Starting phenix.real_space_refine on Mon Jul 6 05:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.cif Found real_map, /net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.map" model { file = "/net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30kw_57864/07_2026/30kw_57864.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20672 2.51 5 N 5488 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31788 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7807 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 9 Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7807 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 9 Chain: "C" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7807 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 9 Chain: "D" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7807 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 9 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.58, per 1000 atoms: 0.24 Number of scatterers: 31788 At special positions: 0 Unit cell: (135.42, 135.42, 165.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 5460 8.00 N 5488 7.00 C 20672 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 9 sheets defined 68.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.939A pdb=" N ILE A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.747A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 178 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.682A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.306A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 395 through 404 removed outlier: 3.848A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.747A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 601 removed outlier: 4.005A pdb=" N ARG A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 682 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 835 Processing helix chain 'A' and resid 852 through 860 Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.569A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.786A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.869A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 removed outlier: 3.569A pdb=" N PHE A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.858A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.687A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.939A pdb=" N MET A 988 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.669A pdb=" N ILE A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1072 removed outlier: 3.523A pdb=" N SER A1054 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A1070 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 4.386A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1143 removed outlier: 3.660A pdb=" N LYS A1120 " --> pdb=" O GLU A1116 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1176 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.017A pdb=" N ILE B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.881A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.921A pdb=" N ARG B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.748A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.870A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 385 Processing helix chain 'B' and resid 395 through 404 removed outlier: 3.770A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.862A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.293A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 585 through 601 removed outlier: 3.869A pdb=" N ARG B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.651A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 682 removed outlier: 3.594A pdb=" N GLY B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 770 through 777 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 860 Processing helix chain 'B' and resid 862 through 884 removed outlier: 3.553A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.788A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 910 Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.908A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 973 removed outlier: 4.824A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.673A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.673A pdb=" N ILE B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1050 through 1068 removed outlier: 3.539A pdb=" N SER B1054 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1087 removed outlier: 4.249A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 3.608A pdb=" N LYS B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1175 Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.037A pdb=" N ILE C 14 " --> pdb=" O TRP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.783A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 178 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 305 through 318 Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.680A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.926A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 385 Processing helix chain 'C' and resid 395 through 404 removed outlier: 3.731A pdb=" N LEU C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.772A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 503 through 512 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 584 through 601 removed outlier: 3.528A pdb=" N LEU C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 removed outlier: 3.529A pdb=" N TRP C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 770 through 777 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 860 Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.551A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.753A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 916 through 924 removed outlier: 3.875A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 removed outlier: 3.949A pdb=" N PHE C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 933 " --> pdb=" O ASP C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 973 removed outlier: 4.847A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.677A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 removed outlier: 3.861A pdb=" N MET C 988 " --> pdb=" O VAL C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.668A pdb=" N ILE C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1050 through 1069 removed outlier: 4.364A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1087 removed outlier: 4.248A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 Processing helix chain 'C' and resid 1143 through 1175 Processing helix chain 'D' and resid 10 through 15 removed outlier: 4.032A pdb=" N ILE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 98 through 108 Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 178 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.729A pdb=" N LEU D 251 " --> pdb=" O ASN D 247 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 305 through 318 Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.781A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 356 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.784A pdb=" N LEU D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.805A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.964A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 601 removed outlier: 3.532A pdb=" N LEU D 590 " --> pdb=" O VAL D 586 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 601 " --> pdb=" O ARG D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 770 through 777 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 835 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 removed outlier: 3.573A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.788A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 910 Processing helix chain 'D' and resid 916 through 924 removed outlier: 3.920A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 removed outlier: 3.863A pdb=" N PHE D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 973 removed outlier: 4.875A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.680A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 removed outlier: 4.070A pdb=" N MET D 988 " --> pdb=" O VAL D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.679A pdb=" N ILE D1033 " --> pdb=" O LEU D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1050 through 1070 removed outlier: 3.524A pdb=" N SER D1054 " --> pdb=" O VAL D1050 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE D1069 " --> pdb=" O LEU D1065 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS D1070 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1087 removed outlier: 4.249A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 Processing helix chain 'D' and resid 1143 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 3.793A pdb=" N SER A 88 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1000 through 1001 removed outlier: 3.543A pdb=" N VAL A1012 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 20 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.971A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 233 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N GLY B 123 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE B 278 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU B 122 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 78 removed outlier: 3.659A pdb=" N SER C 88 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLY C 156 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N VAL C 121 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 16 through 20 Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 3.670A pdb=" N SER D 88 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 231 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) 1836 hydrogen bonds defined for protein. 5400 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: 6.63 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10091 1.34 - 1.46: 6293 1.46 - 1.58: 15833 1.58 - 1.70: 75 1.70 - 1.82: 280 Bond restraints: 32572 Sorted by residual: bond pdb=" C2 CLR A1301 " pdb=" C3 CLR A1301 " ideal model delta sigma weight residual 1.515 1.714 -0.199 2.00e-02 2.50e+03 9.94e+01 bond pdb=" C2 CLR A1304 " pdb=" C3 CLR A1304 " ideal model delta sigma weight residual 1.515 1.714 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C2 CLR D1304 " pdb=" C3 CLR D1304 " ideal model delta sigma weight residual 1.515 1.713 -0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C2 CLR B1303 " pdb=" C3 CLR B1303 " ideal model delta sigma weight residual 1.515 1.712 -0.197 2.00e-02 2.50e+03 9.66e+01 bond pdb=" C2 CLR D1303 " pdb=" C3 CLR D1303 " ideal model delta sigma weight residual 1.515 1.711 -0.196 2.00e-02 2.50e+03 9.64e+01 ... (remaining 32567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.20: 44196 7.20 - 14.39: 40 14.39 - 21.59: 0 21.59 - 28.78: 9 28.78 - 35.98: 3 Bond angle restraints: 44248 Sorted by residual: angle pdb=" C1 CLR C1304 " pdb=" C10 CLR C1304 " pdb=" C19 CLR C1304 " ideal model delta sigma weight residual 109.60 73.62 35.98 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C1 CLR B1302 " pdb=" C10 CLR B1302 " pdb=" C19 CLR B1302 " ideal model delta sigma weight residual 109.60 73.75 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C19 CLR B1302 " pdb=" C10 CLR B1302 " pdb=" C5 CLR B1302 " ideal model delta sigma weight residual 108.37 137.72 -29.35 3.00e+00 1.11e-01 9.57e+01 angle pdb=" C19 CLR C1304 " pdb=" C10 CLR C1304 " pdb=" C5 CLR C1304 " ideal model delta sigma weight residual 108.37 137.05 -28.68 3.00e+00 1.11e-01 9.14e+01 angle pdb=" C1 CLR B1302 " pdb=" C10 CLR B1302 " pdb=" C5 CLR B1302 " ideal model delta sigma weight residual 108.37 80.67 27.70 3.00e+00 1.11e-01 8.53e+01 ... (remaining 44243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 19578 34.24 - 68.47: 580 68.47 - 102.71: 29 102.71 - 136.95: 9 136.95 - 171.18: 12 Dihedral angle restraints: 20208 sinusoidal: 8948 harmonic: 11260 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE D 207 " pdb=" C PHE D 207 " pdb=" N PRO D 208 " pdb=" CA PRO D 208 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N PRO B 208 " pdb=" CA PRO B 208 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 20205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.084: 4997 1.084 - 2.169: 0 2.169 - 3.253: 0 3.253 - 4.338: 0 4.338 - 5.422: 3 Chirality restraints: 5000 Sorted by residual: chirality pdb=" C13 CLR D1301 " pdb=" C12 CLR D1301 " pdb=" C14 CLR D1301 " pdb=" C17 CLR D1301 " both_signs ideal model delta sigma weight residual False -2.93 2.49 -5.42 2.00e-01 2.50e+01 7.35e+02 chirality pdb=" C10 CLR B1302 " pdb=" C1 CLR B1302 " pdb=" C5 CLR B1302 " pdb=" C9 CLR B1302 " both_signs ideal model delta sigma weight residual False -2.85 2.53 -5.38 2.00e-01 2.50e+01 7.22e+02 chirality pdb=" C10 CLR C1304 " pdb=" C1 CLR C1304 " pdb=" C5 CLR C1304 " pdb=" C9 CLR C1304 " both_signs ideal model delta sigma weight residual False -2.85 2.51 -5.36 2.00e-01 2.50e+01 7.17e+02 ... (remaining 4997 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 213 " 0.026 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP D 213 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP D 213 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 213 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 213 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 213 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP D 213 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 213 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 213 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 213 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 691 " -0.018 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP A 691 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 691 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 691 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 691 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 691 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 691 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 691 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 691 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 691 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 691 " -0.015 2.00e-02 2.50e+03 1.95e-02 9.52e+00 pdb=" CG TRP B 691 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 691 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 691 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 691 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 691 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 691 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 691 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 691 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 691 " 0.002 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 12303 2.90 - 3.40: 32704 3.40 - 3.90: 51867 3.90 - 4.40: 57248 4.40 - 4.90: 95363 Nonbonded interactions: 249485 Sorted by model distance: nonbonded pdb=" O GLY B 621 " pdb=" OD1 ASP B 625 " model vdw 2.406 3.040 nonbonded pdb=" O GLY D 621 " pdb=" OD1 ASP D 625 " model vdw 2.410 3.040 nonbonded pdb=" O GLY C 621 " pdb=" OD1 ASP C 625 " model vdw 2.421 3.040 nonbonded pdb=" O GLY A 621 " pdb=" OD1 ASP A 625 " model vdw 2.454 3.040 nonbonded pdb=" C6 CLR B1302 " pdb=" C9 CLR B1302 " model vdw 2.500 3.016 ... (remaining 249480 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 3.160 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.490 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 : 0.012 0.199 32572 Z= 0.598 Angle : 0.903 35.981 44248 Z= 0.385 Chirality : 0.145 5.422 5000 Planarity : 0.004 0.039 5476 Dihedral : 15.937 171.182 12928 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.05 % Allowed : 13.10 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.14), residues: 3844 helix: 1.72 (0.11), residues: 2400 sheet: -0.26 (0.28), residues: 284 loop : -0.04 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 140 TYR 0.016 0.001 TYR D 256 PHE 0.022 0.001 PHE B 249 TRP 0.070 0.002 TRP D 213 HIS 0.006 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.01205 / 0.60 (32572) covalent geometry : angle 0.90259 / 0.38 (44248) hydrogen bonds : bond 0.13190 / 9.05 ( 1836) hydrogen bonds : angle 5.47569 / 3.93 ( 5400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 645 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.2789 (mmt) cc_final: 0.2392 (mmm) REVERT: A 659 MET cc_start: 0.7723 (tmm) cc_final: 0.7464 (ptt) REVERT: A 858 LEU cc_start: 0.8828 (tp) cc_final: 0.8596 (pp) REVERT: A 892 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7708 (ttp-170) REVERT: A 956 ASP cc_start: 0.7925 (m-30) cc_final: 0.7454 (p0) REVERT: A 1164 HIS cc_start: 0.8305 (m170) cc_final: 0.7827 (t70) REVERT: B 155 THR cc_start: 0.4646 (OUTLIER) cc_final: 0.4434 (m) REVERT: B 284 MET cc_start: 0.7539 (ptt) cc_final: 0.6468 (ttt) REVERT: B 399 LEU cc_start: 0.9543 (mt) cc_final: 0.9289 (pp) REVERT: B 509 MET cc_start: 0.6581 (ptp) cc_final: 0.5751 (mmm) REVERT: B 860 LEU cc_start: 0.8944 (mp) cc_final: 0.8646 (mt) REVERT: B 884 THR cc_start: 0.9000 (m) cc_final: 0.8800 (p) REVERT: B 926 MET cc_start: 0.6843 (mmt) cc_final: 0.6522 (mmt) REVERT: B 1132 PHE cc_start: 0.8425 (t80) cc_final: 0.8187 (t80) REVERT: B 1149 LYS cc_start: 0.9409 (ttmm) cc_final: 0.8832 (mmtp) REVERT: B 1156 ASP cc_start: 0.8913 (m-30) cc_final: 0.8473 (m-30) REVERT: B 1162 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 1167 GLU cc_start: 0.8853 (mp0) cc_final: 0.8629 (pt0) REVERT: C 309 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: C 436 ASP cc_start: 0.8466 (t0) cc_final: 0.8251 (t0) REVERT: C 659 MET cc_start: 0.7585 (tmm) cc_final: 0.7292 (ppp) REVERT: C 1156 ASP cc_start: 0.8233 (m-30) cc_final: 0.7900 (m-30) REVERT: C 1162 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7506 (mt) REVERT: D 227 TYR cc_start: 0.2399 (OUTLIER) cc_final: 0.0749 (p90) REVERT: D 253 LEU cc_start: 0.8975 (mm) cc_final: 0.8771 (mm) REVERT: D 439 GLU cc_start: 0.8803 (mp0) cc_final: 0.8298 (pm20) REVERT: D 574 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7207 (mpp) REVERT: D 576 MET cc_start: 0.5807 (tpt) cc_final: 0.5592 (tpt) REVERT: D 622 MET cc_start: 0.6780 (ptm) cc_final: 0.6542 (ptp) REVERT: D 659 MET cc_start: 0.7112 (tmm) cc_final: 0.6894 (tmm) REVERT: D 866 GLN cc_start: 0.7431 (mt0) cc_final: 0.7006 (mp10) REVERT: D 1138 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7722 (ttp-110) REVERT: D 1151 THR cc_start: 0.9288 (m) cc_final: 0.8918 (p) REVERT: D 1155 VAL cc_start: 0.8570 (t) cc_final: 0.8351 (t) REVERT: D 1171 ARG cc_start: 0.8828 (mtt-85) cc_final: 0.8602 (ptt180) outliers start: 68 outliers final: 17 residues processed: 688 average time/residue: 0.2026 time to fit residues: 226.8937 Evaluate side-chains 409 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 386 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 593 CYS Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 147 GLN A 573 GLN A 786 ASN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B1032 ASN ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN C 786 ASN C 990 HIS D 350 GLN D1131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.191778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104502 restraints weight = 62585.925| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.26 r_work: 0.3166 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32572 Z= 0.253 Angle : 0.896 34.012 44248 Z= 0.411 Chirality : 0.054 1.613 5000 Planarity : 0.006 0.059 5476 Dihedral : 9.481 177.711 5633 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.34 % Allowed : 14.49 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 3844 helix: 1.35 (0.10), residues: 2392 sheet: -0.35 (0.29), residues: 284 loop : -0.26 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 405 TYR 0.026 0.002 TYR B 577 PHE 0.029 0.002 PHE D 959 TRP 0.046 0.003 TRP B 681 HIS 0.019 0.002 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (32572) covalent geometry : angle 0.89588 / 0.41 (44248) hydrogen bonds : bond 0.06007 / 4.00 ( 1836) hydrogen bonds : angle 4.52066 / 3.21 ( 5400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 364 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8883 (tmm) cc_final: 0.8529 (ppp) REVERT: A 569 LEU cc_start: 0.9042 (tt) cc_final: 0.8831 (mp) REVERT: A 659 MET cc_start: 0.7957 (tmm) cc_final: 0.7454 (ptt) REVERT: A 678 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 936 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: A 956 ASP cc_start: 0.8570 (m-30) cc_final: 0.7725 (p0) REVERT: A 1055 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8277 (t70) REVERT: A 1119 ARG cc_start: 0.8860 (tpp-160) cc_final: 0.8284 (tpm170) REVERT: A 1149 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8709 (mptt) REVERT: B 239 THR cc_start: 0.0510 (OUTLIER) cc_final: -0.0114 (p) REVERT: B 284 MET cc_start: 0.7432 (ptt) cc_final: 0.6219 (ttt) REVERT: B 309 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: B 509 MET cc_start: 0.6920 (ptp) cc_final: 0.6107 (mmm) REVERT: B 581 MET cc_start: 0.8228 (tpp) cc_final: 0.7943 (tpp) REVERT: B 860 LEU cc_start: 0.8948 (mp) cc_final: 0.8695 (mt) REVERT: B 873 THR cc_start: 0.9171 (m) cc_final: 0.8936 (p) REVERT: B 910 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8057 (t80) REVERT: B 1068 GLU cc_start: 0.8856 (tt0) cc_final: 0.8268 (tm-30) REVERT: B 1146 GLU cc_start: 0.9079 (tp30) cc_final: 0.8653 (tp30) REVERT: B 1156 ASP cc_start: 0.8890 (m-30) cc_final: 0.8489 (m-30) REVERT: B 1167 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: C 309 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: C 381 LEU cc_start: 0.8872 (mm) cc_final: 0.8661 (mm) REVERT: C 397 LEU cc_start: 0.9187 (mp) cc_final: 0.8810 (mm) REVERT: C 399 LEU cc_start: 0.9306 (mt) cc_final: 0.8516 (tp) REVERT: C 438 PRO cc_start: 0.9100 (Cg_exo) cc_final: 0.8573 (Cg_endo) REVERT: C 635 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: C 659 MET cc_start: 0.7867 (tmm) cc_final: 0.7495 (tmm) REVERT: C 784 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7863 (ttm) REVERT: C 831 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: C 902 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: C 1080 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7206 (tt) REVERT: C 1139 ASP cc_start: 0.8971 (m-30) cc_final: 0.8706 (m-30) REVERT: C 1162 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8288 (mm) REVERT: C 1170 GLN cc_start: 0.9010 (tm130) cc_final: 0.8600 (mm110) REVERT: D 355 MET cc_start: 0.1355 (ptm) cc_final: 0.0693 (mmm) REVERT: D 439 GLU cc_start: 0.9004 (mp0) cc_final: 0.8776 (pm20) REVERT: D 574 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8100 (mmt) REVERT: D 632 ARG cc_start: 0.9250 (ttm110) cc_final: 0.8898 (mtm110) REVERT: D 659 MET cc_start: 0.7482 (tmm) cc_final: 0.7201 (tmm) REVERT: D 892 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7487 (ttp-110) REVERT: D 956 ASP cc_start: 0.8725 (m-30) cc_final: 0.8396 (m-30) REVERT: D 1068 GLU cc_start: 0.8668 (tp30) cc_final: 0.8078 (tp30) REVERT: D 1141 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8424 (tpt-90) outliers start: 111 outliers final: 48 residues processed: 456 average time/residue: 0.1865 time to fit residues: 143.1429 Evaluate side-chains 371 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 308 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 910 PHE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1167 GLU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1043 PHE Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 108 optimal weight: 30.0000 chunk 229 optimal weight: 6.9990 chunk 334 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A1017 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 990 HIS D 66 HIS D1131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.189905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113409 restraints weight = 62290.027| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 6.35 r_work: 0.2993 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 32572 Z= 0.209 Angle : 0.718 33.977 44248 Z= 0.340 Chirality : 0.049 1.698 5000 Planarity : 0.005 0.051 5476 Dihedral : 8.746 168.342 5616 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.61 % Allowed : 15.15 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3844 helix: 1.61 (0.11), residues: 2420 sheet: -0.35 (0.29), residues: 284 loop : -0.22 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 632 TYR 0.025 0.002 TYR A 364 PHE 0.023 0.002 PHE C 936 TRP 0.037 0.002 TRP A 403 HIS 0.046 0.002 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (32572) covalent geometry : angle 0.71839 / 0.34 (44248) hydrogen bonds : bond 0.05832 / 3.90 ( 1836) hydrogen bonds : angle 4.39328 / 3.12 ( 5400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 309 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5889 (OUTLIER) cc_final: 0.5460 (mmmt) REVERT: A 659 MET cc_start: 0.8011 (tmm) cc_final: 0.7476 (ptt) REVERT: A 675 LEU cc_start: 0.8695 (mp) cc_final: 0.8446 (tp) REVERT: A 678 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 936 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: A 1139 ASP cc_start: 0.8742 (t0) cc_final: 0.8120 (m-30) REVERT: A 1153 GLN cc_start: 0.9413 (mt0) cc_final: 0.9160 (mm-40) REVERT: B 284 MET cc_start: 0.7347 (ptt) cc_final: 0.5827 (ttt) REVERT: B 298 CYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8766 (t) REVERT: B 309 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: B 509 MET cc_start: 0.7023 (ptp) cc_final: 0.6312 (mmm) REVERT: B 581 MET cc_start: 0.8521 (tpp) cc_final: 0.8301 (tpp) REVERT: B 617 PHE cc_start: 0.9304 (t80) cc_final: 0.8946 (m-80) REVERT: B 675 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 860 LEU cc_start: 0.9058 (mp) cc_final: 0.8779 (mt) REVERT: B 1034 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8187 (tt) REVERT: B 1068 GLU cc_start: 0.8978 (tt0) cc_final: 0.8413 (tm-30) REVERT: B 1146 GLU cc_start: 0.9129 (tp30) cc_final: 0.8630 (tp30) REVERT: B 1156 ASP cc_start: 0.8852 (m-30) cc_final: 0.8453 (m-30) REVERT: B 1167 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8589 (pt0) REVERT: C 117 LEU cc_start: 0.8827 (tp) cc_final: 0.8613 (tt) REVERT: C 275 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8741 (mm) REVERT: C 309 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: C 381 LEU cc_start: 0.8945 (mm) cc_final: 0.8690 (mm) REVERT: C 397 LEU cc_start: 0.9081 (mp) cc_final: 0.8716 (mm) REVERT: C 635 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6373 (pp20) REVERT: C 659 MET cc_start: 0.7993 (tmm) cc_final: 0.7578 (tmm) REVERT: C 936 PHE cc_start: 0.9126 (m-80) cc_final: 0.8873 (m-80) REVERT: C 1139 ASP cc_start: 0.8986 (m-30) cc_final: 0.8714 (m-30) REVERT: D 355 MET cc_start: 0.1713 (ptm) cc_final: 0.1009 (mmm) REVERT: D 439 GLU cc_start: 0.9060 (mp0) cc_final: 0.8857 (pm20) REVERT: D 632 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8765 (mtm110) REVERT: D 659 MET cc_start: 0.7608 (tmm) cc_final: 0.7298 (tmm) REVERT: D 699 CYS cc_start: 0.8041 (t) cc_final: 0.7473 (t) REVERT: D 956 ASP cc_start: 0.8842 (m-30) cc_final: 0.8355 (m-30) REVERT: D 989 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5921 (tm-30) REVERT: D 1055 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.9001 (t70) REVERT: D 1068 GLU cc_start: 0.8824 (tp30) cc_final: 0.8372 (tp30) outliers start: 120 outliers final: 68 residues processed: 399 average time/residue: 0.1811 time to fit residues: 122.4298 Evaluate side-chains 367 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1167 GLU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 957 SER Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain C residue 991 SER Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1055 ASP Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 183 optimal weight: 1.9990 chunk 309 optimal weight: 40.0000 chunk 363 optimal weight: 0.9990 chunk 321 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 148 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 240 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.191815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114252 restraints weight = 62545.255| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 5.84 r_work: 0.3032 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32572 Z= 0.117 Angle : 0.646 33.661 44248 Z= 0.297 Chirality : 0.046 1.686 5000 Planarity : 0.004 0.043 5476 Dihedral : 8.186 172.033 5606 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.80 % Allowed : 15.93 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3844 helix: 1.91 (0.11), residues: 2400 sheet: -0.29 (0.29), residues: 284 loop : -0.15 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 442 TYR 0.020 0.001 TYR B1057 PHE 0.022 0.001 PHE D 249 TRP 0.040 0.001 TRP D 403 HIS 0.009 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (32572) covalent geometry : angle 0.64551 / 0.30 (44248) hydrogen bonds : bond 0.04619 / 3.08 ( 1836) hydrogen bonds : angle 4.07085 / 2.90 ( 5400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 312 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5428 (mmmt) REVERT: A 458 MET cc_start: 0.8963 (tmm) cc_final: 0.8577 (ppp) REVERT: A 565 TRP cc_start: 0.8659 (t60) cc_final: 0.8338 (t60) REVERT: A 659 MET cc_start: 0.8007 (tmm) cc_final: 0.7655 (tmm) REVERT: A 678 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 858 LEU cc_start: 0.9386 (tp) cc_final: 0.9099 (pp) REVERT: A 936 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 1139 ASP cc_start: 0.8703 (t0) cc_final: 0.8031 (m-30) REVERT: A 1153 GLN cc_start: 0.9382 (mt0) cc_final: 0.9132 (mm-40) REVERT: B 284 MET cc_start: 0.7326 (ptt) cc_final: 0.5663 (ttt) REVERT: B 298 CYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8728 (t) REVERT: B 309 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: B 429 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9016 (mp) REVERT: B 509 MET cc_start: 0.7034 (ptp) cc_final: 0.6305 (mmm) REVERT: B 563 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 581 MET cc_start: 0.8573 (tpp) cc_final: 0.8340 (tpp) REVERT: B 617 PHE cc_start: 0.9391 (t80) cc_final: 0.8954 (m-80) REVERT: B 675 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 860 LEU cc_start: 0.9041 (mp) cc_final: 0.8750 (mt) REVERT: B 1068 GLU cc_start: 0.9037 (tt0) cc_final: 0.8502 (tm-30) REVERT: B 1146 GLU cc_start: 0.9153 (tp30) cc_final: 0.8657 (tp30) REVERT: B 1156 ASP cc_start: 0.8879 (m-30) cc_final: 0.8471 (m-30) REVERT: B 1167 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: C 309 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: C 381 LEU cc_start: 0.8900 (mm) cc_final: 0.8627 (mm) REVERT: C 659 MET cc_start: 0.8004 (tmm) cc_final: 0.7762 (tmm) REVERT: C 936 PHE cc_start: 0.9074 (m-80) cc_final: 0.8805 (m-80) REVERT: C 1139 ASP cc_start: 0.8938 (m-30) cc_final: 0.8606 (m-30) REVERT: C 1171 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8519 (mmm160) REVERT: D 355 MET cc_start: 0.1632 (ptm) cc_final: 0.0944 (mmm) REVERT: D 439 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: D 632 ARG cc_start: 0.9170 (ttm110) cc_final: 0.8744 (mtm110) REVERT: D 699 CYS cc_start: 0.7805 (t) cc_final: 0.7179 (t) REVERT: D 956 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: D 989 GLU cc_start: 0.6234 (tm-30) cc_final: 0.6017 (tm-30) REVERT: D 1055 ASP cc_start: 0.9201 (t70) cc_final: 0.8979 (t70) REVERT: D 1068 GLU cc_start: 0.8874 (tp30) cc_final: 0.8420 (tp30) outliers start: 93 outliers final: 57 residues processed: 378 average time/residue: 0.1858 time to fit residues: 118.8903 Evaluate side-chains 356 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1167 GLU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 279 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 389 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN A1084 HIS ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C1053 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.188725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111568 restraints weight = 62283.002| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 6.30 r_work: 0.2950 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32572 Z= 0.217 Angle : 0.708 34.107 44248 Z= 0.330 Chirality : 0.048 1.682 5000 Planarity : 0.005 0.050 5476 Dihedral : 8.297 170.209 5606 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.49 % Allowed : 16.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.14), residues: 3844 helix: 1.69 (0.11), residues: 2424 sheet: -0.35 (0.29), residues: 276 loop : -0.24 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1150 TYR 0.016 0.001 TYR A 364 PHE 0.018 0.002 PHE A 935 TRP 0.022 0.002 TRP D 403 HIS 0.011 0.001 HIS C 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (32572) covalent geometry : angle 0.70827 / 0.33 (44248) hydrogen bonds : bond 0.05951 / 3.97 ( 1836) hydrogen bonds : angle 4.30075 / 3.07 ( 5400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 289 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5391 (mmmt) REVERT: A 458 MET cc_start: 0.8975 (tmm) cc_final: 0.8607 (ppp) REVERT: A 565 TRP cc_start: 0.8784 (t60) cc_final: 0.8492 (t60) REVERT: A 581 MET cc_start: 0.8735 (mmp) cc_final: 0.8495 (mmp) REVERT: A 659 MET cc_start: 0.8211 (tmm) cc_final: 0.7806 (tmm) REVERT: A 678 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 691 TRP cc_start: 0.8313 (p-90) cc_final: 0.8103 (p90) REVERT: A 1139 ASP cc_start: 0.9014 (t0) cc_final: 0.8334 (m-30) REVERT: A 1153 GLN cc_start: 0.9443 (mt0) cc_final: 0.9165 (mm-40) REVERT: B 298 CYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8759 (t) REVERT: B 309 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: B 509 MET cc_start: 0.7196 (ptp) cc_final: 0.6440 (mmm) REVERT: B 581 MET cc_start: 0.8842 (tpp) cc_final: 0.8631 (tpp) REVERT: B 617 PHE cc_start: 0.9389 (t80) cc_final: 0.8956 (m-80) REVERT: B 675 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8361 (tp) REVERT: B 860 LEU cc_start: 0.9142 (mp) cc_final: 0.8851 (mt) REVERT: B 1146 GLU cc_start: 0.9157 (tp30) cc_final: 0.8614 (tp30) REVERT: B 1156 ASP cc_start: 0.8936 (m-30) cc_final: 0.8594 (m-30) REVERT: B 1167 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: C 275 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8724 (mm) REVERT: C 309 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: C 381 LEU cc_start: 0.8956 (mm) cc_final: 0.8752 (mm) REVERT: C 659 MET cc_start: 0.8161 (tmm) cc_final: 0.7891 (tmm) REVERT: C 831 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: C 1139 ASP cc_start: 0.8984 (m-30) cc_final: 0.8644 (m-30) REVERT: C 1162 LEU cc_start: 0.8665 (mm) cc_final: 0.8336 (mm) REVERT: C 1171 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8408 (mmm160) REVERT: D 355 MET cc_start: 0.1748 (ptm) cc_final: 0.1038 (mmm) REVERT: D 439 GLU cc_start: 0.9153 (mp0) cc_final: 0.8915 (pm20) REVERT: D 574 MET cc_start: 0.9101 (tpp) cc_final: 0.8826 (mpp) REVERT: D 632 ARG cc_start: 0.9106 (ttm110) cc_final: 0.8682 (mtm110) REVERT: D 699 CYS cc_start: 0.7911 (t) cc_final: 0.7269 (t) REVERT: D 831 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: D 956 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: D 1068 GLU cc_start: 0.8910 (tp30) cc_final: 0.8482 (tp30) REVERT: D 1141 ARG cc_start: 0.8641 (tpt-90) cc_final: 0.8291 (tpt-90) outliers start: 116 outliers final: 74 residues processed: 377 average time/residue: 0.1823 time to fit residues: 116.6614 Evaluate side-chains 358 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1167 GLU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 957 SER Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 245 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 chunk 373 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 295 optimal weight: 0.0770 chunk 346 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 990 HIS D1131 ASN ** D1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.191472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.113408 restraints weight = 62426.518| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.80 r_work: 0.3016 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32572 Z= 0.115 Angle : 0.648 33.379 44248 Z= 0.295 Chirality : 0.045 1.693 5000 Planarity : 0.004 0.041 5476 Dihedral : 7.893 172.241 5604 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.83 % Allowed : 16.87 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3844 helix: 1.92 (0.11), residues: 2420 sheet: -0.52 (0.29), residues: 284 loop : -0.16 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 442 TYR 0.018 0.001 TYR C 256 PHE 0.016 0.001 PHE D 249 TRP 0.026 0.001 TRP D 403 HIS 0.030 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (32572) covalent geometry : angle 0.64812 / 0.30 (44248) hydrogen bonds : bond 0.04489 / 3.00 ( 1836) hydrogen bonds : angle 4.01898 / 2.87 ( 5400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 299 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5409 (mmmt) REVERT: A 458 MET cc_start: 0.8928 (tmm) cc_final: 0.8588 (ppp) REVERT: A 565 TRP cc_start: 0.8839 (t60) cc_final: 0.8633 (t60) REVERT: A 659 MET cc_start: 0.8174 (tmm) cc_final: 0.7797 (tmm) REVERT: A 678 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 858 LEU cc_start: 0.9381 (tp) cc_final: 0.9096 (pp) REVERT: A 1139 ASP cc_start: 0.8881 (t0) cc_final: 0.8251 (m-30) REVERT: A 1153 GLN cc_start: 0.9434 (mt0) cc_final: 0.9145 (mm-40) REVERT: B 284 MET cc_start: 0.7135 (ptt) cc_final: 0.5449 (ttt) REVERT: B 298 CYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8882 (t) REVERT: B 309 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: B 399 LEU cc_start: 0.9482 (mt) cc_final: 0.9117 (tp) REVERT: B 509 MET cc_start: 0.6991 (ptp) cc_final: 0.6357 (mmm) REVERT: B 617 PHE cc_start: 0.9392 (t80) cc_final: 0.8963 (m-80) REVERT: B 659 MET cc_start: 0.7993 (ptt) cc_final: 0.7255 (tmm) REVERT: B 675 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8392 (tp) REVERT: B 1146 GLU cc_start: 0.9180 (tp30) cc_final: 0.8664 (tp30) REVERT: B 1156 ASP cc_start: 0.8935 (m-30) cc_final: 0.8574 (m-30) REVERT: B 1167 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: C 309 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: C 509 MET cc_start: 0.6785 (mmt) cc_final: 0.6562 (ptp) REVERT: C 574 MET cc_start: 0.9402 (tpp) cc_final: 0.9145 (tpp) REVERT: C 659 MET cc_start: 0.8058 (tmm) cc_final: 0.7769 (tmm) REVERT: C 902 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: C 1139 ASP cc_start: 0.8906 (m-30) cc_final: 0.8554 (m-30) REVERT: C 1162 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8370 (mm) REVERT: C 1167 GLU cc_start: 0.8971 (pt0) cc_final: 0.8654 (pp20) REVERT: C 1171 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8410 (mmm160) REVERT: D 256 TYR cc_start: 0.9281 (m-80) cc_final: 0.9076 (t80) REVERT: D 355 MET cc_start: 0.1744 (ptm) cc_final: 0.1127 (mmm) REVERT: D 574 MET cc_start: 0.9108 (tpp) cc_final: 0.8865 (mpp) REVERT: D 632 ARG cc_start: 0.9092 (ttm110) cc_final: 0.8702 (mtm110) REVERT: D 699 CYS cc_start: 0.7665 (t) cc_final: 0.7139 (t) REVERT: D 956 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: D 1068 GLU cc_start: 0.8952 (tp30) cc_final: 0.8521 (tp30) REVERT: D 1141 ARG cc_start: 0.8635 (tpt-90) cc_final: 0.8194 (tpt-90) outliers start: 94 outliers final: 66 residues processed: 365 average time/residue: 0.1802 time to fit residues: 111.8239 Evaluate side-chains 363 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 288 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1167 GLU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 291 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 390 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 217 optimal weight: 30.0000 chunk 293 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 197 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1170 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS C 990 HIS ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 ASN ** D1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.183826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099289 restraints weight = 62205.586| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 6.37 r_work: 0.2838 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.118 32572 Z= 0.497 Angle : 0.967 35.382 44248 Z= 0.462 Chirality : 0.060 1.666 5000 Planarity : 0.006 0.065 5476 Dihedral : 9.176 165.630 5604 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.13 % Allowed : 16.54 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 3844 helix: 0.99 (0.10), residues: 2416 sheet: -0.47 (0.29), residues: 276 loop : -0.54 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 799 TYR 0.026 0.003 TYR A 968 PHE 0.031 0.003 PHE B 959 TRP 0.031 0.003 TRP D 403 HIS 0.019 0.002 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.01209 / 0.50 (32572) covalent geometry : angle 0.96726 / 0.46 (44248) hydrogen bonds : bond 0.08423 / 5.65 ( 1836) hydrogen bonds : angle 5.03241 / 3.59 ( 5400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 273 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5294 (mmmt) REVERT: A 186 MET cc_start: 0.3785 (OUTLIER) cc_final: 0.3413 (mmt) REVERT: A 440 PHE cc_start: 0.8795 (m-80) cc_final: 0.8152 (m-80) REVERT: A 458 MET cc_start: 0.9038 (tmm) cc_final: 0.8671 (ppp) REVERT: A 565 TRP cc_start: 0.8982 (t60) cc_final: 0.8733 (t60) REVERT: A 581 MET cc_start: 0.9152 (mmp) cc_final: 0.8599 (tpp) REVERT: A 678 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 1130 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8713 (pp20) REVERT: A 1140 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8632 (ttpp) REVERT: A 1142 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8646 (tp30) REVERT: B 509 MET cc_start: 0.7936 (ptp) cc_final: 0.7130 (mmm) REVERT: B 617 PHE cc_start: 0.9489 (t80) cc_final: 0.9016 (m-80) REVERT: B 625 ASP cc_start: 0.8801 (t0) cc_final: 0.8570 (m-30) REVERT: B 659 MET cc_start: 0.8236 (ptt) cc_final: 0.7581 (tmm) REVERT: B 675 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8483 (tp) REVERT: B 805 PHE cc_start: 0.8354 (t80) cc_final: 0.8147 (t80) REVERT: B 1139 ASP cc_start: 0.9187 (m-30) cc_final: 0.8604 (m-30) REVERT: B 1146 GLU cc_start: 0.9278 (tp30) cc_final: 0.8678 (tp30) REVERT: C 275 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8723 (mm) REVERT: C 505 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.7181 (t70) REVERT: C 1139 ASP cc_start: 0.9124 (m-30) cc_final: 0.8813 (m-30) REVERT: C 1144 ASP cc_start: 0.9223 (OUTLIER) cc_final: 0.8943 (p0) REVERT: D 355 MET cc_start: 0.1805 (ptm) cc_final: 0.1146 (mmm) REVERT: D 632 ARG cc_start: 0.8968 (ttm110) cc_final: 0.8556 (mtm110) REVERT: D 691 TRP cc_start: 0.8413 (p-90) cc_final: 0.8197 (p-90) REVERT: D 699 CYS cc_start: 0.8197 (t) cc_final: 0.7589 (t) REVERT: D 831 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: D 956 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: D 1068 GLU cc_start: 0.9098 (tp30) cc_final: 0.8657 (tp30) REVERT: D 1070 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8249 (t-90) REVERT: D 1141 ARG cc_start: 0.8741 (tpt-90) cc_final: 0.8282 (tpt-90) outliers start: 137 outliers final: 89 residues processed: 379 average time/residue: 0.1850 time to fit residues: 117.9588 Evaluate side-chains 354 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 256 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 892 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 957 SER Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1144 ASP Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1043 PHE Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1140 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 267 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 362 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 374 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN A1170 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B1170 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.189181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107718 restraints weight = 62058.753| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.18 r_work: 0.2989 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32572 Z= 0.129 Angle : 0.712 33.652 44248 Z= 0.326 Chirality : 0.047 1.677 5000 Planarity : 0.004 0.043 5476 Dihedral : 8.141 169.970 5602 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.50 % Allowed : 18.34 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.14), residues: 3844 helix: 1.67 (0.11), residues: 2400 sheet: -0.44 (0.30), residues: 276 loop : -0.35 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 405 TYR 0.016 0.001 TYR C 227 PHE 0.030 0.001 PHE D 249 TRP 0.036 0.001 TRP D 403 HIS 0.015 0.001 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (32572) covalent geometry : angle 0.71186 / 0.33 (44248) hydrogen bonds : bond 0.05127 / 3.44 ( 1836) hydrogen bonds : angle 4.25787 / 3.03 ( 5400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 289 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5615 (mmmt) REVERT: A 287 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4665 (tpt170) REVERT: A 300 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8896 (mt) REVERT: A 430 MET cc_start: 0.8762 (mmt) cc_final: 0.8477 (tpp) REVERT: A 439 GLU cc_start: 0.9502 (mp0) cc_final: 0.9043 (pm20) REVERT: A 440 PHE cc_start: 0.8739 (m-80) cc_final: 0.8319 (m-80) REVERT: A 458 MET cc_start: 0.9018 (tmm) cc_final: 0.8644 (ppp) REVERT: A 565 TRP cc_start: 0.9036 (t60) cc_final: 0.8747 (t60) REVERT: A 569 LEU cc_start: 0.8025 (mp) cc_final: 0.7683 (mp) REVERT: A 581 MET cc_start: 0.8932 (mmp) cc_final: 0.8458 (tpp) REVERT: A 659 MET cc_start: 0.7804 (tmm) cc_final: 0.7469 (tmm) REVERT: A 678 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 858 LEU cc_start: 0.9481 (tp) cc_final: 0.9146 (pp) REVERT: A 1130 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8537 (tp30) REVERT: A 1142 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8464 (tp30) REVERT: B 284 MET cc_start: 0.7145 (ptt) cc_final: 0.5320 (ttt) REVERT: B 376 ILE cc_start: 0.9062 (mm) cc_final: 0.8854 (mp) REVERT: B 509 MET cc_start: 0.7728 (ptp) cc_final: 0.6935 (mmm) REVERT: B 617 PHE cc_start: 0.9420 (t80) cc_final: 0.9015 (m-80) REVERT: B 659 MET cc_start: 0.8062 (ptt) cc_final: 0.7565 (tmm) REVERT: B 691 TRP cc_start: 0.8349 (p-90) cc_final: 0.8060 (p-90) REVERT: B 1139 ASP cc_start: 0.8985 (m-30) cc_final: 0.8403 (m-30) REVERT: B 1146 GLU cc_start: 0.9190 (tp30) cc_final: 0.8647 (tp30) REVERT: C 213 TRP cc_start: 0.4586 (t60) cc_final: 0.4325 (t60) REVERT: C 275 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8702 (mm) REVERT: C 458 MET cc_start: 0.9026 (pmm) cc_final: 0.8716 (pmm) REVERT: C 505 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.7124 (t-170) REVERT: C 1139 ASP cc_start: 0.8876 (m-30) cc_final: 0.8580 (m-30) REVERT: C 1146 GLU cc_start: 0.9038 (tp30) cc_final: 0.8618 (tp30) REVERT: C 1167 GLU cc_start: 0.8909 (pt0) cc_final: 0.8580 (pp20) REVERT: D 300 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6322 (mt) REVERT: D 355 MET cc_start: 0.1741 (ptm) cc_final: 0.1102 (mmm) REVERT: D 381 LEU cc_start: 0.8823 (mm) cc_final: 0.8615 (mm) REVERT: D 573 GLN cc_start: 0.7455 (pm20) cc_final: 0.7076 (pp30) REVERT: D 632 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8347 (mtm110) REVERT: D 691 TRP cc_start: 0.8176 (p-90) cc_final: 0.7676 (p90) REVERT: D 956 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: D 1068 GLU cc_start: 0.9096 (tp30) cc_final: 0.8789 (tp30) REVERT: D 1141 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8286 (tpt-90) outliers start: 83 outliers final: 57 residues processed: 347 average time/residue: 0.1924 time to fit residues: 111.4314 Evaluate side-chains 334 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 216 optimal weight: 9.9990 chunk 228 optimal weight: 40.0000 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN A 786 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C1017 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN ** D1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.188803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109900 restraints weight = 61727.822| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 6.28 r_work: 0.2976 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32572 Z= 0.133 Angle : 0.696 33.248 44248 Z= 0.314 Chirality : 0.048 1.706 5000 Planarity : 0.004 0.044 5476 Dihedral : 7.819 171.232 5602 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.56 % Allowed : 18.28 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.14), residues: 3844 helix: 1.81 (0.11), residues: 2396 sheet: -0.55 (0.30), residues: 276 loop : -0.33 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 442 TYR 0.023 0.001 TYR B1057 PHE 0.040 0.001 PHE D 249 TRP 0.025 0.001 TRP C 213 HIS 0.012 0.001 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (32572) covalent geometry : angle 0.69584 / 0.31 (44248) hydrogen bonds : bond 0.04910 / 3.29 ( 1836) hydrogen bonds : angle 4.18008 / 2.99 ( 5400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5489 (mmmt) REVERT: A 300 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8916 (mt) REVERT: A 430 MET cc_start: 0.8867 (mmt) cc_final: 0.8621 (tpp) REVERT: A 440 PHE cc_start: 0.9078 (m-80) cc_final: 0.8422 (m-80) REVERT: A 458 MET cc_start: 0.9018 (tmm) cc_final: 0.8645 (ppp) REVERT: A 581 MET cc_start: 0.8879 (mmp) cc_final: 0.8516 (tpp) REVERT: A 678 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 858 LEU cc_start: 0.9481 (tp) cc_final: 0.9131 (pp) REVERT: A 1130 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8566 (tp30) REVERT: A 1142 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8579 (tp30) REVERT: B 284 MET cc_start: 0.7047 (ptt) cc_final: 0.5139 (ttt) REVERT: B 376 ILE cc_start: 0.9087 (mm) cc_final: 0.8877 (mp) REVERT: B 509 MET cc_start: 0.7723 (ptp) cc_final: 0.6944 (mmm) REVERT: B 565 TRP cc_start: 0.8989 (t60) cc_final: 0.8599 (t60) REVERT: B 617 PHE cc_start: 0.9394 (t80) cc_final: 0.9032 (m-80) REVERT: B 659 MET cc_start: 0.7954 (ptt) cc_final: 0.7518 (tmm) REVERT: B 691 TRP cc_start: 0.8348 (p-90) cc_final: 0.8059 (p-90) REVERT: B 1139 ASP cc_start: 0.8961 (m-30) cc_final: 0.8404 (m-30) REVERT: B 1146 GLU cc_start: 0.9190 (tp30) cc_final: 0.8603 (tp30) REVERT: C 213 TRP cc_start: 0.4609 (t60) cc_final: 0.4309 (t60) REVERT: C 275 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 403 TRP cc_start: 0.9183 (m-10) cc_final: 0.8954 (m-10) REVERT: C 458 MET cc_start: 0.8960 (pmm) cc_final: 0.8661 (pmm) REVERT: C 565 TRP cc_start: 0.9142 (t60) cc_final: 0.8863 (t60) REVERT: C 805 PHE cc_start: 0.8146 (t80) cc_final: 0.7909 (t80) REVERT: C 1139 ASP cc_start: 0.8789 (m-30) cc_final: 0.8454 (m-30) REVERT: C 1146 GLU cc_start: 0.9001 (tp30) cc_final: 0.8599 (tp30) REVERT: D 300 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6308 (mt) REVERT: D 355 MET cc_start: 0.1821 (ptm) cc_final: 0.1176 (mmm) REVERT: D 381 LEU cc_start: 0.8806 (mm) cc_final: 0.8572 (mm) REVERT: D 573 GLN cc_start: 0.7563 (pm20) cc_final: 0.7157 (pp30) REVERT: D 632 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8432 (mtm110) REVERT: D 956 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: D 1068 GLU cc_start: 0.9076 (tp30) cc_final: 0.8775 (tp30) REVERT: D 1141 ARG cc_start: 0.8721 (tpt-90) cc_final: 0.8340 (tpt-90) outliers start: 85 outliers final: 61 residues processed: 337 average time/residue: 0.1924 time to fit residues: 108.1399 Evaluate side-chains 336 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 245 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 128 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1084 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 990 HIS C1017 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.189279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112169 restraints weight = 61876.905| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.75 r_work: 0.2999 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32572 Z= 0.121 Angle : 0.702 33.072 44248 Z= 0.315 Chirality : 0.047 1.708 5000 Planarity : 0.004 0.045 5476 Dihedral : 7.702 171.755 5602 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.05 % Allowed : 18.83 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.14), residues: 3844 helix: 1.86 (0.11), residues: 2396 sheet: -0.52 (0.30), residues: 276 loop : -0.29 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 442 TYR 0.009 0.001 TYR D1057 PHE 0.035 0.001 PHE D 249 TRP 0.079 0.002 TRP D 403 HIS 0.015 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (32572) covalent geometry : angle 0.70197 / 0.31 (44248) hydrogen bonds : bond 0.04598 / 3.07 ( 1836) hydrogen bonds : angle 4.11769 / 2.95 ( 5400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 279 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5471 (mmmt) REVERT: A 300 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 430 MET cc_start: 0.8860 (mmt) cc_final: 0.8624 (tpp) REVERT: A 440 PHE cc_start: 0.8893 (m-80) cc_final: 0.8168 (m-80) REVERT: A 458 MET cc_start: 0.9007 (tmm) cc_final: 0.8636 (ppp) REVERT: A 581 MET cc_start: 0.8855 (mmp) cc_final: 0.8550 (tpp) REVERT: A 678 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 858 LEU cc_start: 0.9486 (tp) cc_final: 0.9143 (pp) REVERT: A 1130 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8568 (tp30) REVERT: A 1142 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8595 (tp30) REVERT: B 284 MET cc_start: 0.7018 (ptt) cc_final: 0.5106 (ttt) REVERT: B 376 ILE cc_start: 0.9084 (mm) cc_final: 0.8870 (mp) REVERT: B 509 MET cc_start: 0.7610 (ptp) cc_final: 0.6815 (mmm) REVERT: B 565 TRP cc_start: 0.8996 (t60) cc_final: 0.8597 (t60) REVERT: B 617 PHE cc_start: 0.9372 (t80) cc_final: 0.9025 (m-80) REVERT: B 659 MET cc_start: 0.7921 (ptt) cc_final: 0.7539 (tmm) REVERT: B 691 TRP cc_start: 0.8300 (p-90) cc_final: 0.8027 (p-90) REVERT: B 1139 ASP cc_start: 0.8934 (m-30) cc_final: 0.8384 (m-30) REVERT: C 213 TRP cc_start: 0.4526 (t60) cc_final: 0.4230 (t60) REVERT: C 275 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8667 (mm) REVERT: C 403 TRP cc_start: 0.9201 (m-10) cc_final: 0.8938 (m-10) REVERT: C 458 MET cc_start: 0.8915 (pmm) cc_final: 0.8605 (pmm) REVERT: C 565 TRP cc_start: 0.9155 (t60) cc_final: 0.8869 (t60) REVERT: C 691 TRP cc_start: 0.8373 (p-90) cc_final: 0.8099 (p-90) REVERT: C 936 PHE cc_start: 0.9065 (m-80) cc_final: 0.8854 (m-80) REVERT: C 1139 ASP cc_start: 0.8818 (m-30) cc_final: 0.8416 (m-30) REVERT: C 1146 GLU cc_start: 0.9007 (tp30) cc_final: 0.8620 (tp30) REVERT: C 1162 LEU cc_start: 0.8919 (mm) cc_final: 0.8551 (mm) REVERT: C 1167 GLU cc_start: 0.8860 (pt0) cc_final: 0.8552 (pp20) REVERT: D 300 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6312 (mt) REVERT: D 355 MET cc_start: 0.1806 (ptm) cc_final: 0.1163 (mmm) REVERT: D 381 LEU cc_start: 0.8801 (mm) cc_final: 0.8591 (mm) REVERT: D 573 GLN cc_start: 0.7620 (pm20) cc_final: 0.7194 (pp30) REVERT: D 632 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8421 (mtm110) REVERT: D 691 TRP cc_start: 0.8315 (p-90) cc_final: 0.7697 (p90) REVERT: D 956 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: D 1068 GLU cc_start: 0.9074 (tp30) cc_final: 0.8761 (tp30) REVERT: D 1141 ARG cc_start: 0.8715 (tpt-90) cc_final: 0.8325 (tpt-90) outliers start: 68 outliers final: 59 residues processed: 331 average time/residue: 0.1893 time to fit residues: 104.5895 Evaluate side-chains 338 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 892 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1138 ARG Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 892 ARG Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 251 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 372 optimal weight: 0.0570 chunk 390 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 110 optimal weight: 40.0000 chunk 320 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C1017 ASN C1153 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.187932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105493 restraints weight = 61780.492| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 7.36 r_work: 0.2932 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.7334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32572 Z= 0.178 Angle : 0.723 33.271 44248 Z= 0.328 Chirality : 0.049 1.712 5000 Planarity : 0.004 0.047 5476 Dihedral : 7.777 170.810 5600 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.44 % Allowed : 18.37 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.14), residues: 3844 helix: 1.84 (0.11), residues: 2380 sheet: -0.54 (0.30), residues: 276 loop : -0.31 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 442 TYR 0.023 0.001 TYR B1057 PHE 0.035 0.001 PHE D 249 TRP 0.060 0.002 TRP D 691 HIS 0.021 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (32572) covalent geometry : angle 0.72339 / 0.33 (44248) hydrogen bonds : bond 0.05351 / 3.58 ( 1836) hydrogen bonds : angle 4.24800 / 3.04 ( 5400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11969.52 seconds wall clock time: 204 minutes 28.53 seconds (12268.53 seconds total)