Starting phenix.real_space_refine on Thu Sep 18 22:15:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rcr_19057/09_2025/8rcr_19057_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rcr_19057/09_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_19057/09_2025/8rcr_19057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rcr_19057/09_2025/8rcr_19057.map" model { file = "/net/cci-nas-00/data/ceres_data/8rcr_19057/09_2025/8rcr_19057_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rcr_19057/09_2025/8rcr_19057_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.65, per 1000 atoms: 0.23 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: 1.77 Conformation dependent library (CDL) restraints added in 710.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.55 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: 3.13 Time building geometry restraints manager: 2.29 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 1202) selection = (chain 'B' and resid 421 through 1402) selection = (chain 'C' and resid 421 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: 0.490 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- 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 20472 Z= 0.605 Angle : 0.801 11.158 27788 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 437 TYR 0.018 0.001 TYR B 631 PHE 0.024 0.002 PHE D 936 TRP 0.070 0.002 TRP B 820 HIS 0.005 0.001 HIS C1164 Details of bonding type rmsd covalent geometry : bond 0.01213 (20468) covalent geometry : angle 0.80067 (27780) SS BOND : bond 0.00180 ( 4) SS BOND : angle 2.01906 ( 8) hydrogen bonds : bond 0.11020 ( 1392) hydrogen bonds : angle 4.75638 ( 4152) *********************** 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 : 0.733 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: 0.7080 (ptt) REVERT: A 625 ASP cc_start: 0.8335 (m-30) cc_final: 0.8122 (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: 0.1149 time to fit residues: 56.5490 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1153 GLN C 570 ASN C 584 ASN 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 = 0.4303 r_free = 0.4303 target = 0.154935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103569 restraints weight = 42696.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106433 restraints weight = 22048.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108312 restraints weight = 14983.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.109254 restraints weight = 12097.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110029 restraints weight = 10789.540| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20472 Z= 0.181 Angle : 0.704 10.684 27788 Z= 0.339 Chirality : 0.042 0.350 3124 Planarity : 0.005 0.043 3388 Dihedral : 7.092 88.166 3444 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 0.81 % Allowed : 9.45 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.17), residues: 2372 helix: 1.61 (0.11), residues: 1904 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.018 0.001 TYR D 631 PHE 0.030 0.001 PHE A 698 TRP 0.024 0.001 TRP A 820 HIS 0.012 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00416 (20468) covalent geometry : angle 0.70413 (27780) SS BOND : bond 0.00013 ( 4) SS BOND : angle 1.51403 ( 8) hydrogen bonds : bond 0.04432 ( 1392) hydrogen bonds : angle 4.18938 ( 4152) *********************** 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 269 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8866 (mt) cc_final: 0.8520 (mt) REVERT: A 622 MET cc_start: 0.8019 (ptt) cc_final: 0.7716 (ptt) REVERT: A 625 ASP cc_start: 0.8390 (m-30) cc_final: 0.8174 (m-30) REVERT: A 684 MET cc_start: 0.8184 (tpt) cc_final: 0.7720 (tpt) REVERT: A 1125 GLU cc_start: 0.9118 (pp20) cc_final: 0.8853 (pp20) REVERT: B 567 LEU cc_start: 0.8857 (mt) cc_final: 0.8514 (mt) REVERT: B 626 LEU cc_start: 0.9465 (tp) cc_final: 0.9235 (pp) REVERT: C 567 LEU cc_start: 0.8908 (mt) cc_final: 0.8571 (mt) REVERT: C 617 PHE cc_start: 0.9089 (m-80) cc_final: 0.8703 (m-80) REVERT: C 622 MET cc_start: 0.8196 (ptt) cc_final: 0.7951 (ptt) REVERT: C 625 ASP cc_start: 0.8661 (m-30) cc_final: 0.8420 (m-30) REVERT: D 567 LEU cc_start: 0.8865 (mt) cc_final: 0.8509 (mt) REVERT: D 698 PHE cc_start: 0.7902 (m-80) cc_final: 0.7466 (m-80) REVERT: D 1153 GLN cc_start: 0.9094 (mp10) cc_final: 0.8891 (mp10) outliers start: 17 outliers final: 8 residues processed: 267 average time/residue: 0.1066 time to fit residues: 47.2671 Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 824 LEU 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 800 VAL Chi-restraints excluded: chain D residue 824 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 0.0870 chunk 218 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B1128 HIS C1164 HIS D 573 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104199 restraints weight = 43051.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107135 restraints weight = 22097.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108995 restraints weight = 14968.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110170 restraints weight = 12016.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110651 restraints weight = 10642.207| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20472 Z= 0.143 Angle : 0.648 13.247 27788 Z= 0.311 Chirality : 0.040 0.335 3124 Planarity : 0.005 0.044 3388 Dihedral : 5.953 59.605 3444 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 12.07 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2372 helix: 1.66 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.013 0.001 TYR D 631 PHE 0.035 0.001 PHE D 910 TRP 0.016 0.001 TRP A 820 HIS 0.009 0.001 HIS C1164 Details of bonding type rmsd covalent geometry : bond 0.00312 (20468) covalent geometry : angle 0.64813 (27780) SS BOND : bond 0.00048 ( 4) SS BOND : angle 1.01115 ( 8) hydrogen bonds : bond 0.04028 ( 1392) hydrogen bonds : angle 4.04405 ( 4152) *********************** 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 288 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8246 (ptp-170) REVERT: A 567 LEU cc_start: 0.8804 (mt) cc_final: 0.8463 (mt) REVERT: A 622 MET cc_start: 0.8091 (ptt) cc_final: 0.7697 (ptt) REVERT: A 1125 GLU cc_start: 0.9148 (pp20) cc_final: 0.8884 (pp20) REVERT: B 567 LEU cc_start: 0.8758 (mt) cc_final: 0.8413 (mt) REVERT: C 567 LEU cc_start: 0.8852 (mt) cc_final: 0.8523 (mt) REVERT: C 622 MET cc_start: 0.8252 (ptt) cc_final: 0.7841 (ptt) REVERT: C 625 ASP cc_start: 0.8657 (m-30) cc_final: 0.8397 (m-30) REVERT: C 827 GLU cc_start: 0.8179 (tt0) cc_final: 0.7750 (tm-30) REVERT: C 1125 GLU cc_start: 0.9139 (pp20) cc_final: 0.8890 (pp20) REVERT: D 567 LEU cc_start: 0.8885 (mt) cc_final: 0.8531 (mt) REVERT: D 1125 GLU cc_start: 0.9137 (pp20) cc_final: 0.8927 (pp20) outliers start: 31 outliers final: 16 residues processed: 284 average time/residue: 0.1126 time to fit residues: 52.5690 Evaluate side-chains 256 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 594 LEU 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 936 PHE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 883 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 76 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 146 optimal weight: 0.0270 chunk 4 optimal weight: 40.0000 chunk 215 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 180 optimal weight: 50.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 786 ASN C 678 GLN D 573 GLN D 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.152062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099882 restraints weight = 42942.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102623 restraints weight = 22893.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104382 restraints weight = 15807.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105475 restraints weight = 12806.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105936 restraints weight = 11374.101| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20472 Z= 0.218 Angle : 0.727 15.932 27788 Z= 0.348 Chirality : 0.043 0.458 3124 Planarity : 0.005 0.045 3388 Dihedral : 6.026 59.017 3444 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 2.29 % Allowed : 14.41 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.17), residues: 2372 helix: 1.60 (0.11), residues: 1912 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 905 TYR 0.015 0.002 TYR C 631 PHE 0.018 0.001 PHE B1132 TRP 0.025 0.002 TRP B 820 HIS 0.007 0.001 HIS B 990 Details of bonding type rmsd covalent geometry : bond 0.00510 (20468) covalent geometry : angle 0.72655 (27780) SS BOND : bond 0.00074 ( 4) SS BOND : angle 1.22172 ( 8) hydrogen bonds : bond 0.04375 ( 1392) hydrogen bonds : angle 4.20700 ( 4152) *********************** 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 304 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.788 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 567 LEU cc_start: 0.8830 (mt) cc_final: 0.8471 (mt) REVERT: A 576 MET cc_start: 0.8789 (ptp) cc_final: 0.8418 (ptm) REVERT: B 437 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8448 (mtt180) REVERT: B 567 LEU cc_start: 0.8820 (mt) cc_final: 0.8439 (mt) REVERT: B 576 MET cc_start: 0.8650 (ptp) cc_final: 0.8248 (ptm) REVERT: B 927 MET cc_start: 0.7956 (mmp) cc_final: 0.7581 (mmt) REVERT: B 951 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8672 (mt) REVERT: C 567 LEU cc_start: 0.8897 (mt) cc_final: 0.8573 (mt) REVERT: C 576 MET cc_start: 0.8857 (ptp) cc_final: 0.8437 (ptm) REVERT: C 622 MET cc_start: 0.8254 (ptt) cc_final: 0.7767 (ptt) REVERT: C 625 ASP cc_start: 0.8633 (m-30) cc_final: 0.8400 (m-30) REVERT: C 659 MET cc_start: 0.6716 (tpt) cc_final: 0.6477 (tpt) REVERT: D 567 LEU cc_start: 0.8840 (mt) cc_final: 0.8497 (mt) REVERT: D 1125 GLU cc_start: 0.9166 (pp20) cc_final: 0.8937 (pp20) outliers start: 48 outliers final: 31 residues processed: 294 average time/residue: 0.1297 time to fit residues: 62.6964 Evaluate side-chains 270 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 509 MET 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 924 SER Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 626 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 951 LEU 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 920 ILE Chi-restraints excluded: chain C residue 1043 PHE 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 864 TRP Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 140 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 196 optimal weight: 0.0070 chunk 131 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 120 optimal weight: 50.0000 chunk 219 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 206 optimal weight: 0.1980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1153 GLN B1131 ASN ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104410 restraints weight = 42639.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107400 restraints weight = 21774.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109302 restraints weight = 14723.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110525 restraints weight = 11792.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111077 restraints weight = 10409.287| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20472 Z= 0.124 Angle : 0.659 17.854 27788 Z= 0.309 Chirality : 0.041 0.464 3124 Planarity : 0.004 0.046 3388 Dihedral : 5.835 56.300 3444 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 1.72 % Allowed : 16.65 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.17), residues: 2372 helix: 1.82 (0.11), residues: 1908 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1136 TYR 0.016 0.001 TYR B 631 PHE 0.034 0.001 PHE D 910 TRP 0.016 0.001 TRP A 820 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00254 (20468) covalent geometry : angle 0.65891 (27780) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.60726 ( 8) hydrogen bonds : bond 0.03895 ( 1392) hydrogen bonds : angle 4.01109 ( 4152) *********************** 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 291 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8811 (mt) cc_final: 0.8475 (mt) REVERT: A 576 MET cc_start: 0.8780 (ptp) cc_final: 0.8420 (ptm) REVERT: A 684 MET cc_start: 0.8003 (tpt) cc_final: 0.7729 (tpt) REVERT: B 567 LEU cc_start: 0.8690 (mt) cc_final: 0.8357 (mt) REVERT: B 576 MET cc_start: 0.8720 (ptp) cc_final: 0.8345 (ptm) REVERT: B 617 PHE cc_start: 0.8587 (m-10) cc_final: 0.8323 (m-80) REVERT: C 567 LEU cc_start: 0.8880 (mt) cc_final: 0.8549 (mt) REVERT: C 576 MET cc_start: 0.8653 (ptp) cc_final: 0.8290 (ptm) REVERT: C 622 MET cc_start: 0.8255 (ptt) cc_final: 0.7785 (ptt) REVERT: C 625 ASP cc_start: 0.8657 (m-30) cc_final: 0.8399 (m-30) REVERT: C 659 MET cc_start: 0.6634 (tpt) cc_final: 0.6411 (tpt) REVERT: C 827 GLU cc_start: 0.8215 (tt0) cc_final: 0.7786 (tm-30) REVERT: D 567 LEU cc_start: 0.8838 (mt) cc_final: 0.8508 (mt) outliers start: 36 outliers final: 25 residues processed: 287 average time/residue: 0.1260 time to fit residues: 59.0660 Evaluate side-chains 263 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG 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 B residue 437 ARG Chi-restraints excluded: chain B residue 594 LEU 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 C residue 824 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain D residue 595 LEU 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 1002 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B1164 HIS ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.155718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104802 restraints weight = 42381.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107801 restraints weight = 21741.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109699 restraints weight = 14634.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.110899 restraints weight = 11731.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111336 restraints weight = 10372.402| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20472 Z= 0.125 Angle : 0.663 17.541 27788 Z= 0.311 Chirality : 0.040 0.442 3124 Planarity : 0.004 0.045 3388 Dihedral : 5.779 53.886 3444 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 1.48 % Allowed : 17.80 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.17), residues: 2372 helix: 1.97 (0.11), residues: 1888 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.016 0.001 TYR C 631 PHE 0.016 0.001 PHE B1132 TRP 0.029 0.001 TRP B 579 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00264 (20468) covalent geometry : angle 0.66265 (27780) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.53790 ( 8) hydrogen bonds : bond 0.03804 ( 1392) hydrogen bonds : angle 3.98704 ( 4152) *********************** 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 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.674 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: 0.8823 (mt) cc_final: 0.8479 (mt) REVERT: A 576 MET cc_start: 0.8778 (ptp) cc_final: 0.8428 (ptm) REVERT: A 1125 GLU cc_start: 0.9156 (pp20) cc_final: 0.8862 (pp20) REVERT: B 458 MET cc_start: 0.7982 (tmm) cc_final: 0.7702 (ptt) REVERT: B 567 LEU cc_start: 0.8711 (mt) cc_final: 0.8368 (mt) REVERT: B 576 MET cc_start: 0.8793 (ptp) cc_final: 0.8390 (ptm) REVERT: B 617 PHE cc_start: 0.8643 (m-10) cc_final: 0.8345 (m-80) REVERT: B 827 GLU cc_start: 0.8150 (tt0) cc_final: 0.7774 (tm-30) REVERT: C 567 LEU cc_start: 0.8888 (mt) cc_final: 0.8571 (mt) REVERT: C 576 MET cc_start: 0.8682 (ptp) cc_final: 0.8348 (ptm) REVERT: C 622 MET cc_start: 0.8186 (ptt) cc_final: 0.7688 (ptt) REVERT: C 625 ASP cc_start: 0.8486 (m-30) cc_final: 0.8274 (m-30) REVERT: C 659 MET cc_start: 0.6623 (tpt) cc_final: 0.6399 (tpt) REVERT: C 827 GLU cc_start: 0.8215 (tt0) cc_final: 0.7796 (tm-30) REVERT: C 1125 GLU cc_start: 0.9179 (pp20) cc_final: 0.8893 (pp20) REVERT: D 567 LEU cc_start: 0.8868 (mt) cc_final: 0.8530 (mt) REVERT: D 626 LEU cc_start: 0.9491 (tp) cc_final: 0.9143 (pp) REVERT: D 1061 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7179 (tm-30) outliers start: 31 outliers final: 26 residues processed: 284 average time/residue: 0.1201 time to fit residues: 55.4548 Evaluate side-chains 269 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL 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 1069 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 626 LEU 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 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain D residue 595 LEU 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 137 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** B1161 GLN ** B1164 HIS ** 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 = 0.4312 r_free = 0.4312 target = 0.155645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104698 restraints weight = 42699.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107686 restraints weight = 21775.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109631 restraints weight = 14707.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.110625 restraints weight = 11776.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111389 restraints weight = 10487.064| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20472 Z= 0.127 Angle : 0.673 15.889 27788 Z= 0.314 Chirality : 0.041 0.436 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.716 53.959 3444 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 1.57 % Allowed : 18.42 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.17), residues: 2372 helix: 2.02 (0.11), residues: 1884 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 508 TYR 0.015 0.001 TYR D 631 PHE 0.025 0.001 PHE B 910 TRP 0.024 0.001 TRP B 565 HIS 0.006 0.001 HIS B1164 Details of bonding type rmsd covalent geometry : bond 0.00275 (20468) covalent geometry : angle 0.67257 (27780) SS BOND : bond 0.00020 ( 4) SS BOND : angle 0.56118 ( 8) hydrogen bonds : bond 0.03752 ( 1392) hydrogen bonds : angle 3.99307 ( 4152) *********************** 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 291 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8814 (mt) cc_final: 0.8474 (mt) REVERT: A 576 MET cc_start: 0.8879 (ptp) cc_final: 0.8492 (ptm) REVERT: A 1125 GLU cc_start: 0.9154 (pp20) cc_final: 0.8850 (pp20) REVERT: B 567 LEU cc_start: 0.8811 (mt) cc_final: 0.8457 (mt) REVERT: B 576 MET cc_start: 0.8789 (ptp) cc_final: 0.8411 (ptm) REVERT: B 617 PHE cc_start: 0.8682 (m-10) cc_final: 0.8355 (m-80) REVERT: B 827 GLU cc_start: 0.8173 (tt0) cc_final: 0.7752 (tm-30) REVERT: B 1061 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 1128 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7954 (m-70) REVERT: C 567 LEU cc_start: 0.8886 (mt) cc_final: 0.8564 (mt) REVERT: C 576 MET cc_start: 0.8670 (ptp) cc_final: 0.8341 (ptm) REVERT: C 622 MET cc_start: 0.8143 (ptt) cc_final: 0.7643 (ptt) REVERT: C 625 ASP cc_start: 0.8471 (m-30) cc_final: 0.8262 (m-30) REVERT: C 659 MET cc_start: 0.6784 (tpt) cc_final: 0.6572 (tpt) REVERT: C 827 GLU cc_start: 0.8211 (tt0) cc_final: 0.7802 (tm-30) REVERT: C 1125 GLU cc_start: 0.9173 (pp20) cc_final: 0.8883 (pp20) REVERT: D 567 LEU cc_start: 0.8866 (mt) cc_final: 0.8531 (mt) REVERT: D 626 LEU cc_start: 0.9477 (tp) cc_final: 0.9197 (pp) REVERT: D 876 LEU cc_start: 0.8083 (tt) cc_final: 0.7882 (tt) REVERT: D 1125 GLU cc_start: 0.9185 (pp20) cc_final: 0.8962 (pp20) REVERT: D 1153 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8411 (pp30) outliers start: 33 outliers final: 28 residues processed: 286 average time/residue: 0.1218 time to fit residues: 56.8123 Evaluate side-chains 280 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 870 VAL 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 1069 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 594 LEU 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 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain D residue 595 LEU 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 923 VAL 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 27 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 B1153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.155271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104216 restraints weight = 42709.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107125 restraints weight = 21887.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.109052 restraints weight = 14777.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110199 restraints weight = 11935.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110682 restraints weight = 10549.754| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20472 Z= 0.134 Angle : 0.681 15.826 27788 Z= 0.320 Chirality : 0.041 0.438 3124 Planarity : 0.004 0.044 3388 Dihedral : 5.716 54.199 3444 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 1.72 % Allowed : 19.13 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.17), residues: 2372 helix: 2.01 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.48 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1136 TYR 0.017 0.001 TYR A 631 PHE 0.039 0.001 PHE D 910 TRP 0.020 0.001 TRP B 579 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00295 (20468) covalent geometry : angle 0.68141 (27780) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.61248 ( 8) hydrogen bonds : bond 0.03783 ( 1392) hydrogen bonds : angle 4.02298 ( 4152) *********************** 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 294 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.8821 (mt) cc_final: 0.8482 (mt) REVERT: A 576 MET cc_start: 0.8856 (ptp) cc_final: 0.8479 (ptm) REVERT: A 684 MET cc_start: 0.8136 (tpt) cc_final: 0.7918 (tpt) REVERT: A 1125 GLU cc_start: 0.9171 (pp20) cc_final: 0.8855 (pp20) REVERT: B 567 LEU cc_start: 0.8778 (mt) cc_final: 0.8445 (mt) REVERT: B 576 MET cc_start: 0.8791 (ptp) cc_final: 0.8422 (ptm) REVERT: B 617 PHE cc_start: 0.8720 (m-10) cc_final: 0.8436 (m-80) REVERT: B 827 GLU cc_start: 0.8174 (tt0) cc_final: 0.7730 (tm-30) REVERT: B 1153 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8279 (pp30) REVERT: C 567 LEU cc_start: 0.8876 (mt) cc_final: 0.8567 (mt) REVERT: C 576 MET cc_start: 0.8881 (ptp) cc_final: 0.8518 (ptm) REVERT: C 622 MET cc_start: 0.8143 (ptt) cc_final: 0.7634 (ptt) REVERT: C 625 ASP cc_start: 0.8477 (m-30) cc_final: 0.8266 (m-30) REVERT: C 659 MET cc_start: 0.6803 (tpt) cc_final: 0.6582 (tpt) REVERT: C 827 GLU cc_start: 0.8245 (tt0) cc_final: 0.7818 (tm-30) REVERT: C 1125 GLU cc_start: 0.9184 (pp20) cc_final: 0.8880 (pp20) REVERT: D 567 LEU cc_start: 0.8859 (mt) cc_final: 0.8528 (mt) REVERT: D 1061 GLN cc_start: 0.7320 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 1125 GLU cc_start: 0.9230 (pp20) cc_final: 0.9001 (pp20) REVERT: D 1153 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8529 (pp30) outliers start: 36 outliers final: 31 residues processed: 286 average time/residue: 0.1147 time to fit residues: 53.7223 Evaluate side-chains 282 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG 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 1069 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 626 LEU 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 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 1002 HIS Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 595 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1032 ASN D1164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.151315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098863 restraints weight = 42682.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101530 restraints weight = 22950.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103212 restraints weight = 16004.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104277 restraints weight = 13045.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104883 restraints weight = 11646.350| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20472 Z= 0.235 Angle : 0.786 15.506 27788 Z= 0.374 Chirality : 0.046 0.465 3124 Planarity : 0.005 0.043 3388 Dihedral : 6.034 59.542 3444 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 19.99 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.17), residues: 2372 helix: 1.78 (0.11), residues: 1888 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1136 TYR 0.020 0.002 TYR C 631 PHE 0.037 0.002 PHE D 910 TRP 0.021 0.002 TRP A 820 HIS 0.008 0.002 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00552 (20468) covalent geometry : angle 0.78588 (27780) SS BOND : bond 0.00060 ( 4) SS BOND : angle 1.36716 ( 8) hydrogen bonds : bond 0.04417 ( 1392) hydrogen bonds : angle 4.34374 ( 4152) *********************** 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 288 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7885 (tmm) cc_final: 0.7592 (ptt) REVERT: A 567 LEU cc_start: 0.8776 (mt) cc_final: 0.8432 (mt) REVERT: A 576 MET cc_start: 0.8884 (ptp) cc_final: 0.8417 (ptm) REVERT: A 695 LEU cc_start: 0.9205 (mp) cc_final: 0.8926 (pp) REVERT: A 698 PHE cc_start: 0.7678 (m-80) cc_final: 0.7467 (m-80) REVERT: A 1125 GLU cc_start: 0.9218 (pp20) cc_final: 0.8883 (pp20) REVERT: B 567 LEU cc_start: 0.8849 (mt) cc_final: 0.8503 (mt) REVERT: B 576 MET cc_start: 0.9011 (ptp) cc_final: 0.8543 (ptm) REVERT: B 622 MET cc_start: 0.8443 (ptt) cc_final: 0.8067 (ptp) REVERT: B 698 PHE cc_start: 0.8020 (m-80) cc_final: 0.7548 (m-80) REVERT: B 927 MET cc_start: 0.8011 (mmp) cc_final: 0.7693 (mmt) REVERT: B 1153 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9004 (mp10) REVERT: C 567 LEU cc_start: 0.8854 (mt) cc_final: 0.8559 (mt) REVERT: C 576 MET cc_start: 0.8880 (ptp) cc_final: 0.8478 (ptm) REVERT: C 622 MET cc_start: 0.8192 (ptt) cc_final: 0.7673 (ptt) REVERT: C 659 MET cc_start: 0.6849 (tpt) cc_final: 0.6620 (tpt) REVERT: C 1061 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 1125 GLU cc_start: 0.9266 (pp20) cc_final: 0.8922 (pp20) REVERT: D 567 LEU cc_start: 0.8858 (mt) cc_final: 0.8546 (mt) REVERT: D 614 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.9069 (p0) REVERT: D 625 ASP cc_start: 0.8789 (t0) cc_final: 0.8180 (m-30) outliers start: 36 outliers final: 33 residues processed: 282 average time/residue: 0.1188 time to fit residues: 54.7889 Evaluate side-chains 270 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG 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 924 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 594 LEU 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 595 LEU 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 920 ILE 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 595 LEU Chi-restraints excluded: chain D residue 614 ASP 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 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 220 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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** D1032 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.149957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097435 restraints weight = 42955.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.100040 restraints weight = 23125.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101787 restraints weight = 16119.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102787 restraints weight = 13144.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103151 restraints weight = 11741.668| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20472 Z= 0.263 Angle : 0.821 19.121 27788 Z= 0.391 Chirality : 0.046 0.458 3124 Planarity : 0.005 0.040 3388 Dihedral : 6.154 55.161 3444 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 1.53 % Allowed : 20.32 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.17), residues: 2372 helix: 1.49 (0.11), residues: 1916 sheet: None (None), residues: 0 loop : -1.61 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 474 TYR 0.016 0.002 TYR B 631 PHE 0.037 0.002 PHE D 910 TRP 0.023 0.002 TRP A 820 HIS 0.008 0.002 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00617 (20468) covalent geometry : angle 0.82039 (27780) SS BOND : bond 0.00121 ( 4) SS BOND : angle 1.48875 ( 8) hydrogen bonds : bond 0.04698 ( 1392) hydrogen bonds : angle 4.53882 ( 4152) ********************** 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 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7896 (tmm) cc_final: 0.7664 (ptt) REVERT: A 567 LEU cc_start: 0.8774 (mt) cc_final: 0.8441 (mt) REVERT: A 576 MET cc_start: 0.8883 (ptp) cc_final: 0.8423 (ptm) REVERT: A 695 LEU cc_start: 0.9297 (mp) cc_final: 0.9022 (pp) REVERT: A 1125 GLU cc_start: 0.9282 (pp20) cc_final: 0.8971 (pp20) REVERT: B 567 LEU cc_start: 0.8873 (mt) cc_final: 0.8535 (mt) REVERT: B 576 MET cc_start: 0.8914 (ptp) cc_final: 0.8514 (ptm) REVERT: B 622 MET cc_start: 0.8568 (ptt) cc_final: 0.8202 (ptp) REVERT: B 827 GLU cc_start: 0.8203 (tt0) cc_final: 0.7715 (tm-30) REVERT: B 927 MET cc_start: 0.8063 (mmp) cc_final: 0.7781 (mmt) REVERT: C 567 LEU cc_start: 0.8816 (mt) cc_final: 0.8527 (mt) REVERT: C 576 MET cc_start: 0.8878 (ptp) cc_final: 0.8433 (ptm) REVERT: C 659 MET cc_start: 0.7013 (tpt) cc_final: 0.6791 (tpt) REVERT: C 1061 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 1125 GLU cc_start: 0.9268 (pp20) cc_final: 0.8940 (pp20) REVERT: D 567 LEU cc_start: 0.8810 (mt) cc_final: 0.8486 (mt) REVERT: D 614 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.9059 (p0) REVERT: D 625 ASP cc_start: 0.8982 (t0) cc_final: 0.8473 (m-30) REVERT: D 698 PHE cc_start: 0.8004 (m-80) cc_final: 0.7791 (m-80) outliers start: 32 outliers final: 29 residues processed: 267 average time/residue: 0.1203 time to fit residues: 53.0598 Evaluate side-chains 261 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ARG 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 930 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 594 LEU 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 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 595 LEU Chi-restraints excluded: chain D residue 614 ASP 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 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 129 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 64 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.154249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102879 restraints weight = 42836.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105795 restraints weight = 21896.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107715 restraints weight = 14844.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108862 restraints weight = 11949.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109292 restraints weight = 10561.134| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20472 Z= 0.135 Angle : 0.727 17.628 27788 Z= 0.340 Chirality : 0.043 0.423 3124 Planarity : 0.005 0.040 3388 Dihedral : 5.903 59.464 3444 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 1.34 % Allowed : 20.90 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.17), residues: 2372 helix: 1.86 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1136 TYR 0.015 0.001 TYR C 631 PHE 0.031 0.001 PHE D 910 TRP 0.020 0.001 TRP B 579 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00288 (20468) covalent geometry : angle 0.72661 (27780) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.52048 ( 8) hydrogen bonds : bond 0.04031 ( 1392) hydrogen bonds : angle 4.20313 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3873.42 seconds wall clock time: 67 minutes 19.74 seconds (4039.74 seconds total)