Starting phenix.real_space_refine on Sat Jan 20 05:13:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iff_35415/01_2024/8iff_35415_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 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 104 5.16 5 C 8705 2.51 5 N 2366 2.21 5 O 2523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 1081": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6800 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6812 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.55 Number of scatterers: 13698 At special positions: 0 Unit cell: (113.05, 122.4, 139.4, 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 104 16.00 O 2523 8.00 N 2366 7.00 C 8705 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.5 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 14 sheets defined 35.3% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 197 through 212 removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 276 through 283 removed outlier: 4.003A pdb=" N MET A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 381 through 425 removed outlier: 3.970A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.969A pdb=" N SER A 434 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 490 through 493 No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 570 through 587 removed outlier: 4.088A pdb=" N ILE A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 815 through 829 removed outlier: 4.143A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 923 removed outlier: 3.780A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Proline residue: A 910 - end of helix removed outlier: 4.412A pdb=" N GLY A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 947 Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.555A pdb=" N THR A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1015 removed outlier: 4.133A pdb=" N VAL A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1025 removed outlier: 3.670A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A1022 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1069 No H-bonds generated for 'chain 'A' and resid 1066 through 1069' Processing helix chain 'A' and resid 1081 through 1096 removed outlier: 4.360A pdb=" N SER A1085 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1095 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.143A pdb=" N GLU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.560A pdb=" N LYS B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 276 through 283 removed outlier: 4.271A pdb=" N MET B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 381 through 401 Processing helix chain 'B' and resid 403 through 416 removed outlier: 3.645A pdb=" N ARG B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 490 through 493 No H-bonds generated for 'chain 'B' and resid 490 through 493' Processing helix chain 'B' and resid 496 through 501 removed outlier: 4.754A pdb=" N LEU B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 587 removed outlier: 3.939A pdb=" N ILE B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'B' and resid 818 through 831 removed outlier: 3.622A pdb=" N ILE B 823 " --> pdb=" O VAL B 819 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 921 removed outlier: 3.619A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 928 through 949 removed outlier: 3.900A pdb=" N GLN B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 981 removed outlier: 3.839A pdb=" N THR B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 No H-bonds generated for 'chain 'B' and resid 998 through 1001' Processing helix chain 'B' and resid 1009 through 1016 removed outlier: 3.743A pdb=" N GLN B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1025 removed outlier: 3.944A pdb=" N MET B1022 " --> pdb=" O PHE B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1072 removed outlier: 3.547A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B1072 " --> pdb=" O LEU B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1094 Processing sheet with id= A, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 Processing sheet with id= C, first strand: chain 'A' and resid 250 through 257 removed outlier: 6.787A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 455 through 460 Processing sheet with id= E, first strand: chain 'A' and resid 837 through 842 removed outlier: 3.534A pdb=" N GLY A 768 " --> pdb=" O GLU A 777 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP A 770 " --> pdb=" O CYS A 775 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS A 775 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1035 through 1037 removed outlier: 4.259A pdb=" N SER A1110 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A1103 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 4.040A pdb=" N HIS A1049 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1117 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.561A pdb=" N PHE B 182 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 86 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 90 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL B 96 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.831A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 447 through 451 Processing sheet with id= K, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.913A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 559 " --> pdb=" O VAL B 530 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.509A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS B 858 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 868 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER B 856 " --> pdb=" O VAL B 868 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS B 870 " --> pdb=" O CYS B 854 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS B 854 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 872 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 852 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 967 through 969 Processing sheet with id= N, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 3.592A pdb=" N LEU B1057 " --> pdb=" O PHE B1111 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3046 1.33 - 1.45: 2848 1.45 - 1.57: 7890 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 13952 Sorted by residual: bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.383 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBC O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.357 1.410 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 13947 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 270 105.76 - 112.82: 7629 112.82 - 119.88: 4517 119.88 - 126.94: 6253 126.94 - 134.00: 170 Bond angle restraints: 18839 Sorted by residual: angle pdb=" CA LYS A 807 " pdb=" CB LYS A 807 " pdb=" CG LYS A 807 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N ASN A 758 " pdb=" CA ASN A 758 " pdb=" C ASN A 758 " ideal model delta sigma weight residual 109.81 102.75 7.06 2.21e+00 2.05e-01 1.02e+01 angle pdb=" C ALA A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta sigma weight residual 121.14 115.76 5.38 1.75e+00 3.27e-01 9.45e+00 angle pdb=" CA LEU A 939 " pdb=" CB LEU A 939 " pdb=" CG LEU A 939 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 9.00e+00 angle pdb=" CA LYS A 807 " pdb=" C LYS A 807 " pdb=" N SER A 808 " ideal model delta sigma weight residual 118.30 114.64 3.66 1.26e+00 6.30e-01 8.44e+00 ... (remaining 18834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7177 18.00 - 36.01: 998 36.01 - 54.01: 287 54.01 - 72.01: 47 72.01 - 90.02: 22 Dihedral angle restraints: 8531 sinusoidal: 3507 harmonic: 5024 Sorted by residual: dihedral pdb=" CA THR A 969 " pdb=" C THR A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A 871 " pdb=" C PHE A 871 " pdb=" N LEU A 872 " pdb=" CA LEU A 872 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " pdb=" OD1 ASP A 441 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1522 0.039 - 0.078: 463 0.078 - 0.117: 121 0.117 - 0.156: 38 0.156 - 0.195: 3 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.52 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2144 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.329 2.00e-02 2.50e+03 2.42e-01 1.47e+03 pdb=" CAP O6E B1201 " -0.118 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.131 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.191 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.087 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.491 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.063 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.383 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.337 2.00e-02 2.50e+03 2.00e-01 1.00e+03 pdb=" CAP O6E A1201 " 0.178 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.136 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.088 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.409 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.128 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " -0.051 2.00e-02 2.50e+03 1.72e-01 7.42e+02 pdb=" CAO O6E A1201 " -0.167 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.295 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " 0.019 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.079 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " 0.024 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.043 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.070 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.407 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 363 2.70 - 3.25: 13097 3.25 - 3.80: 20397 3.80 - 4.35: 25627 4.35 - 4.90: 44222 Nonbonded interactions: 103706 Sorted by model distance: nonbonded pdb=" OG SER A 100 " pdb=" OD1 ASN A 102 " model vdw 2.153 2.440 nonbonded pdb=" O ASN A 909 " pdb=" OG SER A 912 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASN B 330 " pdb=" NE2 HIS B 549 " model vdw 2.256 2.520 nonbonded pdb=" N GLU A 262 " pdb=" OE1 GLU A 262 " model vdw 2.300 2.520 ... (remaining 103701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 through 187 or resid 194 or resid 196 through 1121 or r \ esid 1201)) selection = (chain 'B' and (resid 71 through 187 or resid 195 through 1121 or resid 1201)) } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.310 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 38.360 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13952 Z= 0.275 Angle : 0.634 10.498 18839 Z= 0.322 Chirality : 0.042 0.195 2147 Planarity : 0.010 0.242 2400 Dihedral : 18.236 90.017 5267 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.27 % Allowed : 29.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1712 helix: 1.28 (0.23), residues: 544 sheet: -0.05 (0.30), residues: 303 loop : -1.43 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.006 0.001 HIS A 467 PHE 0.019 0.002 PHE A 871 TYR 0.016 0.001 TYR A 242 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8051 (t) cc_final: 0.7653 (p) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.2601 time to fit residues: 52.5132 Evaluate side-chains 132 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 532 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.4980 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13952 Z= 0.273 Angle : 0.605 9.480 18839 Z= 0.299 Chirality : 0.042 0.166 2147 Planarity : 0.004 0.043 2400 Dihedral : 6.226 82.765 1938 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.46 % Allowed : 25.45 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1712 helix: 1.07 (0.22), residues: 550 sheet: -0.08 (0.30), residues: 314 loop : -1.47 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.022 0.002 PHE A 871 TYR 0.018 0.001 TYR A 242 ARG 0.003 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 137 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 127 THR cc_start: 0.8068 (t) cc_final: 0.7651 (p) REVERT: A 385 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8179 (t80) REVERT: A 742 MET cc_start: 0.6464 (ttt) cc_final: 0.6147 (ttt) REVERT: B 558 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6888 (tp) REVERT: B 920 MET cc_start: 0.1916 (ptm) cc_final: 0.1372 (mtp) outliers start: 82 outliers final: 52 residues processed: 205 average time/residue: 0.2320 time to fit residues: 72.3433 Evaluate side-chains 186 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13952 Z= 0.167 Angle : 0.542 9.090 18839 Z= 0.267 Chirality : 0.040 0.154 2147 Planarity : 0.004 0.041 2400 Dihedral : 5.598 73.035 1938 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.00 % Allowed : 27.38 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1712 helix: 1.34 (0.23), residues: 557 sheet: -0.11 (0.30), residues: 311 loop : -1.33 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.004 0.001 HIS B 249 PHE 0.017 0.001 PHE A 871 TYR 0.014 0.001 TYR A 242 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 139 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.5654 (m170) REVERT: A 127 THR cc_start: 0.8070 (t) cc_final: 0.7667 (p) REVERT: A 128 ASP cc_start: 0.7801 (t0) cc_final: 0.7336 (t0) REVERT: A 385 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8228 (t80) REVERT: A 450 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7824 (tt) REVERT: B 753 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7383 (mttp) REVERT: B 920 MET cc_start: 0.2002 (ptm) cc_final: 0.1409 (mtp) outliers start: 60 outliers final: 45 residues processed: 186 average time/residue: 0.2474 time to fit residues: 68.2192 Evaluate side-chains 184 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 40.0000 chunk 105 optimal weight: 0.0010 chunk 157 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN B 884 HIS B 943 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13952 Z= 0.304 Angle : 0.616 9.665 18839 Z= 0.304 Chirality : 0.043 0.184 2147 Planarity : 0.004 0.040 2400 Dihedral : 5.882 78.059 1936 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.46 % Allowed : 25.65 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1712 helix: 1.01 (0.22), residues: 562 sheet: -0.09 (0.30), residues: 312 loop : -1.37 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.021 0.002 PHE A 871 TYR 0.018 0.002 TYR A 242 ARG 0.003 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 134 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.5644 (m170) REVERT: A 229 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 385 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 89 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5744 (mt) REVERT: B 296 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6781 (tptp) REVERT: B 299 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6312 (ptm160) REVERT: B 325 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7577 (mm) REVERT: B 497 ARG cc_start: 0.7285 (ttt180) cc_final: 0.7046 (ttt180) REVERT: B 920 MET cc_start: 0.2273 (ptm) cc_final: 0.0224 (mmt) REVERT: B 965 MET cc_start: -0.1495 (mmt) cc_final: -0.1728 (mmt) REVERT: B 1001 MET cc_start: 0.2200 (mpp) cc_final: -0.0300 (ttp) outliers start: 97 outliers final: 70 residues processed: 216 average time/residue: 0.2397 time to fit residues: 77.1993 Evaluate side-chains 211 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 135 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 982 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 149 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13952 Z= 0.282 Angle : 0.601 10.073 18839 Z= 0.297 Chirality : 0.042 0.164 2147 Planarity : 0.004 0.041 2400 Dihedral : 5.827 76.814 1936 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.46 % Allowed : 25.85 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1712 helix: 1.03 (0.23), residues: 561 sheet: -0.28 (0.30), residues: 327 loop : -1.35 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.021 0.002 PHE A 871 TYR 0.018 0.001 TYR A 242 ARG 0.003 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 133 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5700 (m170) REVERT: A 130 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7781 (mmt180) REVERT: A 385 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8120 (t80) REVERT: A 508 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8017 (ttm) REVERT: B 89 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5673 (mt) REVERT: B 296 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6793 (tptp) REVERT: B 299 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6287 (ptm160) REVERT: B 325 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7580 (mm) REVERT: B 920 MET cc_start: 0.2394 (ptm) cc_final: 0.0657 (mmm) REVERT: B 1001 MET cc_start: 0.2767 (mpp) cc_final: -0.0241 (ttp) outliers start: 97 outliers final: 74 residues processed: 210 average time/residue: 0.2325 time to fit residues: 75.3245 Evaluate side-chains 209 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 128 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 982 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 50.0000 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13952 Z= 0.259 Angle : 0.598 13.018 18839 Z= 0.293 Chirality : 0.042 0.161 2147 Planarity : 0.004 0.040 2400 Dihedral : 5.794 76.041 1936 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.53 % Allowed : 25.78 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1712 helix: 0.98 (0.22), residues: 571 sheet: -0.27 (0.30), residues: 327 loop : -1.30 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.027 0.002 PHE A 916 TYR 0.017 0.001 TYR B 752 ARG 0.002 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 130 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6025 (OUTLIER) cc_final: 0.5710 (m170) REVERT: A 130 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7751 (mmt180) REVERT: A 309 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.5112 (p0) REVERT: A 385 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8182 (t80) REVERT: A 491 HIS cc_start: 0.6433 (OUTLIER) cc_final: 0.5908 (m-70) REVERT: A 508 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8048 (ttm) REVERT: B 89 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5659 (mt) REVERT: B 296 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6769 (tptp) REVERT: B 299 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6299 (ptm160) REVERT: B 325 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7530 (mm) REVERT: B 470 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 915 MET cc_start: 0.1565 (mtm) cc_final: 0.1053 (tpp) REVERT: B 920 MET cc_start: 0.2426 (ptm) cc_final: 0.0405 (mmt) REVERT: B 1001 MET cc_start: 0.2584 (mpp) cc_final: -0.0326 (ttp) outliers start: 98 outliers final: 76 residues processed: 211 average time/residue: 0.2212 time to fit residues: 71.2896 Evaluate side-chains 214 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 129 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 1020 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 40.0000 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13952 Z= 0.348 Angle : 0.657 12.793 18839 Z= 0.323 Chirality : 0.044 0.203 2147 Planarity : 0.004 0.044 2400 Dihedral : 6.101 77.471 1936 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.60 % Allowed : 26.12 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1712 helix: 0.74 (0.22), residues: 568 sheet: -0.32 (0.30), residues: 326 loop : -1.41 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 366 HIS 0.006 0.001 HIS B 249 PHE 0.028 0.002 PHE A 916 TYR 0.019 0.002 TYR A 242 ARG 0.003 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 132 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.5981 (OUTLIER) cc_final: 0.5746 (m170) REVERT: A 130 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7748 (mmt180) REVERT: A 214 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 309 ASP cc_start: 0.5629 (OUTLIER) cc_final: 0.5415 (p0) REVERT: A 385 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8150 (t80) REVERT: A 491 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5901 (m-70) REVERT: A 508 MET cc_start: 0.8287 (ttm) cc_final: 0.8053 (ttm) REVERT: A 887 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7318 (ttm110) REVERT: A 915 MET cc_start: 0.4397 (mmm) cc_final: 0.3366 (tpp) REVERT: B 89 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5868 (mt) REVERT: B 296 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6769 (tptp) REVERT: B 299 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6324 (ptm160) REVERT: B 325 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7561 (mm) REVERT: B 470 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 915 MET cc_start: 0.1613 (mtm) cc_final: 0.1017 (tpp) REVERT: B 920 MET cc_start: 0.2535 (ptm) cc_final: 0.0651 (mmm) REVERT: B 1001 MET cc_start: 0.2652 (mpp) cc_final: -0.0154 (ttp) outliers start: 99 outliers final: 78 residues processed: 216 average time/residue: 0.2363 time to fit residues: 76.4235 Evaluate side-chains 217 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 130 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 130 optimal weight: 0.0060 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 30.0000 chunk 144 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13952 Z= 0.134 Angle : 0.537 10.657 18839 Z= 0.263 Chirality : 0.039 0.140 2147 Planarity : 0.003 0.041 2400 Dihedral : 5.405 70.851 1936 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.66 % Allowed : 28.71 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1712 helix: 1.27 (0.23), residues: 569 sheet: 0.01 (0.31), residues: 295 loop : -1.32 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.003 0.001 HIS B 172 PHE 0.025 0.001 PHE A 916 TYR 0.017 0.001 TYR B 752 ARG 0.006 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6006 (OUTLIER) cc_final: 0.5796 (m170) REVERT: A 128 ASP cc_start: 0.7864 (t0) cc_final: 0.7463 (t0) REVERT: A 385 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 491 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.5937 (m-70) REVERT: A 915 MET cc_start: 0.4347 (mmm) cc_final: 0.3491 (tpp) REVERT: B 89 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5483 (mt) REVERT: B 299 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6268 (ptm160) REVERT: B 325 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 470 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 920 MET cc_start: 0.2551 (ptm) cc_final: 0.0617 (mmp) REVERT: B 1001 MET cc_start: 0.2418 (mpp) cc_final: -0.0310 (ttp) outliers start: 55 outliers final: 41 residues processed: 178 average time/residue: 0.2695 time to fit residues: 71.7600 Evaluate side-chains 183 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13952 Z= 0.319 Angle : 0.638 11.485 18839 Z= 0.312 Chirality : 0.043 0.176 2147 Planarity : 0.004 0.042 2400 Dihedral : 5.894 73.297 1936 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.13 % Allowed : 28.51 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1712 helix: 0.94 (0.22), residues: 568 sheet: -0.07 (0.31), residues: 313 loop : -1.40 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.006 0.001 HIS B 249 PHE 0.024 0.002 PHE A 916 TYR 0.019 0.002 TYR A 242 ARG 0.005 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 132 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 887 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.7342 (ttm110) REVERT: A 915 MET cc_start: 0.4734 (mmm) cc_final: 0.3994 (tpp) REVERT: B 89 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5789 (mt) REVERT: B 299 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6349 (ptm160) REVERT: B 325 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7625 (mm) REVERT: B 470 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 920 MET cc_start: 0.2515 (ptm) cc_final: 0.0739 (mmm) REVERT: B 1001 MET cc_start: 0.2466 (mpp) cc_final: 0.0200 (ptt) outliers start: 62 outliers final: 51 residues processed: 183 average time/residue: 0.2522 time to fit residues: 68.5459 Evaluate side-chains 186 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 108 optimal weight: 0.0670 chunk 145 optimal weight: 0.0070 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13952 Z= 0.142 Angle : 0.548 10.368 18839 Z= 0.267 Chirality : 0.039 0.136 2147 Planarity : 0.004 0.043 2400 Dihedral : 5.446 69.630 1936 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.40 % Allowed : 29.25 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1712 helix: 1.30 (0.23), residues: 566 sheet: -0.02 (0.31), residues: 302 loop : -1.32 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 366 HIS 0.004 0.001 HIS B 249 PHE 0.023 0.001 PHE A 916 TYR 0.017 0.001 TYR B 752 ARG 0.005 0.000 ARG B 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7861 (t0) cc_final: 0.7453 (t0) REVERT: A 385 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 491 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5935 (m-70) REVERT: A 915 MET cc_start: 0.4817 (mmm) cc_final: 0.4039 (tpp) REVERT: B 89 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5504 (mt) REVERT: B 299 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6351 (ptm160) REVERT: B 325 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7457 (mm) REVERT: B 470 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 920 MET cc_start: 0.2513 (ptm) cc_final: 0.0701 (mmp) REVERT: B 1001 MET cc_start: 0.2382 (mpp) cc_final: 0.0161 (ptt) outliers start: 51 outliers final: 45 residues processed: 180 average time/residue: 0.2664 time to fit residues: 70.6474 Evaluate side-chains 189 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.1980 chunk 125 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.243732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151069 restraints weight = 15458.534| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.03 r_work: 0.3571 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13952 Z= 0.204 Angle : 0.576 10.645 18839 Z= 0.281 Chirality : 0.040 0.154 2147 Planarity : 0.004 0.042 2400 Dihedral : 5.520 68.637 1936 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.86 % Allowed : 28.51 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1712 helix: 1.22 (0.23), residues: 574 sheet: -0.04 (0.31), residues: 307 loop : -1.33 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.022 0.002 PHE A 916 TYR 0.015 0.001 TYR A 242 ARG 0.004 0.000 ARG B 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.33 seconds wall clock time: 55 minutes 49.93 seconds (3349.93 seconds total)