Starting phenix.real_space_refine on Thu Jan 23 18:47:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057.map" model { file = "/net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rcr_19057/01_2025/8rcr_19057_trim.cif" } resolution = 3.6 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= 0.006 sd= 0.033 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 124 5.16 5 C 13120 2.51 5 N 3424 2.21 5 O 3268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19936 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4900 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4900 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4900 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4900 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.56, per 1000 atoms: 0.58 Number of scatterers: 19936 At special positions: 0 Unit cell: (143.748, 143.748, 140.844, 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 124 16.00 O 3268 8.00 N 3424 7.00 C 13120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 605 through 632 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.701A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.753A pdb=" N ASP A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 652' Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.644A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 777 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 835 Processing helix chain 'A' and resid 852 through 861 removed outlier: 3.699A pdb=" N ALA A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.524A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 916 through 926 removed outlier: 3.686A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 Processing helix chain 'A' and resid 958 through 975 removed outlier: 4.803A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.707A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1033 Processing helix chain 'A' and resid 1033 through 1072 removed outlier: 3.540A pdb=" N ASN A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1093 removed outlier: 4.064A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1143 removed outlier: 3.614A pdb=" N ARG A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1163 Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 605 through 632 Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.870A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 4.153A pdb=" N ALA B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 767 through 777 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 835 Processing helix chain 'B' and resid 852 through 861 removed outlier: 3.710A pdb=" N ALA B 861 " --> pdb=" O ARG B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.580A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 916 through 926 removed outlier: 3.740A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 Processing helix chain 'B' and resid 958 through 973 removed outlier: 4.750A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.524A pdb=" N ILE B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1072 removed outlier: 3.547A pdb=" N ASN B1037 " --> pdb=" O ILE B1033 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1093 removed outlier: 4.000A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1143 removed outlier: 3.602A pdb=" N ARG B1119 " --> pdb=" O LYS B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1164 removed outlier: 3.615A pdb=" N LEU B1157 " --> pdb=" O GLN B1153 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 Processing helix chain 'C' and resid 437 through 448 Processing helix chain 'C' and resid 456 through 465 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 605 through 632 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.763A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.571A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 777 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 835 Processing helix chain 'C' and resid 852 through 861 removed outlier: 3.632A pdb=" N ALA C 861 " --> pdb=" O ARG C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.554A pdb=" N GLN C 866 " --> pdb=" O ASP C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.533A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 916 through 926 removed outlier: 3.733A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 Processing helix chain 'C' and resid 958 through 975 removed outlier: 4.792A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.720A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 975 " --> pdb=" O TYR C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.543A pdb=" N ILE C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1072 removed outlier: 5.200A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1093 Processing helix chain 'C' and resid 1114 through 1143 removed outlier: 3.608A pdb=" N ARG C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.824A pdb=" N LEU C1157 " --> pdb=" O GLN C1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 435 Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 456 through 465 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 605 through 632 Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.816A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.500A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 704 removed outlier: 3.523A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 777 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 835 Processing helix chain 'D' and resid 852 through 861 removed outlier: 3.504A pdb=" N ALA D 861 " --> pdb=" O ARG D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 926 through 952 Processing helix chain 'D' and resid 958 through 973 removed outlier: 4.805A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 1016 through 1032 Processing helix chain 'D' and resid 1033 through 1072 removed outlier: 5.271A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D1060 " --> pdb=" O LEU D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1093 Processing helix chain 'D' and resid 1114 through 1143 removed outlier: 3.606A pdb=" N ARG D1119 " --> pdb=" O LYS D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1164 1392 hydrogen bonds defined for protein. 4152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6227 1.34 - 1.46: 4822 1.46 - 1.58: 9142 1.58 - 1.70: 85 1.70 - 1.82: 192 Bond restraints: 20468 Sorted by residual: bond pdb=" C11 CLR B1402 " pdb=" C12 CLR B1402 " ideal model delta sigma weight residual 1.531 1.280 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C11 CLR C1204 " pdb=" C12 CLR C1204 " ideal model delta sigma weight residual 1.531 1.281 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C11 CLR C1202 " pdb=" C12 CLR C1202 " ideal model delta sigma weight residual 1.531 1.282 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C11 CLR A1201 " pdb=" C12 CLR A1201 " ideal model delta sigma weight residual 1.531 1.283 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C11 CLR D1501 " pdb=" C12 CLR D1501 " ideal model delta sigma weight residual 1.531 1.283 0.248 2.00e-02 2.50e+03 1.54e+02 ... (remaining 20463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 27066 2.23 - 4.46: 536 4.46 - 6.69: 141 6.69 - 8.93: 31 8.93 - 11.16: 6 Bond angle restraints: 27780 Sorted by residual: angle pdb=" N SER D 863 " pdb=" CA SER D 863 " pdb=" C SER D 863 " ideal model delta sigma weight residual 112.34 123.50 -11.16 1.30e+00 5.92e-01 7.37e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 112.34 123.19 -10.85 1.30e+00 5.92e-01 6.96e+01 angle pdb=" N ASN D 865 " pdb=" CA ASN D 865 " pdb=" C ASN D 865 " ideal model delta sigma weight residual 111.36 102.32 9.04 1.09e+00 8.42e-01 6.89e+01 angle pdb=" N ASN A 865 " pdb=" CA ASN A 865 " pdb=" C ASN A 865 " ideal model delta sigma weight residual 111.28 103.00 8.28 1.09e+00 8.42e-01 5.76e+01 angle pdb=" N ASN D 865 " pdb=" CA ASN D 865 " pdb=" CB ASN D 865 " ideal model delta sigma weight residual 110.16 119.67 -9.51 1.48e+00 4.57e-01 4.13e+01 ... (remaining 27775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 11963 24.52 - 49.04: 657 49.04 - 73.56: 40 73.56 - 98.08: 20 98.08 - 122.60: 8 Dihedral angle restraints: 12688 sinusoidal: 5640 harmonic: 7048 Sorted by residual: dihedral pdb=" C1 CLR D1502 " pdb=" C2 CLR D1502 " pdb=" C3 CLR D1502 " pdb=" O1 CLR D1502 " ideal model delta sinusoidal sigma weight residual 180.04 57.44 122.60 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C1 CLR D1502 " pdb=" C2 CLR D1502 " pdb=" C3 CLR D1502 " pdb=" C4 CLR D1502 " ideal model delta sinusoidal sigma weight residual 57.41 -63.73 121.14 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C1 CLR C1203 " pdb=" C2 CLR C1203 " pdb=" C3 CLR C1203 " pdb=" O1 CLR C1203 " ideal model delta sinusoidal sigma weight residual 180.04 60.59 119.45 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 12685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3064 0.108 - 0.216: 45 0.216 - 0.324: 2 0.324 - 0.431: 2 0.431 - 0.539: 11 Chirality restraints: 3124 Sorted by residual: chirality pdb=" C14 CLR A1201 " pdb=" C13 CLR A1201 " pdb=" C15 CLR A1201 " pdb=" C8 CLR A1201 " both_signs ideal model delta sigma weight residual False -2.32 -2.86 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" C14 CLR C1204 " pdb=" C13 CLR C1204 " pdb=" C15 CLR C1204 " pdb=" C8 CLR C1204 " both_signs ideal model delta sigma weight residual False -2.32 -2.86 0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C14 CLR C1202 " pdb=" C13 CLR C1202 " pdb=" C15 CLR C1202 " pdb=" C8 CLR C1202 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 3121 not shown) Planarity restraints: 3388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 820 " -0.028 2.00e-02 2.50e+03 2.68e-02 1.80e+01 pdb=" CG TRP B 820 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 820 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 820 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 820 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 820 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 820 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 820 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 820 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 820 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 820 " -0.028 2.00e-02 2.50e+03 2.54e-02 1.62e+01 pdb=" CG TRP A 820 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 820 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 820 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 820 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 820 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 820 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 820 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 820 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 820 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 864 " 0.011 2.00e-02 2.50e+03 1.27e-02 4.05e+00 pdb=" CG TRP B 864 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 864 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 864 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 864 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 864 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 864 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 864 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 864 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 864 " 0.000 2.00e-02 2.50e+03 ... (remaining 3385 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 101 2.50 - 3.10: 15019 3.10 - 3.70: 32520 3.70 - 4.30: 43065 4.30 - 4.90: 70177 Nonbonded interactions: 160882 Sorted by model distance: nonbonded pdb=" OH TYR A1057 " pdb=" O1 CLR A1202 " model vdw 1.903 3.040 nonbonded pdb=" OH TYR C1057 " pdb=" O1 CLR C1204 " model vdw 2.006 3.040 nonbonded pdb=" OD1 ASP A 862 " pdb=" NE1 TRP A 864 " model vdw 2.144 3.120 nonbonded pdb=" O LYS D1149 " pdb=" NE2 GLN D1153 " model vdw 2.153 3.120 nonbonded pdb=" O PHE D 805 " pdb=" OH TYR D 888 " model vdw 2.169 3.040 ... (remaining 160877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 421 through 1168 or resid 1201 through 1202)) selection = (chain 'B' and (resid 421 through 1168 or resid 1401 through 1402)) selection = (chain 'C' and (resid 421 through 1168 or resid 1201 through 1202)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 41.910 Find NCS groups from input model: 1.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 20468 Z= 0.770 Angle : 0.801 11.158 27780 Z= 0.388 Chirality : 0.051 0.539 3124 Planarity : 0.004 0.067 3388 Dihedral : 14.079 122.596 8092 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.17), residues: 2372 helix: 1.62 (0.11), residues: 1880 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 820 HIS 0.005 0.001 HIS C1164 PHE 0.024 0.002 PHE D 936 TYR 0.018 0.001 TYR B 631 ARG 0.004 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.7846 (ptt) cc_final: 0.7056 (ptt) REVERT: A 625 ASP cc_start: 0.8335 (m-30) cc_final: 0.8110 (m-30) REVERT: A 684 MET cc_start: 0.8033 (tpt) cc_final: 0.7669 (tpt) REVERT: A 1125 GLU cc_start: 0.9027 (pp20) cc_final: 0.8787 (pp20) REVERT: C 625 ASP cc_start: 0.8557 (m-30) cc_final: 0.8294 (m-30) REVERT: C 1125 GLU cc_start: 0.9014 (pp20) cc_final: 0.8791 (pp20) REVERT: D 1061 GLN cc_start: 0.7304 (tm-30) cc_final: 0.7035 (tm-30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2776 time to fit residues: 134.3646 Evaluate side-chains 235 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 140 optimal weight: 0.3980 chunk 217 optimal weight: 5.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 ASN ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B1128 HIS ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN C1153 GLN ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D1153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.150878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098392 restraints weight = 42855.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100922 restraints weight = 23202.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102694 restraints weight = 16308.065| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20468 Z= 0.444 Angle : 0.809 10.036 27780 Z= 0.394 Chirality : 0.046 0.335 3124 Planarity : 0.005 0.042 3388 Dihedral : 7.044 76.285 3444 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 1.19 % Allowed : 10.64 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2372 helix: 1.37 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 820 HIS 0.011 0.002 HIS C1164 PHE 0.030 0.002 PHE A 698 TYR 0.022 0.002 TYR D 631 ARG 0.007 0.001 ARG D 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8824 (mt) cc_final: 0.8462 (mt) REVERT: A 622 MET cc_start: 0.8176 (ptt) cc_final: 0.7642 (ptt) REVERT: A 625 ASP cc_start: 0.8444 (m-30) cc_final: 0.8211 (m-30) REVERT: B 567 LEU cc_start: 0.8858 (mt) cc_final: 0.8514 (mt) REVERT: B 577 TYR cc_start: 0.8870 (t80) cc_final: 0.8646 (t80) REVERT: B 622 MET cc_start: 0.8094 (ptt) cc_final: 0.7841 (ptt) REVERT: B 927 MET cc_start: 0.8153 (mmp) cc_final: 0.7850 (mmt) REVERT: B 968 TYR cc_start: 0.8674 (t80) cc_final: 0.8465 (t80) REVERT: C 567 LEU cc_start: 0.8847 (mt) cc_final: 0.8505 (mt) REVERT: C 576 MET cc_start: 0.9067 (ptm) cc_final: 0.8842 (ptp) REVERT: C 622 MET cc_start: 0.8325 (ptt) cc_final: 0.7878 (ptt) REVERT: C 625 ASP cc_start: 0.8670 (m-30) cc_final: 0.8448 (m-30) REVERT: D 567 LEU cc_start: 0.8875 (mt) cc_final: 0.8526 (mt) REVERT: D 909 ILE cc_start: 0.6511 (tt) cc_final: 0.6270 (tt) outliers start: 25 outliers final: 13 residues processed: 273 average time/residue: 0.2834 time to fit residues: 128.1358 Evaluate side-chains 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 787 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1066 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN A1128 HIS A1153 GLN B 570 ASN C 570 ASN ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.155363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103869 restraints weight = 42503.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106785 restraints weight = 21852.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108731 restraints weight = 14828.496| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20468 Z= 0.175 Angle : 0.647 13.537 27780 Z= 0.310 Chirality : 0.040 0.347 3124 Planarity : 0.005 0.044 3388 Dihedral : 5.998 59.081 3444 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 1.53 % Allowed : 13.12 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2372 helix: 1.66 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 565 HIS 0.007 0.001 HIS A 908 PHE 0.032 0.001 PHE D 910 TYR 0.014 0.001 TYR D 631 ARG 0.003 0.000 ARG C 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8851 (mt) cc_final: 0.8507 (mt) REVERT: A 622 MET cc_start: 0.8112 (ptt) cc_final: 0.7527 (ptt) REVERT: A 684 MET cc_start: 0.8283 (tpt) cc_final: 0.7908 (tpt) REVERT: B 567 LEU cc_start: 0.8835 (mt) cc_final: 0.8498 (mt) REVERT: B 622 MET cc_start: 0.7970 (ptt) cc_final: 0.7765 (ptt) REVERT: B 927 MET cc_start: 0.8005 (mmp) cc_final: 0.7445 (mmt) REVERT: B 1159 LEU cc_start: 0.8775 (tt) cc_final: 0.8568 (mt) REVERT: C 567 LEU cc_start: 0.8840 (mt) cc_final: 0.8494 (mt) REVERT: C 622 MET cc_start: 0.8240 (ptt) cc_final: 0.7774 (ptt) REVERT: C 625 ASP cc_start: 0.8665 (m-30) cc_final: 0.8415 (m-30) REVERT: C 827 GLU cc_start: 0.8198 (tt0) cc_final: 0.7780 (tm-30) REVERT: D 567 LEU cc_start: 0.8845 (mt) cc_final: 0.8497 (mt) outliers start: 32 outliers final: 17 residues processed: 287 average time/residue: 0.2940 time to fit residues: 134.3119 Evaluate side-chains 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 890 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 0.5980 chunk 212 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 45 optimal weight: 0.0970 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 GLN D 656 GLN D1164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.155372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.103969 restraints weight = 42891.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106886 restraints weight = 21935.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108846 restraints weight = 14851.799| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20468 Z= 0.181 Angle : 0.650 13.621 27780 Z= 0.309 Chirality : 0.040 0.406 3124 Planarity : 0.005 0.045 3388 Dihedral : 5.892 58.401 3444 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.77 % Allowed : 15.08 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2372 helix: 1.74 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 820 HIS 0.006 0.001 HIS A 908 PHE 0.019 0.001 PHE B 910 TYR 0.011 0.001 TYR C 631 ARG 0.003 0.000 ARG C 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8874 (mt) cc_final: 0.8520 (mt) REVERT: A 576 MET cc_start: 0.8803 (ptp) cc_final: 0.8443 (ptm) REVERT: A 659 MET cc_start: 0.6794 (tpt) cc_final: 0.6549 (tpt) REVERT: B 567 LEU cc_start: 0.8848 (mt) cc_final: 0.8508 (mt) REVERT: B 576 MET cc_start: 0.8673 (ptp) cc_final: 0.8288 (ptm) REVERT: B 1125 GLU cc_start: 0.9140 (pp20) cc_final: 0.8939 (pp20) REVERT: B 1159 LEU cc_start: 0.8835 (tt) cc_final: 0.8625 (mt) REVERT: C 567 LEU cc_start: 0.8844 (mt) cc_final: 0.8503 (mt) REVERT: C 622 MET cc_start: 0.8315 (ptt) cc_final: 0.7695 (ptt) REVERT: C 625 ASP cc_start: 0.8667 (m-30) cc_final: 0.8412 (m-30) REVERT: C 659 MET cc_start: 0.6605 (tpt) cc_final: 0.6353 (tpt) REVERT: C 827 GLU cc_start: 0.8218 (tt0) cc_final: 0.7791 (tm-30) REVERT: D 567 LEU cc_start: 0.8866 (mt) cc_final: 0.8526 (mt) outliers start: 37 outliers final: 30 residues processed: 281 average time/residue: 0.2690 time to fit residues: 123.8593 Evaluate side-chains 263 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 ASN ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102891 restraints weight = 42739.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105686 restraints weight = 22089.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107639 restraints weight = 15091.199| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20468 Z= 0.212 Angle : 0.652 17.680 27780 Z= 0.312 Chirality : 0.040 0.436 3124 Planarity : 0.005 0.072 3388 Dihedral : 5.863 58.250 3444 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 2.24 % Allowed : 16.46 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2372 helix: 1.81 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 820 HIS 0.025 0.001 HIS D1164 PHE 0.035 0.001 PHE D 910 TYR 0.015 0.001 TYR B 631 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8825 (mt) cc_final: 0.8488 (mt) REVERT: A 576 MET cc_start: 0.8795 (ptp) cc_final: 0.8445 (ptm) REVERT: A 622 MET cc_start: 0.7992 (ptt) cc_final: 0.7486 (ptt) REVERT: A 659 MET cc_start: 0.6810 (tpt) cc_final: 0.6571 (tpt) REVERT: A 824 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7190 (tp) REVERT: A 1125 GLU cc_start: 0.9180 (pp20) cc_final: 0.8889 (pp20) REVERT: B 567 LEU cc_start: 0.8827 (mt) cc_final: 0.8469 (mt) REVERT: B 576 MET cc_start: 0.8673 (ptp) cc_final: 0.8312 (ptm) REVERT: B 827 GLU cc_start: 0.8244 (tt0) cc_final: 0.7820 (tm-30) REVERT: B 1125 GLU cc_start: 0.9181 (pp20) cc_final: 0.8976 (pp20) REVERT: C 567 LEU cc_start: 0.8873 (mt) cc_final: 0.8543 (mt) REVERT: C 622 MET cc_start: 0.8341 (ptt) cc_final: 0.7737 (ptt) REVERT: C 625 ASP cc_start: 0.8668 (m-30) cc_final: 0.8418 (m-30) REVERT: C 659 MET cc_start: 0.6653 (tpt) cc_final: 0.6406 (tpt) REVERT: C 827 GLU cc_start: 0.8259 (tt0) cc_final: 0.7806 (tm-30) REVERT: D 567 LEU cc_start: 0.8873 (mt) cc_final: 0.8555 (mt) outliers start: 47 outliers final: 37 residues processed: 292 average time/residue: 0.2728 time to fit residues: 129.6460 Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 234 optimal weight: 40.0000 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 ASN B1161 GLN B1164 HIS ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.154891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103498 restraints weight = 42725.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106401 restraints weight = 21920.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108344 restraints weight = 14830.561| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20468 Z= 0.192 Angle : 0.658 14.105 27780 Z= 0.311 Chirality : 0.042 0.429 3124 Planarity : 0.004 0.045 3388 Dihedral : 5.814 57.245 3444 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 1.81 % Allowed : 18.08 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2372 helix: 1.88 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 565 HIS 0.005 0.001 HIS A 908 PHE 0.025 0.001 PHE B 910 TYR 0.009 0.001 TYR D 631 ARG 0.002 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8831 (mt) cc_final: 0.8513 (mt) REVERT: A 576 MET cc_start: 0.8895 (ptp) cc_final: 0.8518 (ptm) REVERT: A 622 MET cc_start: 0.7992 (ptt) cc_final: 0.7651 (ptt) REVERT: A 659 MET cc_start: 0.6766 (tpt) cc_final: 0.6542 (tpt) REVERT: A 684 MET cc_start: 0.8099 (tpt) cc_final: 0.7831 (tpt) REVERT: A 1125 GLU cc_start: 0.9179 (pp20) cc_final: 0.8880 (pp20) REVERT: B 567 LEU cc_start: 0.8840 (mt) cc_final: 0.8503 (mt) REVERT: B 576 MET cc_start: 0.8781 (ptp) cc_final: 0.8423 (ptm) REVERT: B 827 GLU cc_start: 0.8212 (tt0) cc_final: 0.7783 (tm-30) REVERT: B 1125 GLU cc_start: 0.9174 (pp20) cc_final: 0.8956 (pp20) REVERT: C 567 LEU cc_start: 0.8870 (mt) cc_final: 0.8545 (mt) REVERT: C 622 MET cc_start: 0.8316 (ptt) cc_final: 0.7714 (ptt) REVERT: C 625 ASP cc_start: 0.8492 (m-30) cc_final: 0.8290 (m-30) REVERT: C 659 MET cc_start: 0.6784 (tpt) cc_final: 0.6569 (tpt) REVERT: C 827 GLU cc_start: 0.8259 (tt0) cc_final: 0.7815 (tm-30) REVERT: C 1125 GLU cc_start: 0.9214 (pp20) cc_final: 0.8939 (pp20) REVERT: D 567 LEU cc_start: 0.8878 (mt) cc_final: 0.8546 (mt) REVERT: D 622 MET cc_start: 0.8050 (ppp) cc_final: 0.7846 (ppp) outliers start: 38 outliers final: 33 residues processed: 289 average time/residue: 0.2867 time to fit residues: 133.8436 Evaluate side-chains 275 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 chunk 220 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.154545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103907 restraints weight = 42500.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.107026 restraints weight = 23801.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108286 restraints weight = 14709.493| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20468 Z= 0.198 Angle : 0.669 14.942 27780 Z= 0.315 Chirality : 0.041 0.444 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.802 57.340 3444 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.96 % Allowed : 18.51 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2372 helix: 1.99 (0.11), residues: 1888 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 820 HIS 0.005 0.001 HIS A 908 PHE 0.022 0.001 PHE C 910 TYR 0.016 0.001 TYR A 631 ARG 0.004 0.000 ARG D1150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8846 (mt) cc_final: 0.8513 (mt) REVERT: A 576 MET cc_start: 0.8878 (ptp) cc_final: 0.8485 (ptm) REVERT: A 622 MET cc_start: 0.7934 (ptt) cc_final: 0.7628 (ptt) REVERT: A 824 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7350 (tp) REVERT: A 1125 GLU cc_start: 0.9204 (pp20) cc_final: 0.8881 (pp20) REVERT: B 567 LEU cc_start: 0.8820 (mt) cc_final: 0.8461 (mt) REVERT: B 576 MET cc_start: 0.8839 (ptp) cc_final: 0.8433 (ptm) REVERT: B 622 MET cc_start: 0.7996 (ppp) cc_final: 0.7729 (ppp) REVERT: B 827 GLU cc_start: 0.8233 (tt0) cc_final: 0.7824 (tm-30) REVERT: B 1125 GLU cc_start: 0.9214 (pp20) cc_final: 0.9010 (pp20) REVERT: B 1128 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: C 567 LEU cc_start: 0.8826 (mt) cc_final: 0.8495 (mt) REVERT: C 622 MET cc_start: 0.8280 (ptt) cc_final: 0.7672 (ptt) REVERT: C 625 ASP cc_start: 0.8486 (m-30) cc_final: 0.8283 (m-30) REVERT: C 659 MET cc_start: 0.6936 (tpt) cc_final: 0.6735 (tpt) REVERT: C 827 GLU cc_start: 0.8268 (tt0) cc_final: 0.7823 (tm-30) REVERT: C 1125 GLU cc_start: 0.9229 (pp20) cc_final: 0.8935 (pp20) REVERT: D 567 LEU cc_start: 0.8853 (mt) cc_final: 0.8522 (mt) REVERT: D 626 LEU cc_start: 0.9517 (tp) cc_final: 0.9196 (pp) REVERT: D 1061 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 1153 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8495 (pp30) outliers start: 41 outliers final: 37 residues processed: 286 average time/residue: 0.2715 time to fit residues: 126.5148 Evaluate side-chains 283 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.154697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104089 restraints weight = 42999.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107596 restraints weight = 23664.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108818 restraints weight = 14362.302| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20468 Z= 0.193 Angle : 0.673 14.909 27780 Z= 0.316 Chirality : 0.040 0.435 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.799 57.418 3444 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 1.96 % Allowed : 19.42 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2372 helix: 2.04 (0.11), residues: 1884 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 565 HIS 0.005 0.001 HIS A 908 PHE 0.040 0.001 PHE D 910 TYR 0.017 0.001 TYR D 631 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8860 (mt) cc_final: 0.8535 (mt) REVERT: A 576 MET cc_start: 0.8887 (ptp) cc_final: 0.8503 (ptm) REVERT: A 622 MET cc_start: 0.7965 (ptt) cc_final: 0.7697 (ptt) REVERT: A 684 MET cc_start: 0.8346 (tpt) cc_final: 0.8134 (tpt) REVERT: A 824 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7366 (tp) REVERT: A 1125 GLU cc_start: 0.9235 (pp20) cc_final: 0.8909 (pp20) REVERT: B 567 LEU cc_start: 0.8831 (mt) cc_final: 0.8486 (mt) REVERT: B 576 MET cc_start: 0.8855 (ptp) cc_final: 0.8469 (ptm) REVERT: B 622 MET cc_start: 0.8000 (ppp) cc_final: 0.7688 (ppp) REVERT: B 698 PHE cc_start: 0.8218 (m-80) cc_final: 0.7997 (m-80) REVERT: B 827 GLU cc_start: 0.8225 (tt0) cc_final: 0.7814 (tm-30) REVERT: B 1125 GLU cc_start: 0.9247 (pp20) cc_final: 0.9022 (pp20) REVERT: C 567 LEU cc_start: 0.8840 (mt) cc_final: 0.8521 (mt) REVERT: C 622 MET cc_start: 0.8243 (ptt) cc_final: 0.7598 (ptt) REVERT: C 625 ASP cc_start: 0.8568 (m-30) cc_final: 0.8311 (m-30) REVERT: C 827 GLU cc_start: 0.8293 (tt0) cc_final: 0.7836 (tm-30) REVERT: C 1125 GLU cc_start: 0.9239 (pp20) cc_final: 0.8927 (pp20) REVERT: D 567 LEU cc_start: 0.8867 (mt) cc_final: 0.8544 (mt) REVERT: D 626 LEU cc_start: 0.9543 (tp) cc_final: 0.9082 (pp) REVERT: D 1153 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8477 (pp30) outliers start: 41 outliers final: 37 residues processed: 288 average time/residue: 0.2790 time to fit residues: 129.9652 Evaluate side-chains 283 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1069 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.154914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103741 restraints weight = 42469.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106660 restraints weight = 21806.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108574 restraints weight = 14772.768| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20468 Z= 0.187 Angle : 0.681 15.095 27780 Z= 0.320 Chirality : 0.041 0.435 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.753 57.140 3444 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 1.91 % Allowed : 20.23 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2372 helix: 2.03 (0.11), residues: 1884 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 565 HIS 0.005 0.001 HIS A 908 PHE 0.034 0.001 PHE D 910 TYR 0.013 0.001 TYR D 631 ARG 0.006 0.000 ARG A1136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7922 (tmm) cc_final: 0.7643 (ptt) REVERT: A 567 LEU cc_start: 0.8853 (mt) cc_final: 0.8526 (mt) REVERT: A 576 MET cc_start: 0.8870 (ptp) cc_final: 0.8489 (ptm) REVERT: A 622 MET cc_start: 0.7945 (ptt) cc_final: 0.7731 (ptt) REVERT: A 1125 GLU cc_start: 0.9157 (pp20) cc_final: 0.8825 (pp20) REVERT: B 458 MET cc_start: 0.7875 (tmm) cc_final: 0.7595 (ptt) REVERT: B 567 LEU cc_start: 0.8774 (mt) cc_final: 0.8428 (mt) REVERT: B 576 MET cc_start: 0.8845 (ptp) cc_final: 0.8450 (ptm) REVERT: B 622 MET cc_start: 0.7936 (ppp) cc_final: 0.7592 (ppp) REVERT: B 827 GLU cc_start: 0.8165 (tt0) cc_final: 0.7772 (tm-30) REVERT: B 1125 GLU cc_start: 0.9207 (pp20) cc_final: 0.9001 (pp20) REVERT: B 1128 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.7946 (m-70) REVERT: C 458 MET cc_start: 0.8131 (tmm) cc_final: 0.7907 (ptt) REVERT: C 567 LEU cc_start: 0.8826 (mt) cc_final: 0.8532 (mt) REVERT: C 622 MET cc_start: 0.8204 (ptt) cc_final: 0.7562 (ptt) REVERT: C 625 ASP cc_start: 0.8540 (m-30) cc_final: 0.8290 (m-30) REVERT: C 827 GLU cc_start: 0.8252 (tt0) cc_final: 0.7829 (tm-30) REVERT: C 1125 GLU cc_start: 0.9203 (pp20) cc_final: 0.8891 (pp20) REVERT: D 458 MET cc_start: 0.7858 (tmm) cc_final: 0.7606 (ptt) REVERT: D 567 LEU cc_start: 0.8863 (mt) cc_final: 0.8540 (mt) REVERT: D 599 MET cc_start: 0.8133 (tpt) cc_final: 0.7590 (tpt) REVERT: D 614 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9155 (p0) REVERT: D 625 ASP cc_start: 0.8785 (t0) cc_final: 0.8301 (m-30) REVERT: D 1153 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8463 (pp30) outliers start: 40 outliers final: 37 residues processed: 288 average time/residue: 0.2989 time to fit residues: 139.8043 Evaluate side-chains 281 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1069 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 200 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103760 restraints weight = 42662.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106701 restraints weight = 21877.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108568 restraints weight = 14825.161| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20468 Z= 0.192 Angle : 0.705 15.475 27780 Z= 0.328 Chirality : 0.042 0.435 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.737 57.212 3444 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 2.05 % Allowed : 20.09 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2372 helix: 2.01 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 565 HIS 0.005 0.001 HIS A 908 PHE 0.033 0.001 PHE D 910 TYR 0.012 0.001 TYR D 631 ARG 0.007 0.000 ARG A1136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7975 (tmm) cc_final: 0.7676 (ptt) REVERT: A 567 LEU cc_start: 0.8863 (mt) cc_final: 0.8538 (mt) REVERT: A 576 MET cc_start: 0.8872 (ptp) cc_final: 0.8507 (ptm) REVERT: A 684 MET cc_start: 0.8297 (tpt) cc_final: 0.8026 (tpt) REVERT: A 695 LEU cc_start: 0.9306 (mp) cc_final: 0.9029 (pp) REVERT: A 824 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7370 (tp) REVERT: A 1125 GLU cc_start: 0.9201 (pp20) cc_final: 0.8868 (pp20) REVERT: B 458 MET cc_start: 0.7935 (tmm) cc_final: 0.7625 (ptt) REVERT: B 567 LEU cc_start: 0.8784 (mt) cc_final: 0.8442 (mt) REVERT: B 576 MET cc_start: 0.8848 (ptp) cc_final: 0.8459 (ptm) REVERT: B 622 MET cc_start: 0.7941 (ppp) cc_final: 0.7596 (ppp) REVERT: B 827 GLU cc_start: 0.8172 (tt0) cc_final: 0.7775 (tm-30) REVERT: B 1125 GLU cc_start: 0.9218 (pp20) cc_final: 0.9010 (pp20) REVERT: B 1128 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7969 (m-70) REVERT: C 567 LEU cc_start: 0.8854 (mt) cc_final: 0.8549 (mt) REVERT: C 622 MET cc_start: 0.8171 (ptt) cc_final: 0.7567 (ptt) REVERT: C 625 ASP cc_start: 0.8553 (m-30) cc_final: 0.8300 (m-30) REVERT: C 827 GLU cc_start: 0.8262 (tt0) cc_final: 0.7837 (tm-30) REVERT: C 1061 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7076 (tm-30) REVERT: C 1125 GLU cc_start: 0.9217 (pp20) cc_final: 0.8900 (pp20) REVERT: C 1153 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8952 (mp10) REVERT: D 458 MET cc_start: 0.7929 (tmm) cc_final: 0.7644 (ptt) REVERT: D 567 LEU cc_start: 0.8869 (mt) cc_final: 0.8547 (mt) REVERT: D 614 ASP cc_start: 0.9377 (OUTLIER) cc_final: 0.9161 (p0) REVERT: D 625 ASP cc_start: 0.8803 (t0) cc_final: 0.8305 (m-30) REVERT: D 1153 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8502 (pp30) outliers start: 43 outliers final: 37 residues processed: 288 average time/residue: 0.2759 time to fit residues: 128.9855 Evaluate side-chains 285 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1069 PHE Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 6 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 212 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104120 restraints weight = 42757.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107156 restraints weight = 21832.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108871 restraints weight = 14719.282| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20468 Z= 0.184 Angle : 0.721 19.923 27780 Z= 0.331 Chirality : 0.042 0.435 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.702 56.848 3444 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 1.86 % Allowed : 20.28 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.17), residues: 2372 helix: 2.01 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 565 HIS 0.005 0.001 HIS A 908 PHE 0.023 0.001 PHE B 932 TYR 0.012 0.001 TYR D 631 ARG 0.008 0.000 ARG C1136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6372.46 seconds wall clock time: 115 minutes 6.89 seconds (6906.89 seconds total)