Starting phenix.real_space_refine on Thu Aug 6 07:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7p_41988/08_2026/8u7p_41988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7p_41988/08_2026/8u7p_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_41988/08_2026/8u7p_41988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7p_41988/08_2026/8u7p_41988.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7p_41988/08_2026/8u7p_41988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7p_41988/08_2026/8u7p_41988_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.094 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 10, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'ARG:plan': 9, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 3} 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: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 9, 'ASP:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1} 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: {'RNAv2': 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: {'RNAv2': 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: 2.91, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 633.3 milliseconds 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: 0.24 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: 2.24 Time building geometry restraints manager: 1.30 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: 18982 2.33 - 4.67: 519 4.67 - 7.00: 91 7.00 - 9.34: 41 9.34 - 11.67: 11 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: 8654 28.64 - 57.28: 332 57.28 - 85.93: 47 85.93 - 114.57: 58 114.57 - 143.21: 17 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: 1854 0.057 - 0.113: 509 0.113 - 0.170: 73 0.170 - 0.226: 9 0.226 - 0.283: 7 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=" C2' CMP A1405 " pdb=" C1' CMP A1405 " pdb=" C3' CMP A1405 " pdb=" O2' CMP A1405 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.86e+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: 0.470 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.090 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.968 11.674 19644 Z= 0.450 Chirality : 0.052 0.283 2452 Planarity : 0.005 0.051 2369 Dihedral : 19.144 143.208 5712 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (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 ARG 0.005 0.000 ARG B 128 TYR 0.044 0.002 TYR B 392 PHE 0.040 0.002 PHE A 455 TRP 0.017 0.001 TRP B 635 HIS 0.019 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (14384) covalent geometry : angle 0.96783 / 0.45 (19644) hydrogen bonds : bond 0.12734 / 8.97 ( 965) hydrogen bonds : angle 5.86572 / 4.27 ( 2859) *********************** 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 : 0.403 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: 0.7788 (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: 0.0841 time to fit residues: 40.6202 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3705 r_free = 0.3705 target = 0.094286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.066788 restraints weight = 55238.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066942 restraints weight = 34271.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067744 restraints weight = 25641.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067790 restraints weight = 21231.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067894 restraints weight = 20699.561| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14384 Z= 0.149 Angle : 0.740 10.889 19644 Z= 0.343 Chirality : 0.042 0.232 2452 Planarity : 0.004 0.039 2369 Dihedral : 13.337 127.370 2764 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1792 helix: 0.92 (0.15), residues: 1262 sheet: 1.07 (0.57), residues: 94 loop : -0.22 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.016 0.001 TYR A 309 PHE 0.025 0.001 PHE A 455 TRP 0.015 0.001 TRP A 635 HIS 0.009 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (14384) covalent geometry : angle 0.74009 / 0.34 (19644) hydrogen bonds : bond 0.04696 / 3.14 ( 965) hydrogen bonds : angle 4.33427 / 3.16 ( 2859) *********************** 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 276 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9471 (t) cc_final: 0.9153 (p) REVERT: A 159 PHE cc_start: 0.9097 (t80) cc_final: 0.8883 (t80) REVERT: A 167 CYS cc_start: 0.9370 (p) cc_final: 0.9116 (p) REVERT: A 269 LEU cc_start: 0.8973 (tt) cc_final: 0.8758 (pp) REVERT: A 390 ILE cc_start: 0.9562 (pt) cc_final: 0.9356 (pt) REVERT: A 401 MET cc_start: 0.8642 (tpt) cc_final: 0.8333 (tpp) REVERT: A 524 ASP cc_start: 0.8840 (p0) cc_final: 0.8634 (p0) REVERT: A 578 MET cc_start: 0.8985 (ppp) cc_final: 0.8750 (ppp) REVERT: A 588 LYS cc_start: 0.9338 (pttm) cc_final: 0.8876 (pttt) REVERT: A 591 LYS cc_start: 0.9363 (pttp) cc_final: 0.9010 (pttp) REVERT: A 911 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8415 (tm-30) REVERT: A 925 MET cc_start: 0.9015 (mpp) cc_final: 0.8597 (mpp) REVERT: B 201 PHE cc_start: 0.9083 (t80) cc_final: 0.8844 (t80) REVERT: B 367 MET cc_start: 0.8652 (tpt) cc_final: 0.8416 (tpp) REVERT: B 386 PHE cc_start: 0.8712 (m-80) cc_final: 0.8321 (m-80) REVERT: B 427 TRP cc_start: 0.9178 (m100) cc_final: 0.8937 (m100) REVERT: B 462 ILE cc_start: 0.9376 (pt) cc_final: 0.9167 (pt) REVERT: B 588 LYS cc_start: 0.9342 (pttm) cc_final: 0.9030 (pttm) REVERT: B 591 LYS cc_start: 0.9445 (pttm) cc_final: 0.9156 (pttp) REVERT: B 900 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: B 939 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8610 (mtmm) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.0760 time to fit residues: 33.5537 Evaluate side-chains 232 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 4.9990 chunk 159 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 4 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.094269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066339 restraints weight = 55728.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066680 restraints weight = 36988.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066819 restraints weight = 27458.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067298 restraints weight = 24714.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067760 restraints weight = 21696.385| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14384 Z= 0.146 Angle : 0.705 13.686 19644 Z= 0.329 Chirality : 0.041 0.189 2452 Planarity : 0.003 0.033 2369 Dihedral : 10.142 110.806 2764 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1792 helix: 1.18 (0.15), residues: 1264 sheet: 0.99 (0.55), residues: 104 loop : -0.21 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.016 0.001 TYR A 309 PHE 0.016 0.001 PHE A 455 TRP 0.038 0.001 TRP A 635 HIS 0.007 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14384) covalent geometry : angle 0.70518 / 0.33 (19644) hydrogen bonds : bond 0.04402 / 2.95 ( 965) hydrogen bonds : angle 4.14285 / 3.01 ( 2859) *********************** 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 268 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9503 (t) cc_final: 0.9170 (p) REVERT: A 133 MET cc_start: 0.8886 (mpp) cc_final: 0.8621 (mpp) REVERT: A 159 PHE cc_start: 0.9219 (t80) cc_final: 0.9017 (t80) REVERT: A 167 CYS cc_start: 0.9360 (p) cc_final: 0.9119 (p) REVERT: A 201 PHE cc_start: 0.9120 (t80) cc_final: 0.8807 (t80) REVERT: A 524 ASP cc_start: 0.8946 (p0) cc_final: 0.8663 (p0) REVERT: A 578 MET cc_start: 0.9021 (ppp) cc_final: 0.8795 (ppp) REVERT: A 591 LYS cc_start: 0.9402 (pttp) cc_final: 0.9048 (pttp) REVERT: A 911 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 938 MET cc_start: 0.9354 (tpp) cc_final: 0.9153 (tpp) REVERT: B 133 MET cc_start: 0.8761 (mpp) cc_final: 0.8512 (mpp) REVERT: B 159 PHE cc_start: 0.9224 (t80) cc_final: 0.8966 (t80) REVERT: B 167 CYS cc_start: 0.9399 (p) cc_final: 0.9103 (p) REVERT: B 201 PHE cc_start: 0.9128 (t80) cc_final: 0.8894 (t80) REVERT: B 386 PHE cc_start: 0.8785 (m-80) cc_final: 0.8394 (m-80) REVERT: B 427 TRP cc_start: 0.9228 (m100) cc_final: 0.8962 (m100) REVERT: B 591 LYS cc_start: 0.9484 (pttm) cc_final: 0.9059 (pttp) REVERT: B 911 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 939 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8598 (mtmm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.0762 time to fit residues: 32.7670 Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 175 optimal weight: 40.0000 chunk 116 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3695 r_free = 0.3695 target = 0.093889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065619 restraints weight = 55487.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066291 restraints weight = 33855.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066616 restraints weight = 24538.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066927 restraints weight = 22045.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067234 restraints weight = 20130.740| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1813 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= 0.153 Angle : 0.690 9.252 19644 Z= 0.326 Chirality : 0.041 0.234 2452 Planarity : 0.003 0.031 2369 Dihedral : 8.570 86.388 2764 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1792 helix: 1.29 (0.15), residues: 1264 sheet: 1.27 (0.60), residues: 84 loop : -0.16 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.018 0.001 TYR A 309 PHE 0.014 0.001 PHE B 95 TRP 0.021 0.001 TRP A 635 HIS 0.005 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14384) covalent geometry : angle 0.68993 / 0.33 (19644) hydrogen bonds : bond 0.04277 / 2.86 ( 965) hydrogen bonds : angle 4.06460 / 2.96 ( 2859) *********************** 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 267 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9503 (t) cc_final: 0.9182 (p) REVERT: A 167 CYS cc_start: 0.9441 (p) cc_final: 0.9207 (p) REVERT: A 172 PHE cc_start: 0.8622 (m-10) cc_final: 0.8367 (m-10) REVERT: A 367 MET cc_start: 0.8710 (tpt) cc_final: 0.8387 (tpp) REVERT: A 524 ASP cc_start: 0.8884 (p0) cc_final: 0.8518 (p0) REVERT: A 588 LYS cc_start: 0.9406 (pttm) cc_final: 0.9086 (pttm) REVERT: A 591 LYS cc_start: 0.9382 (pttp) cc_final: 0.9040 (pttp) REVERT: A 594 TYR cc_start: 0.8409 (m-80) cc_final: 0.8118 (m-80) REVERT: A 872 GLU cc_start: 0.8517 (pp20) cc_final: 0.8239 (pp20) REVERT: A 911 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 938 MET cc_start: 0.9275 (tpp) cc_final: 0.9008 (tpp) REVERT: B 133 MET cc_start: 0.8843 (mpp) cc_final: 0.8576 (mpp) REVERT: B 159 PHE cc_start: 0.9191 (t80) cc_final: 0.8964 (t80) REVERT: B 167 CYS cc_start: 0.9399 (p) cc_final: 0.9121 (p) REVERT: B 201 PHE cc_start: 0.9157 (t80) cc_final: 0.8880 (t80) REVERT: B 367 MET cc_start: 0.8667 (tpt) cc_final: 0.8300 (tpp) REVERT: B 386 PHE cc_start: 0.8792 (m-80) cc_final: 0.8390 (m-80) REVERT: B 427 TRP cc_start: 0.9236 (m100) cc_final: 0.8984 (m100) REVERT: B 586 MET cc_start: 0.8994 (mmp) cc_final: 0.8566 (mmp) REVERT: B 588 LYS cc_start: 0.9369 (pttm) cc_final: 0.9141 (pttm) REVERT: B 591 LYS cc_start: 0.9521 (pttm) cc_final: 0.9132 (pttp) REVERT: B 594 TYR cc_start: 0.8445 (m-80) cc_final: 0.8036 (m-80) REVERT: B 911 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 939 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8777 (mtmm) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.0781 time to fit residues: 33.2817 Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 GLN A 831 ASN B 900 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063523 restraints weight = 54850.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065608 restraints weight = 30699.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066916 restraints weight = 21495.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067651 restraints weight = 17275.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068164 restraints weight = 15212.299| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14384 Z= 0.128 Angle : 0.665 8.634 19644 Z= 0.312 Chirality : 0.040 0.220 2452 Planarity : 0.003 0.030 2369 Dihedral : 7.773 77.778 2764 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1792 helix: 1.37 (0.15), residues: 1266 sheet: 0.89 (0.57), residues: 90 loop : -0.09 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.017 0.001 TYR A 309 PHE 0.015 0.001 PHE B 999 TRP 0.017 0.001 TRP A 635 HIS 0.004 0.000 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (14384) covalent geometry : angle 0.66500 / 0.31 (19644) hydrogen bonds : bond 0.04068 / 2.72 ( 965) hydrogen bonds : angle 3.91230 / 2.85 ( 2859) *********************** 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 288 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.500 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: 0.9480 (t) cc_final: 0.9111 (p) REVERT: A 133 MET cc_start: 0.8643 (mpp) cc_final: 0.8294 (mpp) REVERT: A 167 CYS cc_start: 0.9447 (p) cc_final: 0.9212 (p) REVERT: A 172 PHE cc_start: 0.8560 (m-10) cc_final: 0.8182 (m-10) REVERT: A 201 PHE cc_start: 0.9114 (t80) cc_final: 0.8839 (t80) REVERT: A 332 LEU cc_start: 0.9105 (pp) cc_final: 0.8831 (pp) REVERT: A 333 ILE cc_start: 0.9424 (mm) cc_final: 0.9211 (mm) REVERT: A 401 MET cc_start: 0.8561 (tpt) cc_final: 0.8334 (tpp) REVERT: A 524 ASP cc_start: 0.8778 (p0) cc_final: 0.8423 (p0) REVERT: A 578 MET cc_start: 0.8973 (ppp) cc_final: 0.8738 (ppp) REVERT: A 588 LYS cc_start: 0.9375 (pttm) cc_final: 0.9041 (pttm) REVERT: A 591 LYS cc_start: 0.9415 (pttp) cc_final: 0.9150 (pttp) REVERT: A 594 TYR cc_start: 0.8455 (m-80) cc_final: 0.8090 (m-80) REVERT: A 872 GLU cc_start: 0.8459 (pp20) cc_final: 0.8198 (pp20) REVERT: A 911 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 938 MET cc_start: 0.9335 (tpp) cc_final: 0.9023 (tpp) REVERT: A 939 LYS cc_start: 0.9285 (pttp) cc_final: 0.8971 (ptpp) REVERT: B 159 PHE cc_start: 0.9096 (t80) cc_final: 0.8889 (t80) REVERT: B 167 CYS cc_start: 0.9358 (p) cc_final: 0.9068 (p) REVERT: B 201 PHE cc_start: 0.9131 (t80) cc_final: 0.8865 (t80) REVERT: B 367 MET cc_start: 0.8803 (tpt) cc_final: 0.8403 (tpp) REVERT: B 386 PHE cc_start: 0.8700 (m-80) cc_final: 0.8311 (m-80) REVERT: B 427 TRP cc_start: 0.9214 (m100) cc_final: 0.8984 (m100) REVERT: B 586 MET cc_start: 0.8862 (mmp) cc_final: 0.8463 (mmp) REVERT: B 588 LYS cc_start: 0.9379 (pttm) cc_final: 0.9019 (pttm) REVERT: B 591 LYS cc_start: 0.9563 (pttm) cc_final: 0.9143 (pttp) REVERT: B 594 TYR cc_start: 0.8439 (m-80) cc_final: 0.7881 (m-80) REVERT: B 911 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 935 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8130 (tp30) REVERT: B 938 MET cc_start: 0.8953 (tpt) cc_final: 0.8711 (mmm) outliers start: 2 outliers final: 1 residues processed: 287 average time/residue: 0.0770 time to fit residues: 35.4908 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 900 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.095566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064667 restraints weight = 54186.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.066804 restraints weight = 30655.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068142 restraints weight = 21467.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068966 restraints weight = 17198.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069410 restraints weight = 15003.389| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14384 Z= 0.116 Angle : 0.671 8.587 19644 Z= 0.315 Chirality : 0.040 0.216 2452 Planarity : 0.003 0.031 2369 Dihedral : 7.416 75.649 2764 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1792 helix: 1.39 (0.15), residues: 1276 sheet: 0.83 (0.57), residues: 90 loop : -0.18 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.022 0.001 TYR B 392 PHE 0.014 0.001 PHE B 95 TRP 0.054 0.001 TRP A 635 HIS 0.004 0.000 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14384) covalent geometry : angle 0.67090 / 0.32 (19644) hydrogen bonds : bond 0.03939 / 2.64 ( 965) hydrogen bonds : angle 3.86841 / 2.83 ( 2859) *********************** 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 287 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8615 (mpp) cc_final: 0.8256 (mpp) REVERT: A 159 PHE cc_start: 0.9131 (t80) cc_final: 0.8904 (t80) REVERT: A 167 CYS cc_start: 0.9445 (p) cc_final: 0.9200 (p) REVERT: A 172 PHE cc_start: 0.8541 (m-10) cc_final: 0.8153 (m-10) REVERT: A 201 PHE cc_start: 0.9101 (t80) cc_final: 0.8857 (t80) REVERT: A 401 MET cc_start: 0.8558 (tpt) cc_final: 0.8307 (tpp) REVERT: A 503 GLU cc_start: 0.9015 (pm20) cc_final: 0.8719 (pm20) REVERT: A 524 ASP cc_start: 0.8772 (p0) cc_final: 0.8409 (p0) REVERT: A 578 MET cc_start: 0.8955 (ppp) cc_final: 0.8735 (ppp) REVERT: A 588 LYS cc_start: 0.9333 (pttm) cc_final: 0.8992 (pttm) REVERT: A 591 LYS cc_start: 0.9423 (pttp) cc_final: 0.9128 (pttp) REVERT: A 594 TYR cc_start: 0.8391 (m-80) cc_final: 0.7881 (m-80) REVERT: A 872 GLU cc_start: 0.8460 (pp20) cc_final: 0.8179 (pp20) REVERT: A 911 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 938 MET cc_start: 0.9311 (tpp) cc_final: 0.8994 (tpp) REVERT: B 159 PHE cc_start: 0.9104 (t80) cc_final: 0.8883 (t80) REVERT: B 167 CYS cc_start: 0.9395 (p) cc_final: 0.9112 (p) REVERT: B 367 MET cc_start: 0.8711 (tpt) cc_final: 0.8367 (tpp) REVERT: B 386 PHE cc_start: 0.8699 (m-80) cc_final: 0.8339 (m-80) REVERT: B 427 TRP cc_start: 0.9184 (m100) cc_final: 0.8980 (m100) REVERT: B 588 LYS cc_start: 0.9391 (pttm) cc_final: 0.9082 (pttm) REVERT: B 591 LYS cc_start: 0.9548 (pttm) cc_final: 0.9103 (pttp) REVERT: B 594 TYR cc_start: 0.8488 (m-80) cc_final: 0.7858 (m-80) REVERT: B 911 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 938 MET cc_start: 0.9062 (tpt) cc_final: 0.8819 (mmm) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.0820 time to fit residues: 37.6825 Evaluate side-chains 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 0.0570 chunk 164 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 63 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068399 restraints weight = 54002.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068462 restraints weight = 38246.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068849 restraints weight = 27396.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069375 restraints weight = 24106.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069576 restraints weight = 21082.993| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2229 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= 0.114 Angle : 0.676 8.559 19644 Z= 0.314 Chirality : 0.040 0.200 2452 Planarity : 0.003 0.030 2369 Dihedral : 7.230 73.773 2764 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1792 helix: 1.38 (0.15), residues: 1278 sheet: 1.17 (0.60), residues: 84 loop : -0.15 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.016 0.001 TYR B 392 PHE 0.014 0.001 PHE B 95 TRP 0.017 0.001 TRP B 635 HIS 0.007 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (14384) covalent geometry : angle 0.67593 / 0.31 (19644) hydrogen bonds : bond 0.03766 / 2.52 ( 965) hydrogen bonds : angle 3.80728 / 2.78 ( 2859) *********************** 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 297 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8675 (mpp) cc_final: 0.8448 (mpp) REVERT: A 159 PHE cc_start: 0.9197 (t80) cc_final: 0.8974 (t80) REVERT: A 167 CYS cc_start: 0.9457 (p) cc_final: 0.9216 (p) REVERT: A 172 PHE cc_start: 0.8547 (m-10) cc_final: 0.8202 (m-10) REVERT: A 296 ASP cc_start: 0.8833 (t0) cc_final: 0.8343 (t70) REVERT: A 401 MET cc_start: 0.8515 (tpt) cc_final: 0.8278 (tpp) REVERT: A 503 GLU cc_start: 0.8882 (pm20) cc_final: 0.8551 (pm20) REVERT: A 524 ASP cc_start: 0.8784 (p0) cc_final: 0.8405 (p0) REVERT: A 591 LYS cc_start: 0.9388 (pttp) cc_final: 0.9105 (pttp) REVERT: A 594 TYR cc_start: 0.8330 (m-80) cc_final: 0.7653 (m-80) REVERT: A 872 GLU cc_start: 0.8537 (pp20) cc_final: 0.8227 (pp20) REVERT: A 938 MET cc_start: 0.9283 (tpp) cc_final: 0.8962 (tpp) REVERT: B 154 MET cc_start: 0.7402 (mmm) cc_final: 0.7157 (tpp) REVERT: B 159 PHE cc_start: 0.9218 (t80) cc_final: 0.8961 (t80) REVERT: B 167 CYS cc_start: 0.9408 (p) cc_final: 0.9124 (p) REVERT: B 367 MET cc_start: 0.8539 (tpt) cc_final: 0.8255 (tpp) REVERT: B 383 MET cc_start: 0.8157 (ppp) cc_final: 0.7799 (ppp) REVERT: B 386 PHE cc_start: 0.8717 (m-80) cc_final: 0.8443 (m-80) REVERT: B 427 TRP cc_start: 0.9171 (m100) cc_final: 0.8965 (m100) REVERT: B 438 LEU cc_start: 0.9736 (mm) cc_final: 0.9501 (mm) REVERT: B 588 LYS cc_start: 0.9398 (pttm) cc_final: 0.9064 (pttm) REVERT: B 590 GLU cc_start: 0.8528 (mp0) cc_final: 0.7821 (mp0) REVERT: B 591 LYS cc_start: 0.9505 (pttm) cc_final: 0.8937 (pttp) REVERT: B 594 TYR cc_start: 0.8368 (m-80) cc_final: 0.7612 (m-80) REVERT: B 611 LEU cc_start: 0.9557 (tt) cc_final: 0.9128 (tt) REVERT: B 938 MET cc_start: 0.8932 (tpt) cc_final: 0.8707 (mmm) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0836 time to fit residues: 39.8076 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064592 restraints weight = 54795.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066713 restraints weight = 31258.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068036 restraints weight = 21997.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068877 restraints weight = 17653.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069389 restraints weight = 15378.544| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2359 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= 0.128 Angle : 0.686 8.548 19644 Z= 0.323 Chirality : 0.040 0.200 2452 Planarity : 0.003 0.033 2369 Dihedral : 7.202 73.134 2764 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1792 helix: 1.44 (0.15), residues: 1278 sheet: 0.97 (0.59), residues: 86 loop : -0.24 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 856 TYR 0.015 0.001 TYR A 309 PHE 0.014 0.001 PHE B 999 TRP 0.071 0.001 TRP A 635 HIS 0.009 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14384) covalent geometry : angle 0.68587 / 0.32 (19644) hydrogen bonds : bond 0.03809 / 2.56 ( 965) hydrogen bonds : angle 3.82614 / 2.80 ( 2859) *********************** 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 277 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8340 (mp) cc_final: 0.8132 (mm) REVERT: A 159 PHE cc_start: 0.9137 (t80) cc_final: 0.8913 (t80) REVERT: A 167 CYS cc_start: 0.9451 (p) cc_final: 0.9201 (p) REVERT: A 172 PHE cc_start: 0.8538 (m-10) cc_final: 0.8225 (m-10) REVERT: A 367 MET cc_start: 0.8726 (tpt) cc_final: 0.8494 (tpp) REVERT: A 524 ASP cc_start: 0.8794 (p0) cc_final: 0.8430 (p0) REVERT: A 578 MET cc_start: 0.8885 (ppp) cc_final: 0.8668 (ppp) REVERT: A 591 LYS cc_start: 0.9419 (pttp) cc_final: 0.9142 (pttp) REVERT: A 594 TYR cc_start: 0.8430 (m-80) cc_final: 0.8152 (m-80) REVERT: A 872 GLU cc_start: 0.8530 (pp20) cc_final: 0.8267 (pp20) REVERT: A 938 MET cc_start: 0.9321 (tpp) cc_final: 0.9017 (tpp) REVERT: B 154 MET cc_start: 0.7490 (mmm) cc_final: 0.7248 (tpp) REVERT: B 159 PHE cc_start: 0.9116 (t80) cc_final: 0.8875 (t80) REVERT: B 167 CYS cc_start: 0.9377 (p) cc_final: 0.9100 (p) REVERT: B 367 MET cc_start: 0.8647 (tpt) cc_final: 0.8378 (tpp) REVERT: B 383 MET cc_start: 0.8029 (ppp) cc_final: 0.7709 (ppp) REVERT: B 386 PHE cc_start: 0.8685 (m-80) cc_final: 0.8397 (m-80) REVERT: B 588 LYS cc_start: 0.9375 (pttm) cc_final: 0.8981 (pttm) REVERT: B 591 LYS cc_start: 0.9515 (pttm) cc_final: 0.9144 (pttp) REVERT: B 594 TYR cc_start: 0.8518 (m-80) cc_final: 0.7981 (m-80) REVERT: B 611 LEU cc_start: 0.9576 (tt) cc_final: 0.9262 (tt) REVERT: B 938 MET cc_start: 0.8996 (tpt) cc_final: 0.8770 (mmm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.0816 time to fit residues: 36.5020 Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3718 r_free = 0.3718 target = 0.095353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064639 restraints weight = 54984.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066762 restraints weight = 31393.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068051 restraints weight = 22098.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068936 restraints weight = 17729.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069495 restraints weight = 15407.003| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2420 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= 0.131 Angle : 0.691 8.538 19644 Z= 0.325 Chirality : 0.040 0.198 2452 Planarity : 0.003 0.033 2369 Dihedral : 7.225 72.016 2764 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1792 helix: 1.43 (0.15), residues: 1278 sheet: 0.90 (0.58), residues: 86 loop : -0.25 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.016 0.001 TYR B 392 PHE 0.013 0.001 PHE B 406 TRP 0.062 0.001 TRP A 635 HIS 0.008 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14384) covalent geometry : angle 0.69072 / 0.33 (19644) hydrogen bonds : bond 0.03884 / 2.60 ( 965) hydrogen bonds : angle 3.83730 / 2.80 ( 2859) *********************** 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 283 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8490 (mpp) cc_final: 0.8227 (mpp) REVERT: A 159 PHE cc_start: 0.9131 (t80) cc_final: 0.8902 (t80) REVERT: A 167 CYS cc_start: 0.9411 (p) cc_final: 0.9184 (p) REVERT: A 172 PHE cc_start: 0.8655 (m-10) cc_final: 0.8381 (m-10) REVERT: A 201 PHE cc_start: 0.9147 (t80) cc_final: 0.8896 (t80) REVERT: A 401 MET cc_start: 0.8570 (tpt) cc_final: 0.8277 (tpt) REVERT: A 524 ASP cc_start: 0.8808 (p0) cc_final: 0.8451 (p0) REVERT: A 578 MET cc_start: 0.8880 (ppp) cc_final: 0.8675 (ppp) REVERT: A 591 LYS cc_start: 0.9408 (pttp) cc_final: 0.9156 (pttp) REVERT: A 594 TYR cc_start: 0.8480 (m-80) cc_final: 0.8191 (m-80) REVERT: A 872 GLU cc_start: 0.8485 (pp20) cc_final: 0.8224 (pp20) REVERT: A 938 MET cc_start: 0.9283 (tpp) cc_final: 0.9005 (tpp) REVERT: A 939 LYS cc_start: 0.9292 (pttp) cc_final: 0.8976 (ptpp) REVERT: B 159 PHE cc_start: 0.9117 (t80) cc_final: 0.8882 (t80) REVERT: B 167 CYS cc_start: 0.9379 (p) cc_final: 0.9099 (p) REVERT: B 367 MET cc_start: 0.8630 (tpt) cc_final: 0.8372 (tpp) REVERT: B 383 MET cc_start: 0.7932 (ppp) cc_final: 0.7545 (ppp) REVERT: B 386 PHE cc_start: 0.8682 (m-80) cc_final: 0.8388 (m-80) REVERT: B 427 TRP cc_start: 0.9120 (m100) cc_final: 0.8760 (m100) REVERT: B 438 LEU cc_start: 0.9754 (mm) cc_final: 0.9546 (mm) REVERT: B 591 LYS cc_start: 0.9540 (pttm) cc_final: 0.9163 (pttp) REVERT: B 594 TYR cc_start: 0.8557 (m-80) cc_final: 0.8094 (m-80) REVERT: B 939 LYS cc_start: 0.9201 (ptmt) cc_final: 0.8962 (ptmt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0714 time to fit residues: 32.8759 Evaluate side-chains 227 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3723 r_free = 0.3723 target = 0.095743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068286 restraints weight = 54390.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068139 restraints weight = 32217.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068900 restraints weight = 25131.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069105 restraints weight = 20208.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069240 restraints weight = 19653.364| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2482 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= 0.125 Angle : 0.697 8.503 19644 Z= 0.326 Chirality : 0.040 0.194 2452 Planarity : 0.003 0.031 2369 Dihedral : 7.189 71.126 2764 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1792 helix: 1.45 (0.15), residues: 1278 sheet: 0.88 (0.58), residues: 86 loop : -0.28 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 856 TYR 0.016 0.001 TYR B 392 PHE 0.037 0.001 PHE A 95 TRP 0.059 0.001 TRP A 635 HIS 0.008 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14384) covalent geometry : angle 0.69666 / 0.33 (19644) hydrogen bonds : bond 0.03838 / 2.58 ( 965) hydrogen bonds : angle 3.82349 / 2.79 ( 2859) ********************** 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 284 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9187 (t80) cc_final: 0.8960 (t80) REVERT: A 167 CYS cc_start: 0.9427 (p) cc_final: 0.9195 (p) REVERT: A 172 PHE cc_start: 0.8697 (m-10) cc_final: 0.8428 (m-80) REVERT: A 233 GLU cc_start: 0.9173 (pt0) cc_final: 0.8956 (pt0) REVERT: A 401 MET cc_start: 0.8619 (tpt) cc_final: 0.8318 (tpt) REVERT: A 524 ASP cc_start: 0.8772 (p0) cc_final: 0.8386 (p0) REVERT: A 578 MET cc_start: 0.8923 (ppp) cc_final: 0.8720 (ppp) REVERT: A 591 LYS cc_start: 0.9378 (pttp) cc_final: 0.9111 (pttp) REVERT: A 594 TYR cc_start: 0.8426 (m-80) cc_final: 0.8137 (m-80) REVERT: A 823 LEU cc_start: 0.9658 (mt) cc_final: 0.9390 (pp) REVERT: A 872 GLU cc_start: 0.8542 (pp20) cc_final: 0.8258 (pp20) REVERT: A 938 MET cc_start: 0.9281 (tpp) cc_final: 0.8999 (tpp) REVERT: B 159 PHE cc_start: 0.9167 (t80) cc_final: 0.8932 (t80) REVERT: B 167 CYS cc_start: 0.9409 (p) cc_final: 0.9130 (p) REVERT: B 367 MET cc_start: 0.8513 (tpt) cc_final: 0.8248 (tpp) REVERT: B 383 MET cc_start: 0.8049 (ppp) cc_final: 0.7646 (ppp) REVERT: B 386 PHE cc_start: 0.8723 (m-80) cc_final: 0.8403 (m-80) REVERT: B 427 TRP cc_start: 0.9041 (m100) cc_final: 0.8581 (m100) REVERT: B 438 LEU cc_start: 0.9752 (mm) cc_final: 0.9521 (mm) REVERT: B 444 ASN cc_start: 0.8936 (m-40) cc_final: 0.8686 (t0) REVERT: B 591 LYS cc_start: 0.9521 (pttm) cc_final: 0.9114 (pttp) REVERT: B 594 TYR cc_start: 0.8378 (m-80) cc_final: 0.7912 (m-80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.0808 time to fit residues: 37.3763 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 165 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3730 r_free = 0.3730 target = 0.096149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065590 restraints weight = 54347.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067617 restraints weight = 31648.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068960 restraints weight = 22457.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069797 restraints weight = 18105.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070247 restraints weight = 15783.248| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14384 Z= 0.118 Angle : 0.698 8.475 19644 Z= 0.326 Chirality : 0.040 0.190 2452 Planarity : 0.003 0.032 2369 Dihedral : 7.127 70.302 2764 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1792 helix: 1.44 (0.15), residues: 1278 sheet: 0.93 (0.57), residues: 88 loop : -0.21 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 856 TYR 0.017 0.001 TYR B 536 PHE 0.031 0.001 PHE A 95 TRP 0.058 0.001 TRP A 635 HIS 0.007 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14384) covalent geometry : angle 0.69828 / 0.33 (19644) hydrogen bonds : bond 0.03773 / 2.53 ( 965) hydrogen bonds : angle 3.77991 / 2.75 ( 2859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.36 seconds wall clock time: 36 minutes 28.74 seconds (2188.74 seconds total)