Starting phenix.real_space_refine on Sun May 3 09:59:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.map" model { file = "/net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uco_64049/05_2026/9uco_64049.cif" } resolution = 3.58 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= 0.525 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 56 5.16 5 C 7898 2.51 5 N 2016 2.21 5 O 2174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12144 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2491 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 26, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 20, 'ARG:plan': 9, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 830 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2484 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 28, 'TRANS': 320} Chain breaks: 3 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 23, 'ARG:plan': 13, 'PHE:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 204 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 874 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1846 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1847 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.78, per 1000 atoms: 0.23 Number of scatterers: 12144 At special positions: 0 Unit cell: (179.4, 104.88, 131.56, 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 56 16.00 O 2174 8.00 N 2016 7.00 C 7898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS R 710 " - pdb=" SG CYS R 787 " distance=2.03 Simple disulfide: pdb=" SG CYS H 710 " - pdb=" SG CYS H 787 " 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: 1.03 Conformation dependent library (CDL) restraints added in 603.1 milliseconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3112 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 22 sheets defined 24.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'R' and resid 646 through 672 removed outlier: 3.685A pdb=" N CYS R 661 " --> pdb=" O ILE R 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU R 671 " --> pdb=" O ALA R 667 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS R 672 " --> pdb=" O THR R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 677 through 700 removed outlier: 3.772A pdb=" N TYR R 681 " --> pdb=" O ASN R 677 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET R 682 " --> pdb=" O HIS R 678 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS R 683 " --> pdb=" O ASN R 679 " (cutoff:3.500A) Processing helix chain 'R' and resid 706 through 741 removed outlier: 4.854A pdb=" N GLY R 715 " --> pdb=" O ALA R 711 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE R 716 " --> pdb=" O ILE R 712 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS R 718 " --> pdb=" O ALA R 714 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA R 732 " --> pdb=" O MET R 728 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 777 removed outlier: 3.918A pdb=" N LEU R 765 " --> pdb=" O PHE R 761 " (cutoff:3.500A) Proline residue: R 766 - end of helix Processing helix chain 'R' and resid 796 through 821 Proline residue: R 802 - end of helix removed outlier: 3.507A pdb=" N MET R 805 " --> pdb=" O GLY R 801 " (cutoff:3.500A) Processing helix chain 'R' and resid 839 through 852 removed outlier: 4.026A pdb=" N ILE R 849 " --> pdb=" O ALA R 845 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE R 850 " --> pdb=" O ILE R 846 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE R 851 " --> pdb=" O ALA R 847 " (cutoff:3.500A) Processing helix chain 'R' and resid 853 through 860 removed outlier: 3.610A pdb=" N LEU R 858 " --> pdb=" O SER R 855 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE R 860 " --> pdb=" O VAL R 857 " (cutoff:3.500A) Processing helix chain 'R' and resid 867 through 879 Processing helix chain 'R' and resid 880 through 889 Processing helix chain 'R' and resid 893 through 904 removed outlier: 3.642A pdb=" N LYS R 902 " --> pdb=" O ASP R 898 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 903 " --> pdb=" O GLU R 899 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 904 " --> pdb=" O TYR R 900 " (cutoff:3.500A) Processing helix chain 'H' and resid 646 through 672 removed outlier: 3.561A pdb=" N ILE H 650 " --> pdb=" O SER H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 700 Processing helix chain 'H' and resid 706 through 741 removed outlier: 4.938A pdb=" N GLY H 715 " --> pdb=" O ALA H 711 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 716 " --> pdb=" O ILE H 712 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N HIS H 718 " --> pdb=" O ALA H 714 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 719 " --> pdb=" O GLY H 715 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN H 741 " --> pdb=" O LEU H 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 754 through 777 removed outlier: 3.682A pdb=" N ALA H 760 " --> pdb=" O LEU H 756 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE H 761 " --> pdb=" O HIS H 757 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU H 765 " --> pdb=" O PHE H 761 " (cutoff:3.500A) Proline residue: H 766 - end of helix Processing helix chain 'H' and resid 796 through 822 Proline residue: H 802 - end of helix removed outlier: 3.593A pdb=" N ARG H 822 " --> pdb=" O LEU H 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 839 through 852 removed outlier: 3.565A pdb=" N ILE H 849 " --> pdb=" O ALA H 845 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE H 850 " --> pdb=" O ILE H 846 " (cutoff:3.500A) Processing helix chain 'H' and resid 853 through 860 removed outlier: 4.017A pdb=" N LEU H 858 " --> pdb=" O SER H 855 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE H 860 " --> pdb=" O VAL H 857 " (cutoff:3.500A) Processing helix chain 'H' and resid 867 through 879 Processing helix chain 'H' and resid 880 through 891 removed outlier: 3.817A pdb=" N LEU H 891 " --> pdb=" O LEU H 887 " (cutoff:3.500A) Processing helix chain 'H' and resid 893 through 904 removed outlier: 4.130A pdb=" N LEU H 903 " --> pdb=" O GLU H 899 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 4.016A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.739A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 316 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 242 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 251 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.727A pdb=" N SER B 10 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 24 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.715A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 55 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N SER B 35 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 112 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG B 103 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU B 110 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.715A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 55 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N SER B 35 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.599A pdb=" N THR F 6 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 20 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 76 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.710A pdb=" N LEU F 12 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.846A pdb=" N TYR F 50 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 12 removed outlier: 4.097A pdb=" N GLY C 39 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.874A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 80 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 61 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP C 78 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.649A pdb=" N THR C 186 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 199 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.907A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 330 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL C 228 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.579A pdb=" N SER D 10 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 24 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 14 removed outlier: 5.997A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 61 through 63 removed outlier: 6.735A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG D 103 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU D 110 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.614A pdb=" N TYR E 37 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.922A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1575 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: 2.11 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1892 1.31 - 1.43: 3408 1.43 - 1.56: 7043 1.56 - 1.69: 2 1.69 - 1.81: 83 Bond restraints: 12428 Sorted by residual: bond pdb=" CA GLU A 66 " pdb=" C GLU A 66 " ideal model delta sigma weight residual 1.525 1.446 0.079 1.25e-02 6.40e+03 4.00e+01 bond pdb=" N ASP A 67 " pdb=" CA ASP A 67 " ideal model delta sigma weight residual 1.456 1.396 0.060 1.21e-02 6.83e+03 2.48e+01 bond pdb=" CA ASP A 67 " pdb=" C ASP A 67 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.20e-02 6.94e+03 1.75e+01 bond pdb=" CG LEU H 659 " pdb=" CD1 LEU H 659 " ideal model delta sigma weight residual 1.521 1.393 0.128 3.30e-02 9.18e+02 1.50e+01 bond pdb=" CA ASP A 69 " pdb=" CB ASP A 69 " ideal model delta sigma weight residual 1.530 1.466 0.064 1.69e-02 3.50e+03 1.42e+01 ... (remaining 12423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 16764 2.35 - 4.69: 201 4.69 - 7.04: 37 7.04 - 9.38: 7 9.38 - 11.73: 2 Bond angle restraints: 17011 Sorted by residual: angle pdb=" N LEU A 68 " pdb=" CA LEU A 68 " pdb=" C LEU A 68 " ideal model delta sigma weight residual 107.75 96.02 11.73 1.86e+00 2.89e-01 3.98e+01 angle pdb=" N THR A 74 " pdb=" CA THR A 74 " pdb=" C THR A 74 " ideal model delta sigma weight residual 112.34 105.50 6.84 1.30e+00 5.92e-01 2.77e+01 angle pdb=" C GLU A 66 " pdb=" N ASP A 67 " pdb=" CA ASP A 67 " ideal model delta sigma weight residual 123.00 115.87 7.13 1.38e+00 5.25e-01 2.67e+01 angle pdb=" N PHE A 75 " pdb=" CA PHE A 75 " pdb=" C PHE A 75 " ideal model delta sigma weight residual 109.86 117.55 -7.69 1.55e+00 4.16e-01 2.46e+01 angle pdb=" CA ASP A 69 " pdb=" CB ASP A 69 " pdb=" CG ASP A 69 " ideal model delta sigma weight residual 112.60 107.91 4.69 1.00e+00 1.00e+00 2.20e+01 ... (remaining 17006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6315 17.67 - 35.34: 730 35.34 - 53.00: 181 53.00 - 70.67: 31 70.67 - 88.34: 6 Dihedral angle restraints: 7263 sinusoidal: 2444 harmonic: 4819 Sorted by residual: dihedral pdb=" CB CYS R 710 " pdb=" SG CYS R 710 " pdb=" SG CYS R 787 " pdb=" CB CYS R 787 " ideal model delta sinusoidal sigma weight residual 93.00 163.20 -70.20 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N LYS A 106 " pdb=" CA LYS A 106 " ideal model delta harmonic sigma weight residual 180.00 146.57 33.43 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CB CYS H 710 " pdb=" SG CYS H 710 " pdb=" SG CYS H 787 " pdb=" CB CYS H 787 " ideal model delta sinusoidal sigma weight residual -86.00 -139.38 53.38 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 7260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1611 0.048 - 0.095: 344 0.095 - 0.143: 96 0.143 - 0.191: 5 0.191 - 0.238: 2 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CG LEU H 659 " pdb=" CB LEU H 659 " pdb=" CD1 LEU H 659 " pdb=" CD2 LEU H 659 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA THR A 74 " pdb=" N THR A 74 " pdb=" C THR A 74 " pdb=" CB THR A 74 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU R 852 " pdb=" CB LEU R 852 " pdb=" CD1 LEU R 852 " pdb=" CD2 LEU R 852 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 2055 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 69 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ASP A 69 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP A 69 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL A 70 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 222 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C ASN A 222 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN A 222 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 223 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 87 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 88 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.029 5.00e-02 4.00e+02 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 190 2.66 - 3.22: 10833 3.22 - 3.78: 17798 3.78 - 4.34: 22957 4.34 - 4.90: 39270 Nonbonded interactions: 91048 Sorted by model distance: nonbonded pdb=" OD2 ASP A 290 " pdb=" OG SER A 302 " model vdw 2.099 3.040 nonbonded pdb=" OG SER R 773 " pdb=" OG SER R 798 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP A 204 " pdb=" OH TYR A 208 " model vdw 2.148 3.040 nonbonded pdb=" O THR A 136 " pdb=" OG SER H 749 " model vdw 2.204 3.040 nonbonded pdb=" O MET F 5 " pdb=" NE2 GLN F 101 " model vdw 2.208 3.120 ... (remaining 91043 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 6 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 45 or (resid 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 61 or (resi \ d 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throug \ h 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or re \ sid 70 through 75 or (resid 76 and (name N or name CA or name C or name O or nam \ e CB )) or resid 77 through 199 or (resid 200 through 201 and (name N or name CA \ or name C or name O or name CB )) or resid 202 through 235 or (resid 236 and (n \ ame N or name CA or name C or name O or name CB )) or resid 237 through 244 or ( \ resid 245 and (name N or name CA or name C or name O or name CB )) or resid 246 \ through 276 or (resid 277 and (name N or name CA or name C or name O or name CB \ )) or resid 278 through 281 or (resid 282 through 283 and (name N or name CA or \ name C or name O or name CB )) or resid 284 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 369)) selection = (chain 'C' and (resid 6 through 9 or (resid 10 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 37 or (resid 38 and (name \ N or name CA or name C or name O or name CB )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB )) or resid 45 through \ 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or res \ id 72 through 89 or resid 97 through 106 or (resid 107 and (name N or name CA or \ name C or name O or name CB )) or resid 108 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 159 through \ 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) or r \ esid 182 through 274 or (resid 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 291 or (resid 292 through 293 and (name N or na \ me CA or name C or name O or name CB )) or resid 294 through 321 or (resid 322 a \ nd (name N or name CA or name C or name O or name CB )) or resid 323 through 369 \ )) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 5 through 12 or resid 14 through 21 or (resid 22 and (name \ N or name CA or name C or name O or name CB )) or resid 23 through 29 or (resid \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 40 or (resid 41 through 43 and (name N or name CA or name C or name O or name C \ B )) or resid 44 through 69 or (resid 70 and (name N or name CA or name C or nam \ e O or name CB )) or resid 71 through 100 or (resid 101 through 103 and (name N \ or name CA or name C or name O or name CB )) or resid 104 through 121)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = (chain 'H' and (resid 645 through 657 or (resid 658 and (name N or name CA or na \ me C or name O or name CB )) or resid 659 through 661 or (resid 662 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 68 \ 1 or (resid 682 and (name N or name CA or name C or name O or name CB )) or resi \ d 683 through 719 or (resid 720 and (name N or name CA or name C or name O or na \ me CB )) or resid 721 or (resid 722 through 723 and (name N or name CA or name C \ or name O or name CB )) or resid 724 through 751 or (resid 752 and (name N or n \ ame CA or name C or name O or name CB )) or resid 753 through 822 or resid 838 o \ r (resid 839 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 40 through 904)) selection = (chain 'R' and (resid 645 through 663 or (resid 664 through 665 and (name N or n \ ame CA or name C or name O or name CB )) or resid 666 through 677 or (resid 678 \ through 679 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 0 through 691 or (resid 692 through 693 and (name N or name CA or name C or name \ O or name CB )) or resid 694 through 742 or resid 749 through 756 or (resid 757 \ and (name N or name CA or name C or name O or name CB )) or resid 758 or (resid \ 759 through 760 and (name N or name CA or name C or name O or name CB )) or res \ id 761 through 772 or (resid 773 through 774 and (name N or name CA or name C or \ name O or name CB )) or resid 775 through 854 or (resid 855 and (name N or name \ CA or name C or name O or name CB )) or resid 856 through 902 or (resid 903 and \ (name N or name CA or name C or name O or name CB )) or resid 904)) } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 : 0.005 0.128 12434 Z= 0.237 Angle : 0.665 11.728 17023 Z= 0.358 Chirality : 0.043 0.238 2058 Planarity : 0.005 0.052 2119 Dihedral : 16.103 88.337 4133 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.58 % Allowed : 29.03 % Favored : 70.39 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1613 helix: 0.35 (0.27), residues: 368 sheet: 0.27 (0.24), residues: 508 loop : -1.79 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.015 0.001 TYR A 63 PHE 0.019 0.001 PHE D 71 TRP 0.010 0.001 TRP H 856 HIS 0.005 0.001 HIS H 683 Details of bonding type rmsd covalent geometry : bond 0.00477 (12428) covalent geometry : angle 0.66487 (17011) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.51298 ( 12) hydrogen bonds : bond 0.12865 ( 544) hydrogen bonds : angle 6.87014 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.496 Fit side-chains REVERT: H 721 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7955 (t80) REVERT: H 781 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7813 (t80) outliers start: 7 outliers final: 2 residues processed: 146 average time/residue: 0.0984 time to fit residues: 21.6534 Evaluate side-chains 139 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 781 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS F 39 GLN F 101 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.041135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.038477 restraints weight = 58158.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.039250 restraints weight = 23580.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.039727 restraints weight = 12125.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.040014 restraints weight = 7289.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.040179 restraints weight = 4946.678| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12434 Z= 0.224 Angle : 0.626 9.432 17023 Z= 0.325 Chirality : 0.044 0.376 2058 Planarity : 0.005 0.049 2119 Dihedral : 5.234 53.760 1757 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.05 % Allowed : 26.72 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1613 helix: 0.49 (0.26), residues: 387 sheet: 0.28 (0.24), residues: 507 loop : -1.67 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 62 TYR 0.018 0.001 TYR F 50 PHE 0.015 0.002 PHE R 874 TRP 0.013 0.002 TRP R 797 HIS 0.003 0.001 HIS R 784 Details of bonding type rmsd covalent geometry : bond 0.00514 (12428) covalent geometry : angle 0.62604 (17011) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.81920 ( 12) hydrogen bonds : bond 0.04720 ( 544) hydrogen bonds : angle 5.48341 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.515 Fit side-chains REVERT: R 685 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7036 (m170) REVERT: H 721 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7591 (t80) REVERT: H 781 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7879 (t80) outliers start: 49 outliers final: 24 residues processed: 181 average time/residue: 0.0960 time to fit residues: 26.3626 Evaluate side-chains 161 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 701 ILE Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Chi-restraints excluded: chain H residue 849 ILE Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 146 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.042875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.040152 restraints weight = 57829.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.040941 restraints weight = 23498.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.041425 restraints weight = 12128.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.041722 restraints weight = 7341.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.041916 restraints weight = 5007.587| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12434 Z= 0.119 Angle : 0.547 10.080 17023 Z= 0.281 Chirality : 0.041 0.206 2058 Planarity : 0.004 0.049 2119 Dihedral : 4.771 56.995 1753 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.39 % Allowed : 28.37 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1613 helix: 0.66 (0.26), residues: 391 sheet: 0.33 (0.24), residues: 505 loop : -1.58 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.014 0.001 TYR A 63 PHE 0.010 0.001 PHE R 874 TRP 0.012 0.001 TRP R 797 HIS 0.009 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00273 (12428) covalent geometry : angle 0.54676 (17011) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.63223 ( 12) hydrogen bonds : bond 0.03749 ( 544) hydrogen bonds : angle 5.03588 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.513 Fit side-chains REVERT: H 721 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7568 (t80) REVERT: H 781 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7976 (t80) outliers start: 41 outliers final: 19 residues processed: 182 average time/residue: 0.1040 time to fit residues: 28.1269 Evaluate side-chains 162 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 0.0000 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS B 87 ASN ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.040151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.037520 restraints weight = 58254.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.038288 restraints weight = 23577.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.038755 restraints weight = 12138.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.039041 restraints weight = 7297.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.039222 restraints weight = 4962.506| |-----------------------------------------------------------------------------| r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12434 Z= 0.269 Angle : 0.665 9.711 17023 Z= 0.342 Chirality : 0.044 0.164 2058 Planarity : 0.005 0.049 2119 Dihedral : 5.237 59.154 1753 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.29 % Allowed : 26.30 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1613 helix: 0.31 (0.25), residues: 391 sheet: 0.15 (0.24), residues: 507 loop : -1.60 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.019 0.002 TYR F 50 PHE 0.018 0.002 PHE C 115 TRP 0.014 0.002 TRP H 819 HIS 0.004 0.001 HIS R 784 Details of bonding type rmsd covalent geometry : bond 0.00623 (12428) covalent geometry : angle 0.66427 (17011) SS BOND : bond 0.00414 ( 6) SS BOND : angle 0.96246 ( 12) hydrogen bonds : bond 0.04774 ( 544) hydrogen bonds : angle 5.41110 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.459 Fit side-chains REVERT: E 12 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8442 (tt) REVERT: H 781 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7914 (t80) outliers start: 64 outliers final: 44 residues processed: 190 average time/residue: 0.0958 time to fit residues: 27.6005 Evaluate side-chains 179 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 692 LEU Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 768 LEU Chi-restraints excluded: chain R residue 811 SER Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain R residue 876 ILE Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Chi-restraints excluded: chain H residue 783 MET Chi-restraints excluded: chain H residue 849 ILE Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 73 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.041083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.038417 restraints weight = 58495.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.039190 restraints weight = 23611.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.039670 restraints weight = 12121.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.039962 restraints weight = 7285.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.040148 restraints weight = 4938.116| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12434 Z= 0.183 Angle : 0.600 10.260 17023 Z= 0.309 Chirality : 0.043 0.218 2058 Planarity : 0.005 0.050 2119 Dihedral : 5.066 56.278 1753 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.05 % Allowed : 26.63 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1613 helix: 0.37 (0.25), residues: 392 sheet: 0.15 (0.24), residues: 506 loop : -1.58 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.014 0.001 TYR F 50 PHE 0.012 0.001 PHE C 115 TRP 0.014 0.001 TRP R 797 HIS 0.008 0.001 HIS R 685 Details of bonding type rmsd covalent geometry : bond 0.00425 (12428) covalent geometry : angle 0.60022 (17011) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.76611 ( 12) hydrogen bonds : bond 0.04181 ( 544) hydrogen bonds : angle 5.25494 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 0.420 Fit side-chains REVERT: F 32 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.8958 (t) REVERT: E 12 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8436 (tt) outliers start: 61 outliers final: 44 residues processed: 194 average time/residue: 0.0958 time to fit residues: 28.2527 Evaluate side-chains 184 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 768 LEU Chi-restraints excluded: chain R residue 811 SER Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain R residue 858 LEU Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Chi-restraints excluded: chain H residue 800 LEU Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS B 87 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.042049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.039362 restraints weight = 57622.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.040136 restraints weight = 23362.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.040616 restraints weight = 12039.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.040910 restraints weight = 7269.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.041080 restraints weight = 4951.946| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12434 Z= 0.137 Angle : 0.569 12.783 17023 Z= 0.290 Chirality : 0.043 0.446 2058 Planarity : 0.005 0.050 2119 Dihedral : 4.846 53.716 1753 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.80 % Allowed : 26.39 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1613 helix: 0.60 (0.25), residues: 392 sheet: 0.24 (0.24), residues: 506 loop : -1.58 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.012 0.001 TYR A 63 PHE 0.013 0.001 PHE H 691 TRP 0.012 0.001 TRP R 797 HIS 0.006 0.001 HIS R 685 Details of bonding type rmsd covalent geometry : bond 0.00315 (12428) covalent geometry : angle 0.56874 (17011) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.68936 ( 12) hydrogen bonds : bond 0.03764 ( 544) hydrogen bonds : angle 5.07637 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: B 9 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: F 32 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8856 (t) REVERT: E 12 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8407 (tt) REVERT: H 659 LEU cc_start: 0.8775 (mm) cc_final: 0.8513 (mp) outliers start: 58 outliers final: 37 residues processed: 195 average time/residue: 0.0979 time to fit residues: 28.6830 Evaluate side-chains 181 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain R residue 858 LEU Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 724 CYS Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 0.0040 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.042666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.039971 restraints weight = 57008.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.040741 restraints weight = 23225.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.041224 restraints weight = 11994.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.041493 restraints weight = 7258.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.041702 restraints weight = 5082.940| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12434 Z= 0.123 Angle : 0.553 11.183 17023 Z= 0.282 Chirality : 0.042 0.366 2058 Planarity : 0.004 0.051 2119 Dihedral : 4.729 51.670 1753 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.38 % Allowed : 26.80 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1613 helix: 0.81 (0.26), residues: 391 sheet: 0.26 (0.24), residues: 507 loop : -1.57 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.013 0.001 TYR A 63 PHE 0.010 0.001 PHE H 691 TRP 0.011 0.001 TRP H 727 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00282 (12428) covalent geometry : angle 0.55283 (17011) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.69123 ( 12) hydrogen bonds : bond 0.03555 ( 544) hydrogen bonds : angle 4.93399 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.464 Fit side-chains REVERT: A 352 MET cc_start: 0.8940 (ttm) cc_final: 0.8705 (ttp) REVERT: B 61 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8658 (m) REVERT: E 12 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 53 outliers final: 45 residues processed: 194 average time/residue: 0.0946 time to fit residues: 27.5215 Evaluate side-chains 194 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 768 LEU Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain R residue 858 LEU Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 724 CYS Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 781 TYR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 849 ILE Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 87 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.041111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.038445 restraints weight = 58127.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.039217 restraints weight = 23497.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.039689 restraints weight = 12083.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.039954 restraints weight = 7265.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.040142 restraints weight = 5101.088| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12434 Z= 0.207 Angle : 0.612 10.551 17023 Z= 0.313 Chirality : 0.043 0.147 2058 Planarity : 0.005 0.050 2119 Dihedral : 4.943 49.947 1753 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.05 % Allowed : 26.14 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1613 helix: 0.56 (0.25), residues: 394 sheet: 0.20 (0.24), residues: 506 loop : -1.55 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.015 0.001 TYR F 50 PHE 0.014 0.001 PHE C 115 TRP 0.011 0.002 TRP R 797 HIS 0.006 0.001 HIS R 685 Details of bonding type rmsd covalent geometry : bond 0.00480 (12428) covalent geometry : angle 0.61206 (17011) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.84130 ( 12) hydrogen bonds : bond 0.04183 ( 544) hydrogen bonds : angle 5.15503 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 0.396 Fit side-chains REVERT: B 9 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: F 32 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8917 (t) REVERT: E 12 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 61 outliers final: 50 residues processed: 195 average time/residue: 0.0970 time to fit residues: 28.5833 Evaluate side-chains 192 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 768 LEU Chi-restraints excluded: chain R residue 811 SER Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 649 ILE Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 724 CYS Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 849 ILE Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.041245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.038593 restraints weight = 57777.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.039355 restraints weight = 23377.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.039826 restraints weight = 12033.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.040117 restraints weight = 7287.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.040308 restraints weight = 4956.601| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12434 Z= 0.190 Angle : 0.611 11.133 17023 Z= 0.312 Chirality : 0.043 0.251 2058 Planarity : 0.005 0.050 2119 Dihedral : 4.821 46.105 1751 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.80 % Allowed : 26.63 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1613 helix: 0.50 (0.25), residues: 394 sheet: 0.17 (0.24), residues: 506 loop : -1.58 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.014 0.001 TYR F 50 PHE 0.013 0.001 PHE C 115 TRP 0.012 0.001 TRP R 797 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00442 (12428) covalent geometry : angle 0.61120 (17011) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.76898 ( 12) hydrogen bonds : bond 0.04097 ( 544) hydrogen bonds : angle 5.16603 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8886 (ttm) cc_final: 0.8659 (ttp) REVERT: B 9 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: F 5 MET cc_start: 0.8701 (mmp) cc_final: 0.8362 (mmp) REVERT: F 32 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8948 (t) REVERT: E 12 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 58 outliers final: 51 residues processed: 193 average time/residue: 0.0980 time to fit residues: 28.5366 Evaluate side-chains 196 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 701 ILE Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 768 LEU Chi-restraints excluded: chain R residue 811 SER Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 649 ILE Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 724 CYS Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 849 ILE Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 141 optimal weight: 0.0770 chunk 142 optimal weight: 0.9980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS B 87 ASN ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.043421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.040700 restraints weight = 57069.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.041489 restraints weight = 23146.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041971 restraints weight = 11971.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.042243 restraints weight = 7241.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.042453 restraints weight = 5104.360| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12434 Z= 0.105 Angle : 0.551 10.335 17023 Z= 0.280 Chirality : 0.041 0.215 2058 Planarity : 0.004 0.052 2119 Dihedral : 4.506 45.116 1751 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.47 % Allowed : 28.04 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1613 helix: 0.82 (0.26), residues: 393 sheet: 0.29 (0.24), residues: 505 loop : -1.57 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.016 0.001 TYR C 47 PHE 0.009 0.001 PHE H 795 TRP 0.014 0.001 TRP H 727 HIS 0.007 0.001 HIS R 685 Details of bonding type rmsd covalent geometry : bond 0.00242 (12428) covalent geometry : angle 0.55130 (17011) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.62356 ( 12) hydrogen bonds : bond 0.03332 ( 544) hydrogen bonds : angle 4.84601 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8884 (ttm) cc_final: 0.8633 (ttp) REVERT: B 9 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: E 12 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8471 (tt) outliers start: 42 outliers final: 32 residues processed: 186 average time/residue: 0.0976 time to fit residues: 27.3323 Evaluate side-chains 177 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain R residue 680 THR Chi-restraints excluded: chain R residue 681 TYR Chi-restraints excluded: chain R residue 685 HIS Chi-restraints excluded: chain R residue 701 ILE Chi-restraints excluded: chain R residue 849 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 652 HIS Chi-restraints excluded: chain H residue 666 ILE Chi-restraints excluded: chain H residue 677 ASN Chi-restraints excluded: chain H residue 710 CYS Chi-restraints excluded: chain H residue 721 PHE Chi-restraints excluded: chain H residue 724 CYS Chi-restraints excluded: chain H residue 739 VAL Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 857 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** R 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 685 HIS H 881 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.042673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.039968 restraints weight = 57646.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.040741 restraints weight = 23442.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.041225 restraints weight = 12162.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.041523 restraints weight = 7343.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.041718 restraints weight = 5009.575| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12434 Z= 0.143 Angle : 0.569 10.494 17023 Z= 0.292 Chirality : 0.042 0.219 2058 Planarity : 0.005 0.051 2119 Dihedral : 4.558 44.866 1751 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.39 % Allowed : 28.21 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1613 helix: 0.79 (0.26), residues: 394 sheet: 0.27 (0.24), residues: 515 loop : -1.58 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.016 0.001 TYR C 47 PHE 0.011 0.001 PHE H 795 TRP 0.011 0.001 TRP H 727 HIS 0.004 0.001 HIS H 683 Details of bonding type rmsd covalent geometry : bond 0.00331 (12428) covalent geometry : angle 0.56892 (17011) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.69680 ( 12) hydrogen bonds : bond 0.03641 ( 544) hydrogen bonds : angle 4.86921 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.66 seconds wall clock time: 32 minutes 28.33 seconds (1948.33 seconds total)