Starting phenix.real_space_refine on Sat May 17 18:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964.map" model { file = "/net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u6z_41964/05_2025/8u6z_41964_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.048 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 82 5.16 5 C 10499 2.51 5 N 2608 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7842 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 969} Chain breaks: 5 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7842 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 969} Chain breaks: 5 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 23 Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 200 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 23 Time building chain proxies: 9.25, per 1000 atoms: 0.58 Number of scatterers: 16046 At special positions: 0 Unit cell: (109.02, 142.14, 126.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 3 15.00 O 2854 8.00 N 2608 7.00 C 10499 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: 3.79 Conformation dependent library (CDL) restraints added in 2.1 seconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3764 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 9 sheets defined 75.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.539A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.623A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.734A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.675A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.908A pdb=" N SER A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.101A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 297 through 319 Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.204A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 377 removed outlier: 3.955A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.882A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.792A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.443A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.567A pdb=" N CYS A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.274A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 653 removed outlier: 3.606A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 699 removed outlier: 4.072A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 3.578A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 756 removed outlier: 4.007A pdb=" N SER A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 777 removed outlier: 3.676A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 807 through 816 removed outlier: 4.219A pdb=" N MET A 810 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 854 removed outlier: 3.906A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 4.112A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.162A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.689A pdb=" N LEU A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix removed outlier: 3.715A pdb=" N MET A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.577A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.398A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.624A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 154 removed outlier: 3.620A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.654A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.882A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.145A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.504A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.155A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 380 removed outlier: 4.233A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 removed outlier: 3.886A pdb=" N LEU B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.836A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 481 removed outlier: 3.528A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.588A pdb=" N CYS B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 601 Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.266A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 640 through 653 removed outlier: 3.610A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 699 removed outlier: 4.085A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 731 through 756 removed outlier: 4.027A pdb=" N SER B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 777 removed outlier: 3.700A pdb=" N LYS B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 777 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 807 through 816 removed outlier: 4.223A pdb=" N MET B 810 " --> pdb=" O GLY B 807 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 815 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 854 removed outlier: 3.943A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 840 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.077A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.179A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'B' and resid 952 through 959 removed outlier: 3.579A pdb=" N LEU B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 977 Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix removed outlier: 3.597A pdb=" N MET B1107 " --> pdb=" O ILE B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1123 removed outlier: 3.578A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.216A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1033 through 1037 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.721A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A1149 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1189 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A1145 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.631A pdb=" N TYR A1153 " --> pdb=" O THR A1175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.229A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1033 through 1036 Processing sheet with id=AA7, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AA8, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 5.836A pdb=" N VAL B1145 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B1189 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B1149 " --> pdb=" O ARG B1185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1151 through 1153 1123 hydrogen bonds defined for protein. 3306 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: 4.83 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2710 1.32 - 1.45: 4007 1.45 - 1.57: 9504 1.57 - 1.69: 6 1.69 - 1.82: 150 Bond restraints: 16377 Sorted by residual: bond pdb=" C26 AJP A1402 " pdb=" O25 AJP A1402 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C26 AJP B1404 " pdb=" O25 AJP B1404 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C26 AJP B1403 " pdb=" O25 AJP B1403 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C35 AJP A1403 " pdb=" O34 AJP A1403 " ideal model delta sigma weight residual 1.380 1.409 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.404 -0.029 2.00e-02 2.50e+03 2.11e+00 ... (remaining 16372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21503 1.69 - 3.38: 580 3.38 - 5.08: 109 5.08 - 6.77: 48 6.77 - 8.46: 18 Bond angle restraints: 22258 Sorted by residual: angle pdb=" C PHE A 365 " pdb=" N MET A 366 " pdb=" CA MET A 366 " ideal model delta sigma weight residual 120.31 115.25 5.06 1.52e+00 4.33e-01 1.11e+01 angle pdb=" C PHE B 294 " pdb=" N ASN B 295 " pdb=" CA ASN B 295 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C ALA B 272 " pdb=" N VAL B 273 " pdb=" CA VAL B 273 " ideal model delta sigma weight residual 122.97 119.86 3.11 9.80e-01 1.04e+00 1.01e+01 angle pdb=" C PHE B 365 " pdb=" N MET B 366 " pdb=" CA MET B 366 " ideal model delta sigma weight residual 120.31 115.69 4.62 1.52e+00 4.33e-01 9.23e+00 angle pdb=" CA MET B1107 " pdb=" CB MET B1107 " pdb=" CG MET B1107 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 ... (remaining 22253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 9460 23.30 - 46.59: 699 46.59 - 69.89: 79 69.89 - 93.19: 15 93.19 - 116.49: 18 Dihedral angle restraints: 10271 sinusoidal: 4467 harmonic: 5804 Sorted by residual: dihedral pdb=" C02 AJP A1403 " pdb=" C85 AJP A1403 " pdb=" O84 AJP A1403 " pdb=" C05 AJP A1403 " ideal model delta sinusoidal sigma weight residual -57.60 58.89 -116.49 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C02 AJP B1403 " pdb=" C85 AJP B1403 " pdb=" O84 AJP B1403 " pdb=" C05 AJP B1403 " ideal model delta sinusoidal sigma weight residual -57.60 58.05 -115.65 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C02 AJP A1402 " pdb=" C85 AJP A1402 " pdb=" O84 AJP A1402 " pdb=" C05 AJP A1402 " ideal model delta sinusoidal sigma weight residual -57.60 56.46 -114.06 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 10268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1958 0.043 - 0.086: 593 0.086 - 0.129: 142 0.129 - 0.172: 19 0.172 - 0.215: 9 Chirality restraints: 2721 Sorted by residual: chirality pdb=" C10 AJP B1404 " pdb=" C08 AJP B1404 " pdb=" C11 AJP B1404 " pdb=" O82 AJP B1404 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C10 AJP A1402 " pdb=" C08 AJP A1402 " pdb=" C11 AJP A1402 " pdb=" O82 AJP A1402 " both_signs ideal model delta sigma weight residual False 2.61 2.40 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C10 AJP B1403 " pdb=" C08 AJP B1403 " pdb=" C11 AJP B1403 " pdb=" O82 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.61 2.41 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2718 not shown) Planarity restraints: 2685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 635 " 0.016 2.00e-02 2.50e+03 1.99e-02 9.87e+00 pdb=" CG TRP B 635 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 635 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 635 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 635 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 635 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 635 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 635 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 635 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 635 " -0.016 2.00e-02 2.50e+03 1.98e-02 9.75e+00 pdb=" CG TRP A 635 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 635 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 635 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 635 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 635 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 635 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 635 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 635 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 635 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 642 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.043 5.00e-02 4.00e+02 ... (remaining 2682 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1309 2.74 - 3.28: 16191 3.28 - 3.82: 26232 3.82 - 4.36: 26565 4.36 - 4.90: 48569 Nonbonded interactions: 118866 Sorted by model distance: nonbonded pdb=" OE2 GLU A 872 " pdb=" NH2 ARG A 875 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU B 872 " pdb=" NH2 ARG B 875 " model vdw 2.200 3.120 nonbonded pdb=" OG SER B1132 " pdb=" O GLN B1135 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A1132 " pdb=" O GLN A1135 " model vdw 2.237 3.040 nonbonded pdb=" O PHE A 288 " pdb=" OG SER A 291 " model vdw 2.286 3.040 ... (remaining 118861 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 1193 or (resid 1401 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P or name C210 or name C211 or name C212 or name C213 or name C214 or na \ me C215 or name C310 or name C311 or name C312)) or (resid 1403 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C0 \ 8 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ name C23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C32 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ e C41 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 or \ name O31 or name O33 or name O34 or name O40 or name O42 or name O43 or name O4 \ 4 or name O54 or name O77 or name O78 or name O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 76 through 1193 or resid 1401 or resid 1403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 34.510 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.051 16377 Z= 0.181 Angle : 0.719 8.462 22258 Z= 0.337 Chirality : 0.044 0.215 2721 Planarity : 0.005 0.078 2685 Dihedral : 15.933 116.486 6507 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 1974 helix: 1.59 (0.14), residues: 1442 sheet: 1.40 (0.57), residues: 98 loop : -0.90 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 635 HIS 0.003 0.001 HIS B 908 PHE 0.044 0.002 PHE B 201 TYR 0.015 0.001 TYR B 309 ARG 0.003 0.000 ARG A 573 Details of bonding type rmsd hydrogen bonds : bond 0.10668 ( 1123) hydrogen bonds : angle 4.24055 ( 3306) covalent geometry : bond 0.00405 (16377) covalent geometry : angle 0.71869 (22258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8548 (ttp) cc_final: 0.8270 (ttm) REVERT: A 318 TRP cc_start: 0.6267 (t60) cc_final: 0.5851 (m100) REVERT: A 319 LEU cc_start: 0.6790 (mp) cc_final: 0.6452 (mp) REVERT: A 1047 VAL cc_start: 0.9512 (m) cc_final: 0.9165 (t) REVERT: B 154 MET cc_start: 0.8481 (ttp) cc_final: 0.8243 (ttm) REVERT: B 186 MET cc_start: 0.8063 (ttm) cc_final: 0.7855 (mtt) REVERT: B 318 TRP cc_start: 0.6446 (t60) cc_final: 0.5926 (m100) REVERT: B 319 LEU cc_start: 0.6710 (mp) cc_final: 0.6370 (mp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2387 time to fit residues: 59.8931 Evaluate side-chains 120 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN B 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092486 restraints weight = 32768.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095349 restraints weight = 60876.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096338 restraints weight = 32456.640| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 16377 Z= 0.318 Angle : 0.749 9.177 22258 Z= 0.370 Chirality : 0.043 0.160 2721 Planarity : 0.005 0.076 2685 Dihedral : 8.664 83.939 2873 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.12 % Allowed : 8.27 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 1974 helix: 1.63 (0.13), residues: 1454 sheet: 0.87 (0.52), residues: 110 loop : -0.88 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 635 HIS 0.004 0.001 HIS B 132 PHE 0.028 0.002 PHE B 201 TYR 0.021 0.002 TYR B 312 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.06208 ( 1123) hydrogen bonds : angle 4.11552 ( 3306) covalent geometry : bond 0.00753 (16377) covalent geometry : angle 0.74915 (22258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.754 Fit side-chains REVERT: A 318 TRP cc_start: 0.6477 (t60) cc_final: 0.5566 (m100) REVERT: A 319 LEU cc_start: 0.7298 (mp) cc_final: 0.6490 (mp) REVERT: B 318 TRP cc_start: 0.6654 (t60) cc_final: 0.5845 (m100) REVERT: B 319 LEU cc_start: 0.7201 (mp) cc_final: 0.6478 (mp) REVERT: B 578 MET cc_start: 0.8258 (mmt) cc_final: 0.8047 (mmm) outliers start: 19 outliers final: 17 residues processed: 141 average time/residue: 0.2279 time to fit residues: 51.4388 Evaluate side-chains 133 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 54 optimal weight: 0.0670 chunk 177 optimal weight: 7.9990 chunk 195 optimal weight: 0.0370 chunk 145 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099392 restraints weight = 32045.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102319 restraints weight = 54114.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103268 restraints weight = 30439.699| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16377 Z= 0.113 Angle : 0.513 8.356 22258 Z= 0.251 Chirality : 0.037 0.180 2721 Planarity : 0.004 0.078 2685 Dihedral : 7.414 81.391 2873 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.71 % Allowed : 11.41 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.20), residues: 1974 helix: 2.18 (0.14), residues: 1446 sheet: 0.91 (0.49), residues: 126 loop : -0.78 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 635 HIS 0.004 0.001 HIS B 908 PHE 0.021 0.001 PHE B 201 TYR 0.016 0.001 TYR B 312 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1123) hydrogen bonds : angle 3.53869 ( 3306) covalent geometry : bond 0.00226 (16377) covalent geometry : angle 0.51327 (22258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.748 Fit side-chains REVERT: A 233 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 318 TRP cc_start: 0.6044 (t60) cc_final: 0.5546 (m100) REVERT: A 319 LEU cc_start: 0.6917 (mp) cc_final: 0.6359 (mp) REVERT: A 1088 TYR cc_start: 0.7737 (t80) cc_final: 0.7323 (t80) REVERT: B 233 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 318 TRP cc_start: 0.6394 (t60) cc_final: 0.5789 (m100) REVERT: B 319 LEU cc_start: 0.6649 (mp) cc_final: 0.6216 (mp) REVERT: B 1088 TYR cc_start: 0.7877 (t80) cc_final: 0.7488 (t80) outliers start: 12 outliers final: 7 residues processed: 146 average time/residue: 0.2267 time to fit residues: 53.6726 Evaluate side-chains 136 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 140 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 41 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.127619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098859 restraints weight = 32019.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100240 restraints weight = 53012.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101144 restraints weight = 37101.998| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16377 Z= 0.112 Angle : 0.514 7.979 22258 Z= 0.248 Chirality : 0.037 0.194 2721 Planarity : 0.004 0.076 2685 Dihedral : 7.250 82.110 2873 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.65 % Allowed : 12.83 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.20), residues: 1974 helix: 2.25 (0.14), residues: 1446 sheet: 1.24 (0.52), residues: 114 loop : -0.80 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.022 0.001 PHE B 201 TYR 0.014 0.001 TYR B 312 ARG 0.001 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1123) hydrogen bonds : angle 3.46982 ( 3306) covalent geometry : bond 0.00250 (16377) covalent geometry : angle 0.51353 (22258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.616 Fit side-chains REVERT: A 233 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 318 TRP cc_start: 0.6127 (t60) cc_final: 0.5538 (m100) REVERT: A 319 LEU cc_start: 0.7023 (mp) cc_final: 0.6792 (mp) REVERT: A 578 MET cc_start: 0.8225 (mmt) cc_final: 0.7898 (mmm) REVERT: A 733 ARG cc_start: 0.7518 (mmt180) cc_final: 0.5986 (ttt180) REVERT: A 1038 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9141 (p) REVERT: A 1088 TYR cc_start: 0.7960 (t80) cc_final: 0.7597 (t80) REVERT: A 1107 MET cc_start: 0.5185 (OUTLIER) cc_final: 0.4760 (tpp) REVERT: B 233 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 290 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8924 (mp) REVERT: B 318 TRP cc_start: 0.6395 (t60) cc_final: 0.5773 (m100) REVERT: B 319 LEU cc_start: 0.6775 (mp) cc_final: 0.6309 (mp) REVERT: B 1038 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9112 (p) REVERT: B 1088 TYR cc_start: 0.8038 (t80) cc_final: 0.7671 (t80) outliers start: 28 outliers final: 13 residues processed: 146 average time/residue: 0.2433 time to fit residues: 56.6403 Evaluate side-chains 140 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1107 MET Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 1038 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103040 restraints weight = 32544.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103770 restraints weight = 59337.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103856 restraints weight = 27429.074| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16377 Z= 0.125 Angle : 0.515 8.364 22258 Z= 0.252 Chirality : 0.037 0.207 2721 Planarity : 0.004 0.076 2685 Dihedral : 7.246 80.943 2873 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.54 % Allowed : 13.48 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1974 helix: 2.27 (0.14), residues: 1446 sheet: 1.32 (0.52), residues: 114 loop : -0.74 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 643 HIS 0.003 0.000 HIS B 908 PHE 0.021 0.001 PHE B 201 TYR 0.016 0.001 TYR B 309 ARG 0.001 0.000 ARG B1092 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1123) hydrogen bonds : angle 3.46404 ( 3306) covalent geometry : bond 0.00289 (16377) covalent geometry : angle 0.51516 (22258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.662 Fit side-chains REVERT: A 233 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 318 TRP cc_start: 0.6015 (t60) cc_final: 0.5453 (m100) REVERT: A 578 MET cc_start: 0.7823 (mmt) cc_final: 0.7612 (mmm) REVERT: A 733 ARG cc_start: 0.7132 (mmt180) cc_final: 0.5763 (ttt180) REVERT: A 1088 TYR cc_start: 0.7799 (t80) cc_final: 0.7462 (t80) REVERT: A 1104 MET cc_start: 0.8055 (tpp) cc_final: 0.7760 (tpp) REVERT: B 233 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 290 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9041 (mp) REVERT: B 318 TRP cc_start: 0.6221 (t60) cc_final: 0.5714 (m100) REVERT: B 319 LEU cc_start: 0.6717 (mp) cc_final: 0.6259 (mp) REVERT: B 1088 TYR cc_start: 0.7794 (t80) cc_final: 0.7443 (t80) outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 0.2464 time to fit residues: 56.8508 Evaluate side-chains 139 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 811 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100393 restraints weight = 31850.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103780 restraints weight = 54289.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104485 restraints weight = 28898.154| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16377 Z= 0.105 Angle : 0.511 10.930 22258 Z= 0.246 Chirality : 0.036 0.223 2721 Planarity : 0.004 0.077 2685 Dihedral : 7.028 79.300 2873 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 14.48 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.20), residues: 1974 helix: 2.33 (0.14), residues: 1446 sheet: 1.43 (0.52), residues: 114 loop : -0.72 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.021 0.001 PHE B 201 TYR 0.013 0.001 TYR B 309 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 1123) hydrogen bonds : angle 3.38952 ( 3306) covalent geometry : bond 0.00231 (16377) covalent geometry : angle 0.51150 (22258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.866 Fit side-chains REVERT: A 233 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 318 TRP cc_start: 0.6034 (t60) cc_final: 0.5563 (m100) REVERT: A 578 MET cc_start: 0.8059 (mmt) cc_final: 0.7822 (mmm) REVERT: A 586 MET cc_start: 0.8638 (ttm) cc_final: 0.8408 (ttp) REVERT: A 733 ARG cc_start: 0.7310 (mmt180) cc_final: 0.5883 (ttt180) REVERT: A 1088 TYR cc_start: 0.7836 (t80) cc_final: 0.7521 (t80) REVERT: A 1104 MET cc_start: 0.8106 (tpp) cc_final: 0.7847 (tpp) REVERT: B 233 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 290 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8939 (mp) REVERT: B 318 TRP cc_start: 0.6288 (t60) cc_final: 0.5720 (m100) REVERT: B 319 LEU cc_start: 0.6847 (mp) cc_final: 0.6459 (mp) REVERT: B 1088 TYR cc_start: 0.7829 (t80) cc_final: 0.7500 (t80) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 0.2400 time to fit residues: 58.0606 Evaluate side-chains 143 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102962 restraints weight = 32535.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103121 restraints weight = 58727.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103123 restraints weight = 27595.073| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16377 Z= 0.166 Angle : 0.556 7.000 22258 Z= 0.271 Chirality : 0.038 0.217 2721 Planarity : 0.004 0.076 2685 Dihedral : 7.288 79.832 2873 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 15.13 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1974 helix: 2.26 (0.14), residues: 1446 sheet: 1.34 (0.52), residues: 114 loop : -0.71 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 643 HIS 0.003 0.001 HIS B 908 PHE 0.021 0.001 PHE B 201 TYR 0.019 0.001 TYR B 309 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 1123) hydrogen bonds : angle 3.52568 ( 3306) covalent geometry : bond 0.00394 (16377) covalent geometry : angle 0.55599 (22258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.655 Fit side-chains REVERT: A 233 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 318 TRP cc_start: 0.6166 (t60) cc_final: 0.5688 (m100) REVERT: A 733 ARG cc_start: 0.7131 (mmt180) cc_final: 0.5798 (ttt180) REVERT: A 1088 TYR cc_start: 0.7744 (t80) cc_final: 0.7463 (t80) REVERT: A 1104 MET cc_start: 0.8101 (tpp) cc_final: 0.7899 (tpp) REVERT: B 233 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 318 TRP cc_start: 0.6235 (t60) cc_final: 0.5755 (m100) REVERT: B 319 LEU cc_start: 0.6883 (mp) cc_final: 0.6399 (mp) REVERT: B 733 ARG cc_start: 0.7180 (mmt180) cc_final: 0.6264 (ttt180) REVERT: B 1088 TYR cc_start: 0.7832 (t80) cc_final: 0.7535 (t80) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.2743 time to fit residues: 62.9242 Evaluate side-chains 141 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097611 restraints weight = 32329.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101317 restraints weight = 56660.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101786 restraints weight = 29404.162| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16377 Z= 0.123 Angle : 0.542 13.768 22258 Z= 0.259 Chirality : 0.037 0.234 2721 Planarity : 0.004 0.077 2685 Dihedral : 7.095 79.890 2873 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.24 % Allowed : 15.37 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.20), residues: 1974 helix: 2.31 (0.14), residues: 1446 sheet: 1.44 (0.52), residues: 114 loop : -0.67 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 643 HIS 0.003 0.000 HIS B 908 PHE 0.011 0.001 PHE B 201 TYR 0.015 0.001 TYR B 309 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1123) hydrogen bonds : angle 3.44558 ( 3306) covalent geometry : bond 0.00284 (16377) covalent geometry : angle 0.54170 (22258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.811 Fit side-chains REVERT: A 233 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 249 MET cc_start: 0.9187 (tmm) cc_final: 0.8805 (tmm) REVERT: A 318 TRP cc_start: 0.6150 (t60) cc_final: 0.5699 (m100) REVERT: A 733 ARG cc_start: 0.7364 (mmt180) cc_final: 0.5894 (ttt180) REVERT: A 1088 TYR cc_start: 0.7942 (t80) cc_final: 0.7673 (t80) REVERT: A 1104 MET cc_start: 0.8185 (tpp) cc_final: 0.7935 (tpp) REVERT: B 233 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 318 TRP cc_start: 0.6251 (t60) cc_final: 0.5841 (m100) REVERT: B 319 LEU cc_start: 0.6930 (mp) cc_final: 0.6539 (mp) REVERT: B 733 ARG cc_start: 0.7363 (mmt180) cc_final: 0.6124 (ttt180) REVERT: B 1088 TYR cc_start: 0.7920 (t80) cc_final: 0.7602 (t80) outliers start: 21 outliers final: 15 residues processed: 147 average time/residue: 0.2406 time to fit residues: 56.2472 Evaluate side-chains 144 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 58 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.126870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097847 restraints weight = 32234.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101114 restraints weight = 56880.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101902 restraints weight = 30041.477| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16377 Z= 0.135 Angle : 0.549 7.618 22258 Z= 0.263 Chirality : 0.038 0.237 2721 Planarity : 0.004 0.076 2685 Dihedral : 7.061 80.137 2873 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.18 % Allowed : 15.96 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.20), residues: 1974 helix: 2.30 (0.14), residues: 1446 sheet: 1.42 (0.52), residues: 114 loop : -0.66 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 643 HIS 0.003 0.001 HIS A 908 PHE 0.023 0.001 PHE B 201 TYR 0.016 0.001 TYR B 309 ARG 0.001 0.000 ARG B1092 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1123) hydrogen bonds : angle 3.45912 ( 3306) covalent geometry : bond 0.00315 (16377) covalent geometry : angle 0.54881 (22258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.657 Fit side-chains REVERT: A 233 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 249 MET cc_start: 0.9193 (tmm) cc_final: 0.8821 (tmm) REVERT: A 318 TRP cc_start: 0.6154 (t60) cc_final: 0.5725 (m100) REVERT: A 578 MET cc_start: 0.8126 (mmt) cc_final: 0.7843 (mmm) REVERT: A 733 ARG cc_start: 0.7314 (mmt180) cc_final: 0.5940 (ttt180) REVERT: A 1088 TYR cc_start: 0.7836 (t80) cc_final: 0.7557 (t80) REVERT: A 1104 MET cc_start: 0.8173 (tpp) cc_final: 0.7963 (tpp) REVERT: B 233 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 318 TRP cc_start: 0.6245 (t60) cc_final: 0.5811 (m100) REVERT: B 319 LEU cc_start: 0.6943 (mp) cc_final: 0.6504 (mp) REVERT: B 733 ARG cc_start: 0.7317 (mmt180) cc_final: 0.6116 (ttt180) REVERT: B 1088 TYR cc_start: 0.7905 (t80) cc_final: 0.7618 (t80) outliers start: 20 outliers final: 18 residues processed: 144 average time/residue: 0.2359 time to fit residues: 53.9254 Evaluate side-chains 144 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102123 restraints weight = 31970.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105350 restraints weight = 54644.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106151 restraints weight = 27310.897| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16377 Z= 0.100 Angle : 0.533 8.414 22258 Z= 0.250 Chirality : 0.036 0.247 2721 Planarity : 0.004 0.078 2685 Dihedral : 6.662 78.098 2873 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 16.25 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1974 helix: 2.42 (0.14), residues: 1446 sheet: 1.52 (0.53), residues: 114 loop : -0.61 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 643 HIS 0.004 0.000 HIS A 908 PHE 0.022 0.001 PHE B 201 TYR 0.013 0.001 TYR B 312 ARG 0.002 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1123) hydrogen bonds : angle 3.33526 ( 3306) covalent geometry : bond 0.00216 (16377) covalent geometry : angle 0.53290 (22258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.645 Fit side-chains REVERT: A 199 MET cc_start: 0.8381 (tpp) cc_final: 0.8092 (tpp) REVERT: A 233 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 249 MET cc_start: 0.9125 (tmm) cc_final: 0.8730 (tmm) REVERT: A 318 TRP cc_start: 0.6056 (t60) cc_final: 0.5599 (m100) REVERT: A 733 ARG cc_start: 0.7016 (mmt180) cc_final: 0.5799 (ttt180) REVERT: A 1088 TYR cc_start: 0.7762 (t80) cc_final: 0.7473 (t80) REVERT: B 233 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 318 TRP cc_start: 0.6129 (t60) cc_final: 0.5699 (m100) REVERT: B 319 LEU cc_start: 0.6692 (mp) cc_final: 0.6382 (mp) REVERT: B 733 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6099 (ttt180) REVERT: B 1088 TYR cc_start: 0.7760 (t80) cc_final: 0.7462 (t80) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.2332 time to fit residues: 57.7679 Evaluate side-chains 152 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 58 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098044 restraints weight = 32196.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100089 restraints weight = 56947.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101226 restraints weight = 34374.776| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16377 Z= 0.132 Angle : 0.559 12.974 22258 Z= 0.264 Chirality : 0.037 0.235 2721 Planarity : 0.004 0.076 2685 Dihedral : 6.811 78.549 2873 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.06 % Allowed : 16.67 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1974 helix: 2.38 (0.14), residues: 1446 sheet: 1.50 (0.53), residues: 114 loop : -0.59 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 643 HIS 0.003 0.001 HIS B 908 PHE 0.026 0.001 PHE B 201 TYR 0.015 0.001 TYR B 309 ARG 0.002 0.000 ARG A 940 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1123) hydrogen bonds : angle 3.40522 ( 3306) covalent geometry : bond 0.00311 (16377) covalent geometry : angle 0.55871 (22258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.58 seconds wall clock time: 65 minutes 41.58 seconds (3941.58 seconds total)