p0) REVERT: A 578 MET cc_start: 0.9015 (ppp) cc_final: 0.8793 (ppp) REVERT: A 591 LYS cc_start: 0.9384 (pttp) cc_final: 0.9124 (pttp) REVERT: A 938 MET cc_start: 0.9217 (tpt) cc_final: 0.8976 (tpp) REVERT: B 159 PHE cc_start: 0.9218 (t80) cc_final: 0.8960 (t80) REVERT: B 167 CYS cc_start: 0.9431 (p) cc_final: 0.9143 (p) REVERT: B 367 MET cc_start: 0.8550 (tpt) cc_final: 0.8258 (tpp) REVERT: B 383 MET cc_start: 0.8217 (ppp) cc_final: 0.7821 (ppp) REVERT: B 386 PHE cc_start: 0.8761 (m-80) cc_final: 0.8453 (m-80) REVERT: B 427 TRP cc_start: 0.9143 (m100) cc_final: 0.8895 (m100) REVERT: B 438 LEU cc_start: 0.9748 (mm) cc_final: 0.9517 (mm) REVERT: B 444 ASN cc_start: 0.8921 (m-40) cc_final: 0.8633 (t0) REVERT: B 591 LYS cc_start: 0.9507 (pttm) cc_final: 0.9001 (pttp) REVERT: B 594 TYR cc_start: 0.8403 (m-80) cc_final: 0.7688 (m-80) REVERT: B 611 LEU cc_start: 0.9523 (tt) cc_final: 0.9125 (tp) REVERT: B 616 GLU cc_start: 0.9164 (tp30) cc_final: 0.8842 (tp30) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2022 time to fit residues: 92.2471 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067992 restraints weight = 54307.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068517 restraints weight = 36838.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068933 restraints weight = 26486.556| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14384 Z= 0.119 Angle : 0.668 7.813 19644 Z= 0.319 Chirality : 0.039 0.197 2452 Planarity : 0.003 0.029 2369 Dihedral : 8.008 134.612 2764 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1792 helix: 1.42 (0.15), residues: 1276 sheet: 1.04 (0.58), residues: 88 loop : -0.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.009 0.001 HIS A 458 PHE 0.013 0.001 PHE A 406 TYR 0.016 0.001 TYR B 392 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 965) hydrogen bonds : angle 3.81514 ( 2859) covalent geometry : bond 0.00245 (14384) covalent geometry : angle 0.66785 (19644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9235 (t80) cc_final: 0.9010 (t80) REVERT: A 167 CYS cc_start: 0.9474 (p) cc_final: 0.9231 (p) REVERT: A 172 PHE cc_start: 0.8578 (m-10) cc_final: 0.8247 (m-10) REVERT: A 218 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8851 (mmmt) REVERT: A 296 ASP cc_start: 0.8829 (t0) cc_final: 0.8297 (t70) REVERT: A 354 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 438 LEU cc_start: 0.9744 (mm) cc_final: 0.9538 (mm) REVERT: A 524 ASP cc_start: 0.8873 (p0) cc_final: 0.8504 (p0) REVERT: A 578 MET cc_start: 0.9022 (ppp) cc_final: 0.8808 (ppp) REVERT: A 591 LYS cc_start: 0.9351 (pttp) cc_final: 0.9068 (pttp) REVERT: A 594 TYR cc_start: 0.8299 (m-80) cc_final: 0.7718 (m-80) REVERT: A 823 LEU cc_start: 0.9665 (mt) cc_final: 0.9364 (pp) REVERT: A 932 LEU cc_start: 0.9513 (mt) cc_final: 0.9116 (mt) REVERT: A 938 MET cc_start: 0.9232 (tpt) cc_final: 0.8853 (tpp) REVERT: B 159 PHE cc_start: 0.9222 (t80) cc_final: 0.8955 (t80) REVERT: B 167 CYS cc_start: 0.9432 (p) cc_final: 0.9142 (p) REVERT: B 367 MET cc_start: 0.8519 (tpt) cc_final: 0.8258 (tpp) REVERT: B 383 MET cc_start: 0.8177 (ppp) cc_final: 0.7787 (ppp) REVERT: B 386 PHE cc_start: 0.8774 (m-80) cc_final: 0.8466 (m-80) REVERT: B 427 TRP cc_start: 0.9119 (m100) cc_final: 0.8684 (m100) REVERT: B 444 ASN cc_start: 0.8868 (m-40) cc_final: 0.8604 (t0) REVERT: B 591 LYS cc_start: 0.9477 (pttm) cc_final: 0.9109 (pttp) REVERT: B 594 TYR cc_start: 0.8383 (m-80) cc_final: 0.7715 (m-80) REVERT: B 611 LEU cc_start: 0.9529 (tt) cc_final: 0.9119 (tt) REVERT: B 616 GLU cc_start: 0.9179 (tp30) cc_final: 0.8892 (tp30) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2092 time to fit residues: 96.5559 Evaluate side-chains 240 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 97 optimal weight: 0.0570 chunk 133 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 0.0040 chunk 29 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 173 optimal weight: 0.0050 overall best weight: 0.9526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 GLN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.096657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068891 restraints weight = 53931.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068894 restraints weight = 32411.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069491 restraints weight = 26236.213| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14384 Z= 0.122 Angle : 0.687 7.969 19644 Z= 0.329 Chirality : 0.040 0.195 2452 Planarity : 0.003 0.034 2369 Dihedral : 7.942 134.663 2764 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1792 helix: 1.39 (0.15), residues: 1278 sheet: 1.03 (0.57), residues: 88 loop : -0.24 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.008 0.001 HIS A 458 PHE 0.015 0.001 PHE A 406 TYR 0.016 0.001 TYR B 392 ARG 0.003 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 965) hydrogen bonds : angle 3.80729 ( 2859) covalent geometry : bond 0.00255 (14384) covalent geometry : angle 0.68696 (19644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9195 (t80) cc_final: 0.8987 (t80) REVERT: A 167 CYS cc_start: 0.9450 (p) cc_final: 0.9226 (p) REVERT: A 172 PHE cc_start: 0.8532 (m-10) cc_final: 0.8262 (m-10) REVERT: A 354 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 401 MET cc_start: 0.8410 (tpt) cc_final: 0.8138 (tpp) REVERT: A 438 LEU cc_start: 0.9754 (mm) cc_final: 0.9545 (mm) REVERT: A 444 ASN cc_start: 0.8809 (m-40) cc_final: 0.8543 (t0) REVERT: A 524 ASP cc_start: 0.8867 (p0) cc_final: 0.8499 (p0) REVERT: A 578 MET cc_start: 0.9013 (ppp) cc_final: 0.8801 (ppp) REVERT: A 591 LYS cc_start: 0.9344 (pttp) cc_final: 0.9066 (pttp) REVERT: A 594 TYR cc_start: 0.8302 (m-80) cc_final: 0.7713 (m-80) REVERT: A 823 LEU cc_start: 0.9658 (mt) cc_final: 0.9356 (pp) REVERT: A 932 LEU cc_start: 0.9522 (mt) cc_final: 0.9141 (mt) REVERT: A 938 MET cc_start: 0.9287 (tpt) cc_final: 0.8954 (tpp) REVERT: B 133 MET cc_start: 0.8666 (mpp) cc_final: 0.8355 (mpp) REVERT: B 154 MET cc_start: 0.8059 (mmp) cc_final: 0.7831 (mmt) REVERT: B 159 PHE cc_start: 0.9178 (t80) cc_final: 0.8922 (t80) REVERT: B 167 CYS cc_start: 0.9428 (p) cc_final: 0.9146 (p) REVERT: B 383 MET cc_start: 0.8150 (ppp) cc_final: 0.7759 (ppp) REVERT: B 386 PHE cc_start: 0.8765 (m-80) cc_final: 0.8424 (m-80) REVERT: B 427 TRP cc_start: 0.9093 (m100) cc_final: 0.8621 (m100) REVERT: B 438 LEU cc_start: 0.9750 (mm) cc_final: 0.9525 (mm) REVERT: B 591 LYS cc_start: 0.9493 (pttm) cc_final: 0.9094 (pttp) REVERT: B 594 TYR cc_start: 0.8321 (m-80) cc_final: 0.7675 (m-80) REVERT: B 611 LEU cc_start: 0.9539 (tt) cc_final: 0.9108 (tt) REVERT: B 616 GLU cc_start: 0.9147 (tp30) cc_final: 0.8843 (tp30) REVERT: B 939 LYS cc_start: 0.9142 (ptmt) cc_final: 0.8854 (mtmm) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1969 time to fit residues: 90.7721 Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 160 optimal weight: 50.0000 chunk 30 optimal weight: 0.0570 chunk 51 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.094678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.063771 restraints weight = 54639.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065802 restraints weight = 31374.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067075 restraints weight = 22267.948| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14384 Z= 0.159 Angle : 0.720 8.073 19644 Z= 0.354 Chirality : 0.041 0.228 2452 Planarity : 0.003 0.034 2369 Dihedral : 8.005 135.273 2764 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1792 helix: 1.37 (0.15), residues: 1280 sheet: 0.95 (0.57), residues: 88 loop : -0.26 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.007 0.001 HIS A 458 PHE 0.037 0.001 PHE A 95 TYR 0.016 0.001 TYR B 392 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 965) hydrogen bonds : angle 3.94377 ( 2859) covalent geometry : bond 0.00348 (14384) covalent geometry : angle 0.71981 (19644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 CYS cc_start: 0.9439 (p) cc_final: 0.9208 (p) REVERT: A 172 PHE cc_start: 0.8651 (m-10) cc_final: 0.8414 (m-10) REVERT: A 401 MET cc_start: 0.8431 (tpt) cc_final: 0.8181 (tpp) REVERT: A 438 LEU cc_start: 0.9769 (mm) cc_final: 0.9549 (mm) REVERT: A 524 ASP cc_start: 0.8818 (p0) cc_final: 0.8425 (p0) REVERT: A 578 MET cc_start: 0.8978 (ppp) cc_final: 0.8759 (ppp) REVERT: A 591 LYS cc_start: 0.9379 (pttp) cc_final: 0.9115 (pttp) REVERT: A 938 MET cc_start: 0.9266 (tpt) cc_final: 0.8958 (tpp) REVERT: B 167 CYS cc_start: 0.9407 (p) cc_final: 0.9123 (p) REVERT: B 201 PHE cc_start: 0.9156 (t80) cc_final: 0.8873 (t80) REVERT: B 383 MET cc_start: 0.8063 (ppp) cc_final: 0.7729 (ppp) REVERT: B 386 PHE cc_start: 0.8742 (m-80) cc_final: 0.8409 (m-80) REVERT: B 427 TRP cc_start: 0.9138 (m100) cc_final: 0.8674 (m100) REVERT: B 438 LEU cc_start: 0.9774 (mm) cc_final: 0.9565 (mm) REVERT: B 591 LYS cc_start: 0.9486 (pttm) cc_final: 0.9152 (pttp) REVERT: B 594 TYR cc_start: 0.8544 (m-80) cc_final: 0.8124 (m-80) REVERT: B 616 GLU cc_start: 0.9096 (tp30) cc_final: 0.8766 (tp30) REVERT: B 939 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8813 (mtmm) outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.2423 time to fit residues: 106.4018 Evaluate side-chains 234 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 75 optimal weight: 40.0000 chunk 108 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 900 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 = 0.3701 r_free = 0.3701 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067123 restraints weight = 54750.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067422 restraints weight = 33132.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068139 restraints weight = 25337.518| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14384 Z= 0.154 Angle : 0.727 11.431 19644 Z= 0.354 Chirality : 0.042 0.218 2452 Planarity : 0.003 0.034 2369 Dihedral : 8.059 135.393 2764 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1792 helix: 1.36 (0.15), residues: 1280 sheet: 0.84 (0.57), residues: 88 loop : -0.31 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.007 0.001 HIS A 458 PHE 0.032 0.001 PHE A 95 TYR 0.017 0.001 TYR B 392 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 965) hydrogen bonds : angle 3.96211 ( 2859) covalent geometry : bond 0.00335 (14384) covalent geometry : angle 0.72651 (19644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4554.55 seconds wall clock time: 80 minutes 1.12 seconds (4801.12 seconds total)