Starting phenix.real_space_refine on Sat Dec 28 04:30:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa2_38192/12_2024/8xa2_38192_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 300 5.16 5 C 32173 2.51 5 N 8940 2.21 5 O 9220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50633 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "E" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "F" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "R" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1847 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 235} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 49 Chain: "V" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1975 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2221 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 21.51, per 1000 atoms: 0.42 Number of scatterers: 50633 At special positions: 0 Unit cell: (184.95, 160.65, 180.9, 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 300 16.00 O 9220 8.00 N 8940 7.00 C 32173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 846 " - pdb=" SG CYS A 985 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS E 846 " - pdb=" SG CYS E 985 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 985 " distance=2.03 Simple disulfide: pdb=" SG CYS G 846 " - pdb=" SG CYS G 985 " 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: 9.21 Conformation dependent library (CDL) restraints added in 4.9 seconds 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12318 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 63 sheets defined 36.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.684A pdb=" N VAL A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.848A pdb=" N ASN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 203 removed outlier: 3.779A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 222 through 241 removed outlier: 3.794A pdb=" N ALA A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.822A pdb=" N ILE A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.389A pdb=" N GLY A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.433A pdb=" N MET A 475 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 476 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.678A pdb=" N LEU A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.709A pdb=" N GLU A 558 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.780A pdb=" N ILE A 598 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 623 through 635 Processing helix chain 'A' and resid 641 through 651 Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 660 through 676 removed outlier: 3.813A pdb=" N GLN A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.173A pdb=" N LEU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 724 removed outlier: 3.586A pdb=" N ILE A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.895A pdb=" N ALA A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 842 removed outlier: 4.184A pdb=" N GLY A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.542A pdb=" N TYR A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 901 " --> pdb=" O TYR A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.825A pdb=" N ALA A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 removed outlier: 3.758A pdb=" N ARG A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1014 removed outlier: 3.547A pdb=" N LEU A1013 " --> pdb=" O PRO A1010 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A1014 " --> pdb=" O PRO A1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1010 through 1014' Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.648A pdb=" N ALA A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1047 Processing helix chain 'A' and resid 1051 through 1062 Processing helix chain 'A' and resid 1159 through 1172 Processing helix chain 'A' and resid 1214 through 1219 removed outlier: 4.164A pdb=" N PHE A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A1219 " --> pdb=" O LEU A1215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1214 through 1219' Processing helix chain 'A' and resid 1358 through 1365 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.700A pdb=" N VAL C 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 100 removed outlier: 4.488A pdb=" N ALA C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.870A pdb=" N ASN C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 203 removed outlier: 3.709A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 222 through 241 removed outlier: 3.839A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.780A pdb=" N ILE C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 removed outlier: 4.161A pdb=" N GLY C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.021A pdb=" N MET C 475 " --> pdb=" O ARG C 472 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 476 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 485 removed outlier: 3.758A pdb=" N LEU C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 494 Processing helix chain 'C' and resid 516 through 528 removed outlier: 3.674A pdb=" N MET C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.578A pdb=" N GLU C 558 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 598 removed outlier: 3.778A pdb=" N ILE C 598 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 641 through 651 Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 660 through 676 removed outlier: 3.782A pdb=" N GLN C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 675 " --> pdb=" O TYR C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 693 removed outlier: 4.044A pdb=" N LEU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET C 688 " --> pdb=" O PHE C 684 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR C 689 " --> pdb=" O HIS C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 724 removed outlier: 3.587A pdb=" N ILE C 704 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 756 through 766 removed outlier: 3.892A pdb=" N ALA C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 4.110A pdb=" N GLY C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 827 " --> pdb=" O ARG C 823 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 837 " --> pdb=" O TYR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix Processing helix chain 'C' and resid 851 through 860 Proline residue: C 857 - end of helix removed outlier: 3.546A pdb=" N GLN C 860 " --> pdb=" O TYR C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 901 removed outlier: 3.556A pdb=" N TYR C 897 " --> pdb=" O SER C 893 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 901 " --> pdb=" O TYR C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 934 through 938 removed outlier: 3.679A pdb=" N ALA C 938 " --> pdb=" O ALA C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.825A pdb=" N ALA C 990 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.807A pdb=" N ARG C1000 " --> pdb=" O THR C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1014 removed outlier: 3.589A pdb=" N LEU C1013 " --> pdb=" O PRO C1010 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C1014 " --> pdb=" O PRO C1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1010 through 1014' Processing helix chain 'C' and resid 1022 through 1031 removed outlier: 3.613A pdb=" N ALA C1026 " --> pdb=" O ARG C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1047 Processing helix chain 'C' and resid 1051 through 1062 Processing helix chain 'C' and resid 1159 through 1172 Processing helix chain 'C' and resid 1214 through 1219 removed outlier: 4.143A pdb=" N PHE C1218 " --> pdb=" O ASP C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1358 through 1364 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.620A pdb=" N VAL E 89 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 100 removed outlier: 4.552A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 100' Processing helix chain 'E' and resid 148 through 159 removed outlier: 3.655A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 203 removed outlier: 3.841A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 222 through 241 removed outlier: 3.806A pdb=" N ALA E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 227 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.782A pdb=" N ILE E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 303 removed outlier: 4.052A pdb=" N GLY E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 Processing helix chain 'E' and resid 472 through 477 removed outlier: 4.411A pdb=" N MET E 475 " --> pdb=" O ARG E 472 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY E 476 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 485 removed outlier: 3.693A pdb=" N LEU E 483 " --> pdb=" O HIS E 480 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 485 " --> pdb=" O SER E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 494 Processing helix chain 'E' and resid 516 through 528 removed outlier: 3.718A pdb=" N MET E 520 " --> pdb=" O LEU E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 548 Processing helix chain 'E' and resid 554 through 558 removed outlier: 3.728A pdb=" N GLU E 558 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 598 removed outlier: 3.797A pdb=" N ILE E 598 " --> pdb=" O ASN E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 616 Processing helix chain 'E' and resid 623 through 635 Processing helix chain 'E' and resid 641 through 651 Processing helix chain 'E' and resid 653 through 658 Processing helix chain 'E' and resid 660 through 676 removed outlier: 3.780A pdb=" N GLN E 674 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER E 675 " --> pdb=" O TYR E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 693 removed outlier: 4.176A pdb=" N LEU E 687 " --> pdb=" O ASN E 683 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N MET E 688 " --> pdb=" O PHE E 684 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR E 689 " --> pdb=" O HIS E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 700 through 724 removed outlier: 3.590A pdb=" N ILE E 704 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 741 Processing helix chain 'E' and resid 756 through 766 removed outlier: 3.917A pdb=" N ALA E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 842 removed outlier: 4.269A pdb=" N GLY E 826 " --> pdb=" O ASP E 822 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 827 " --> pdb=" O ARG E 823 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE E 837 " --> pdb=" O TYR E 833 " (cutoff:3.500A) Proline residue: E 838 - end of helix Processing helix chain 'E' and resid 851 through 860 Proline residue: E 857 - end of helix removed outlier: 3.607A pdb=" N GLN E 860 " --> pdb=" O TYR E 856 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 902 removed outlier: 3.589A pdb=" N TYR E 897 " --> pdb=" O SER E 893 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 901 " --> pdb=" O TYR E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 906 through 912 Processing helix chain 'E' and resid 912 through 917 Processing helix chain 'E' and resid 934 through 938 removed outlier: 3.785A pdb=" N ALA E 938 " --> pdb=" O ALA E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 992 removed outlier: 3.801A pdb=" N ALA E 990 " --> pdb=" O GLU E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 996 through 1004 removed outlier: 3.809A pdb=" N ARG E1000 " --> pdb=" O THR E 996 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1014 removed outlier: 3.577A pdb=" N LEU E1013 " --> pdb=" O PRO E1010 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E1014 " --> pdb=" O PRO E1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1010 through 1014' Processing helix chain 'E' and resid 1022 through 1031 removed outlier: 3.605A pdb=" N ALA E1026 " --> pdb=" O ARG E1022 " (cutoff:3.500A) Processing helix chain 'E' and resid 1036 through 1047 Processing helix chain 'E' and resid 1051 through 1062 Processing helix chain 'E' and resid 1159 through 1172 Processing helix chain 'E' and resid 1214 through 1219 removed outlier: 4.180A pdb=" N PHE E1218 " --> pdb=" O ASP E1214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E1219 " --> pdb=" O LEU E1215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1214 through 1219' Processing helix chain 'E' and resid 1358 through 1364 Processing helix chain 'E' and resid 1365 through 1367 No H-bonds generated for 'chain 'E' and resid 1365 through 1367' Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.691A pdb=" N VAL F 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100 removed outlier: 4.529A pdb=" N ALA F 100 " --> pdb=" O PRO F 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 100' Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.815A pdb=" N ASN F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 202 removed outlier: 3.747A pdb=" N PHE F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Proline residue: F 212 - end of helix Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.794A pdb=" N ALA F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 227 " --> pdb=" O ASN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 251 through 264 removed outlier: 3.819A pdb=" N ILE F 255 " --> pdb=" O GLU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 303 removed outlier: 4.300A pdb=" N GLY F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 477 removed outlier: 4.522A pdb=" N MET F 475 " --> pdb=" O ARG F 472 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY F 476 " --> pdb=" O ASP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 485 removed outlier: 3.679A pdb=" N LEU F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP F 485 " --> pdb=" O SER F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 494 Processing helix chain 'F' and resid 517 through 528 Processing helix chain 'F' and resid 543 through 548 Processing helix chain 'F' and resid 554 through 558 removed outlier: 3.655A pdb=" N GLU F 558 " --> pdb=" O LEU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 598 removed outlier: 3.816A pdb=" N ILE F 598 " --> pdb=" O ASN F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 616 Processing helix chain 'F' and resid 623 through 635 Processing helix chain 'F' and resid 641 through 651 Processing helix chain 'F' and resid 653 through 658 Processing helix chain 'F' and resid 660 through 676 removed outlier: 3.765A pdb=" N GLN F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER F 675 " --> pdb=" O TYR F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 693 removed outlier: 4.152A pdb=" N LEU F 687 " --> pdb=" O ASN F 683 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET F 688 " --> pdb=" O PHE F 684 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR F 689 " --> pdb=" O HIS F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 724 removed outlier: 3.589A pdb=" N ILE F 704 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 741 Processing helix chain 'F' and resid 756 through 766 removed outlier: 3.829A pdb=" N ALA F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 842 removed outlier: 4.122A pdb=" N GLY F 826 " --> pdb=" O ASP F 822 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 827 " --> pdb=" O ARG F 823 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE F 837 " --> pdb=" O TYR F 833 " (cutoff:3.500A) Proline residue: F 838 - end of helix Processing helix chain 'F' and resid 851 through 860 Proline residue: F 857 - end of helix removed outlier: 3.573A pdb=" N GLN F 860 " --> pdb=" O TYR F 856 " (cutoff:3.500A) Processing helix chain 'F' and resid 893 through 901 removed outlier: 3.605A pdb=" N TYR F 897 " --> pdb=" O SER F 893 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 901 " --> pdb=" O TYR F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 912 Processing helix chain 'F' and resid 912 through 917 Processing helix chain 'F' and resid 934 through 938 removed outlier: 3.704A pdb=" N ALA F 938 " --> pdb=" O ALA F 935 " (cutoff:3.500A) Processing helix chain 'F' and resid 987 through 992 removed outlier: 3.823A pdb=" N ALA F 990 " --> pdb=" O GLU F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 996 through 1004 removed outlier: 3.828A pdb=" N ARG F1000 " --> pdb=" O THR F 996 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1014 removed outlier: 3.576A pdb=" N LEU F1013 " --> pdb=" O PRO F1010 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F1014 " --> pdb=" O PRO F1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1010 through 1014' Processing helix chain 'F' and resid 1022 through 1031 removed outlier: 3.661A pdb=" N ALA F1026 " --> pdb=" O ARG F1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 1036 through 1047 Processing helix chain 'F' and resid 1051 through 1062 Processing helix chain 'F' and resid 1159 through 1172 Processing helix chain 'F' and resid 1214 through 1219 removed outlier: 4.184A pdb=" N PHE F1218 " --> pdb=" O ASP F1214 " (cutoff:3.500A) Processing helix chain 'F' and resid 1358 through 1364 removed outlier: 3.597A pdb=" N LEU F1362 " --> pdb=" O ASP F1358 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.601A pdb=" N VAL G 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 100 removed outlier: 4.517A pdb=" N ALA G 100 " --> pdb=" O PRO G 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 100' Processing helix chain 'G' and resid 148 through 159 removed outlier: 3.654A pdb=" N ASN G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 203 removed outlier: 3.914A pdb=" N PHE G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Proline residue: G 212 - end of helix Processing helix chain 'G' and resid 222 through 241 removed outlier: 3.822A pdb=" N ALA G 226 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 264 removed outlier: 3.803A pdb=" N ILE G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 303 removed outlier: 4.260A pdb=" N GLY G 302 " --> pdb=" O GLN G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 477 removed outlier: 4.915A pdb=" N MET G 475 " --> pdb=" O ARG G 472 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY G 476 " --> pdb=" O ASP G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 485 removed outlier: 3.700A pdb=" N LEU G 483 " --> pdb=" O HIS G 480 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 484 " --> pdb=" O SER G 481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 485 " --> pdb=" O SER G 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 480 through 485' Processing helix chain 'G' and resid 486 through 494 Processing helix chain 'G' and resid 516 through 528 removed outlier: 3.726A pdb=" N MET G 520 " --> pdb=" O LEU G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 548 Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.704A pdb=" N GLU G 558 " --> pdb=" O LEU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 598 removed outlier: 3.795A pdb=" N ILE G 598 " --> pdb=" O ASN G 595 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 616 Processing helix chain 'G' and resid 623 through 635 Processing helix chain 'G' and resid 641 through 651 Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 660 through 676 removed outlier: 3.508A pdb=" N LEU G 664 " --> pdb=" O LEU G 660 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN G 674 " --> pdb=" O GLY G 670 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER G 675 " --> pdb=" O TYR G 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 693 removed outlier: 4.198A pdb=" N LEU G 687 " --> pdb=" O ASN G 683 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET G 688 " --> pdb=" O PHE G 684 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 689 " --> pdb=" O HIS G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 700 through 724 removed outlier: 3.564A pdb=" N ILE G 704 " --> pdb=" O PRO G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 735 through 741 Processing helix chain 'G' and resid 756 through 766 removed outlier: 3.912A pdb=" N ALA G 766 " --> pdb=" O ARG G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 842 removed outlier: 4.222A pdb=" N GLY G 826 " --> pdb=" O ASP G 822 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE G 827 " --> pdb=" O ARG G 823 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE G 837 " --> pdb=" O TYR G 833 " (cutoff:3.500A) Proline residue: G 838 - end of helix Processing helix chain 'G' and resid 851 through 860 Proline residue: G 857 - end of helix removed outlier: 3.574A pdb=" N GLN G 860 " --> pdb=" O TYR G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 893 through 901 removed outlier: 3.590A pdb=" N TYR G 897 " --> pdb=" O SER G 893 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA G 901 " --> pdb=" O TYR G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 906 through 912 Processing helix chain 'G' and resid 912 through 917 Processing helix chain 'G' and resid 934 through 938 removed outlier: 3.720A pdb=" N ALA G 938 " --> pdb=" O ALA G 935 " (cutoff:3.500A) Processing helix chain 'G' and resid 987 through 992 removed outlier: 3.787A pdb=" N ALA G 990 " --> pdb=" O GLU G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 996 through 1004 removed outlier: 3.802A pdb=" N ARG G1000 " --> pdb=" O THR G 996 " (cutoff:3.500A) Processing helix chain 'G' and resid 1010 through 1014 removed outlier: 3.591A pdb=" N LEU G1013 " --> pdb=" O PRO G1010 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY G1014 " --> pdb=" O PRO G1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1010 through 1014' Processing helix chain 'G' and resid 1022 through 1031 removed outlier: 3.596A pdb=" N ALA G1026 " --> pdb=" O ARG G1022 " (cutoff:3.500A) Processing helix chain 'G' and resid 1036 through 1047 Processing helix chain 'G' and resid 1051 through 1062 Processing helix chain 'G' and resid 1159 through 1172 Processing helix chain 'G' and resid 1214 through 1219 removed outlier: 4.194A pdb=" N PHE G1218 " --> pdb=" O ASP G1214 " (cutoff:3.500A) Processing helix chain 'G' and resid 1358 through 1364 removed outlier: 3.524A pdb=" N LEU G1362 " --> pdb=" O ASP G1358 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 26 Processing helix chain 'R' and resid 43 through 47 Processing helix chain 'R' and resid 59 through 70 Processing helix chain 'R' and resid 145 through 159 Processing helix chain 'R' and resid 208 through 220 Processing helix chain 'R' and resid 230 through 236 Processing helix chain 'R' and resid 251 through 256 removed outlier: 3.631A pdb=" N GLU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA R 256 " --> pdb=" O ILE R 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 251 through 256' Processing helix chain 'R' and resid 268 through 287 Processing helix chain 'V' and resid 17 through 27 Processing helix chain 'V' and resid 42 through 47 removed outlier: 3.514A pdb=" N ALA V 47 " --> pdb=" O VAL V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 52 Processing helix chain 'V' and resid 59 through 70 Processing helix chain 'V' and resid 145 through 163 removed outlier: 3.937A pdb=" N ALA V 163 " --> pdb=" O GLU V 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 209 removed outlier: 3.803A pdb=" N PHE V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 226 Processing helix chain 'V' and resid 269 through 287 removed outlier: 3.952A pdb=" N ILE V 273 " --> pdb=" O ILE V 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 151 removed outlier: 3.516A pdb=" N ASP Z 150 " --> pdb=" O HIS Z 147 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU Z 151 " --> pdb=" O PRO Z 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 147 through 151' Processing helix chain 'Z' and resid 165 through 178 Processing helix chain 'Z' and resid 198 through 205 Processing helix chain 'Z' and resid 212 through 223 Processing helix chain 'Z' and resid 230 through 248 Processing helix chain 'Z' and resid 300 through 302 No H-bonds generated for 'chain 'Z' and resid 300 through 302' Processing helix chain 'Z' and resid 307 through 311 Processing helix chain 'Z' and resid 350 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.649A pdb=" N ILE G 107 " --> pdb=" O LYS G 134 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET G 132 " --> pdb=" O PHE G 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 95 removed outlier: 5.953A pdb=" N ILE A 92 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A1094 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 94 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 95 removed outlier: 5.953A pdb=" N ILE A 92 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A1094 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 94 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.831A pdb=" N MET A 132 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 107 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 removed outlier: 4.802A pdb=" N THR A 309 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP A 383 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 394 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 289 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1080 " --> pdb=" O ALA A1132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 422 Processing sheet with id=AA7, first strand: chain 'A' and resid 456 through 460 Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 568 Processing sheet with id=AA9, first strand: chain 'A' and resid 752 through 753 Processing sheet with id=AB1, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AB2, first strand: chain 'A' and resid 1355 through 1356 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 95 removed outlier: 5.873A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 95 removed outlier: 5.873A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.615A pdb=" N MET C 132 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 107 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 308 through 312 removed outlier: 4.768A pdb=" N THR C 309 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP C 383 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 394 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU C 289 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU C1080 " --> pdb=" O ALA C1132 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C1084 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 422 Processing sheet with id=AB8, first strand: chain 'C' and resid 456 through 460 Processing sheet with id=AB9, first strand: chain 'C' and resid 563 through 568 Processing sheet with id=AC1, first strand: chain 'C' and resid 752 through 753 Processing sheet with id=AC2, first strand: chain 'C' and resid 955 through 958 removed outlier: 3.825A pdb=" N GLY C 849 " --> pdb=" O TYR C 975 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1355 through 1356 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 95 removed outlier: 5.969A pdb=" N ILE E 92 " --> pdb=" O TYR E1092 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL E1094 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 94 " --> pdb=" O VAL E1094 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 95 removed outlier: 5.969A pdb=" N ILE E 92 " --> pdb=" O TYR E1092 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL E1094 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 94 " --> pdb=" O VAL E1094 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 132 through 135 removed outlier: 3.669A pdb=" N MET E 132 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 107 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 308 through 312 removed outlier: 4.825A pdb=" N THR E 309 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP E 383 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 394 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU E 289 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU E1080 " --> pdb=" O ALA E1132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E1084 " --> pdb=" O VAL E1128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 417 through 422 Processing sheet with id=AC9, first strand: chain 'E' and resid 456 through 460 removed outlier: 3.532A pdb=" N PHE E 459 " --> pdb=" O THR E 467 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 563 through 568 Processing sheet with id=AD2, first strand: chain 'E' and resid 752 through 753 Processing sheet with id=AD3, first strand: chain 'E' and resid 955 through 958 removed outlier: 3.664A pdb=" N GLY E 849 " --> pdb=" O TYR E 975 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1139 through 1140 Processing sheet with id=AD5, first strand: chain 'E' and resid 1355 through 1356 Processing sheet with id=AD6, first strand: chain 'F' and resid 92 through 95 removed outlier: 5.869A pdb=" N ILE F 92 " --> pdb=" O TYR F1092 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL F1094 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR F 94 " --> pdb=" O VAL F1094 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 132 through 135 removed outlier: 3.534A pdb=" N MET F 132 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE F 107 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AD9, first strand: chain 'F' and resid 308 through 312 removed outlier: 4.845A pdb=" N THR F 309 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASP F 383 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 394 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU F 289 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU F1080 " --> pdb=" O ALA F1132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 417 through 422 Processing sheet with id=AE2, first strand: chain 'F' and resid 466 through 470 Processing sheet with id=AE3, first strand: chain 'F' and resid 563 through 569 Processing sheet with id=AE4, first strand: chain 'F' and resid 752 through 753 Processing sheet with id=AE5, first strand: chain 'F' and resid 955 through 958 removed outlier: 3.669A pdb=" N GLY F 849 " --> pdb=" O TYR F 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 91 through 95 removed outlier: 5.970A pdb=" N ILE G 92 " --> pdb=" O TYR G1092 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL G1094 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR G 94 " --> pdb=" O VAL G1094 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 91 through 95 removed outlier: 5.970A pdb=" N ILE G 92 " --> pdb=" O TYR G1092 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL G1094 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR G 94 " --> pdb=" O VAL G1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 308 through 312 removed outlier: 4.951A pdb=" N THR G 309 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP G 383 " --> pdb=" O LEU G 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 394 " --> pdb=" O ASP G 383 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU G 289 " --> pdb=" O GLU G 395 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU G1080 " --> pdb=" O ALA G1132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 417 through 422 Processing sheet with id=AF1, first strand: chain 'G' and resid 456 through 460 Processing sheet with id=AF2, first strand: chain 'G' and resid 563 through 568 Processing sheet with id=AF3, first strand: chain 'G' and resid 752 through 753 Processing sheet with id=AF4, first strand: chain 'G' and resid 955 through 958 removed outlier: 3.731A pdb=" N GLY G 849 " --> pdb=" O TYR G 975 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1355 through 1356 Processing sheet with id=AF6, first strand: chain 'R' and resid 31 through 34 removed outlier: 6.787A pdb=" N LEU R 84 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL R 78 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA R 41 " --> pdb=" O GLU R 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU R 11 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 107 through 108 Processing sheet with id=AF8, first strand: chain 'R' and resid 139 through 141 removed outlier: 3.552A pdb=" N LEU R 116 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE R 113 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU R 293 " --> pdb=" O ILE R 113 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 126 through 128 Processing sheet with id=AG1, first strand: chain 'V' and resid 31 through 34 removed outlier: 6.938A pdb=" N LEU V 84 " --> pdb=" O THR V 76 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL V 78 " --> pdb=" O LYS V 82 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS V 82 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA V 41 " --> pdb=" O GLU V 7 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU V 9 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 98 through 100 removed outlier: 3.991A pdb=" N LEU V 293 " --> pdb=" O ILE V 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.660A pdb=" N ILE V 135 " --> pdb=" O ILE V 126 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 176 through 177 removed outlier: 3.612A pdb=" N TYR V 184 " --> pdb=" O ILE V 177 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 122 through 127 Processing sheet with id=AG6, first strand: chain 'Z' and resid 195 through 197 removed outlier: 5.795A pdb=" N ILE Z 144 " --> pdb=" O PHE Z 258 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE Z 258 " --> pdb=" O ILE Z 144 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 280 through 281 removed outlier: 6.989A pdb=" N VAL Z 321 " --> pdb=" O ILE Z 436 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR Z 438 " --> pdb=" O LYS Z 319 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS Z 319 " --> pdb=" O THR Z 438 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG Z 337 " --> pdb=" O VAL Z 326 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP Z 305 " --> pdb=" O LEU Z 342 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 280 through 281 Processing sheet with id=AG9, first strand: chain 'Z' and resid 451 through 452 removed outlier: 3.579A pdb=" N VAL Z 458 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) 1775 hydrogen bonds defined for protein. 4941 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: 17.70 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16904 1.34 - 1.46: 11225 1.46 - 1.58: 23222 1.58 - 1.70: 0 1.70 - 1.83: 471 Bond restraints: 51822 Sorted by residual: bond pdb=" CA GLU G 729 " pdb=" CB GLU G 729 " ideal model delta sigma weight residual 1.528 1.562 -0.034 1.51e-02 4.39e+03 5.05e+00 bond pdb=" CA GLU A 729 " pdb=" CB GLU A 729 " ideal model delta sigma weight residual 1.528 1.562 -0.034 1.51e-02 4.39e+03 5.01e+00 bond pdb=" CA GLU E 729 " pdb=" CB GLU E 729 " ideal model delta sigma weight residual 1.528 1.560 -0.032 1.51e-02 4.39e+03 4.48e+00 bond pdb=" CA GLU F 729 " pdb=" CB GLU F 729 " ideal model delta sigma weight residual 1.528 1.560 -0.032 1.51e-02 4.39e+03 4.46e+00 bond pdb=" CA GLU C 729 " pdb=" CB GLU C 729 " ideal model delta sigma weight residual 1.528 1.560 -0.032 1.51e-02 4.39e+03 4.36e+00 ... (remaining 51817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 69766 3.58 - 7.15: 775 7.15 - 10.73: 91 10.73 - 14.31: 23 14.31 - 17.88: 4 Bond angle restraints: 70659 Sorted by residual: angle pdb=" C HIS Z 253 " pdb=" N ARG Z 254 " pdb=" CA ARG Z 254 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C GLY A 413 " pdb=" N ASN A 414 " pdb=" CA ASN A 414 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C GLY G 413 " pdb=" N ASN G 414 " pdb=" CA ASN G 414 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 angle pdb=" C ALA C1085 " pdb=" N GLU C1086 " pdb=" CA GLU C1086 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" CA LEU E 155 " pdb=" CB LEU E 155 " pdb=" CG LEU E 155 " ideal model delta sigma weight residual 116.30 134.18 -17.88 3.50e+00 8.16e-02 2.61e+01 ... (remaining 70654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 28184 17.75 - 35.51: 2380 35.51 - 53.26: 384 53.26 - 71.02: 37 71.02 - 88.77: 52 Dihedral angle restraints: 31037 sinusoidal: 11967 harmonic: 19070 Sorted by residual: dihedral pdb=" CB CYS F 846 " pdb=" SG CYS F 846 " pdb=" SG CYS F 985 " pdb=" CB CYS F 985 " ideal model delta sinusoidal sigma weight residual -86.00 -3.01 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS E 846 " pdb=" SG CYS E 846 " pdb=" SG CYS E 985 " pdb=" CB CYS E 985 " ideal model delta sinusoidal sigma weight residual -86.00 -4.21 -81.79 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS A 846 " pdb=" SG CYS A 846 " pdb=" SG CYS A 985 " pdb=" CB CYS A 985 " ideal model delta sinusoidal sigma weight residual -86.00 -5.06 -80.94 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 31034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 7073 0.082 - 0.163: 1008 0.163 - 0.245: 51 0.245 - 0.327: 8 0.327 - 0.408: 2 Chirality restraints: 8142 Sorted by residual: chirality pdb=" CB ILE E 25 " pdb=" CA ILE E 25 " pdb=" CG1 ILE E 25 " pdb=" CG2 ILE E 25 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CB ILE R 292 " pdb=" CA ILE R 292 " pdb=" CG1 ILE R 292 " pdb=" CG2 ILE R 292 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE A 25 " pdb=" CA ILE A 25 " pdb=" CG1 ILE A 25 " pdb=" CG2 ILE A 25 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 8139 not shown) Planarity restraints: 9235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 823 " 0.645 9.50e-02 1.11e+02 2.89e-01 5.23e+01 pdb=" NE ARG F 823 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG F 823 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 823 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 823 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 17 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO R 18 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO R 18 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 18 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 237 " -0.198 9.50e-02 1.11e+02 8.95e-02 6.67e+00 pdb=" NE ARG Z 237 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG Z 237 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 237 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 237 " 0.001 2.00e-02 2.50e+03 ... (remaining 9232 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 8093 2.76 - 3.30: 48743 3.30 - 3.83: 85626 3.83 - 4.37: 94985 4.37 - 4.90: 162540 Nonbonded interactions: 399987 Sorted by model distance: nonbonded pdb=" OE2 GLU C 729 " pdb=" NH2 ARG C1060 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR Z 328 " pdb=" O GLY Z 335 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR C1144 " pdb=" O SER C1202 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP G 194 " pdb=" OH TYR G 402 " model vdw 2.260 3.040 nonbonded pdb=" OG SER G 149 " pdb=" O GLY G1106 " model vdw 2.262 3.040 ... (remaining 399982 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' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.090 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: 0.060 Extract box with map and model: 1.410 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 84.430 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 51822 Z= 0.259 Angle : 0.983 17.883 70659 Z= 0.503 Chirality : 0.054 0.408 8142 Planarity : 0.008 0.289 9235 Dihedral : 13.669 88.773 18704 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.62 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 6510 helix: -1.35 (0.10), residues: 1941 sheet: -1.13 (0.17), residues: 899 loop : -1.85 (0.10), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 462 HIS 0.010 0.001 HIS R 39 PHE 0.033 0.002 PHE A 634 TYR 0.022 0.002 TYR C1092 ARG 0.024 0.001 ARG Z 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.7425 (tpt) cc_final: 0.7127 (tpt) REVERT: A 429 ASN cc_start: 0.7408 (m110) cc_final: 0.7084 (m110) REVERT: A 475 MET cc_start: 0.7603 (mpp) cc_final: 0.5551 (ttm) REVERT: A 848 MET cc_start: 0.1233 (pmm) cc_final: 0.0233 (pmm) REVERT: C 421 MET cc_start: 0.8120 (tpt) cc_final: 0.7589 (tpp) REVERT: C 848 MET cc_start: 0.0343 (pmm) cc_final: -0.0460 (pmm) REVERT: C 959 MET cc_start: 0.4198 (mtt) cc_final: 0.3824 (mmt) REVERT: C 1055 LEU cc_start: 0.9038 (mm) cc_final: 0.8333 (pp) REVERT: E 421 MET cc_start: 0.7613 (tpt) cc_final: 0.7063 (tpp) REVERT: E 429 ASN cc_start: 0.6335 (t0) cc_final: 0.5986 (t0) REVERT: E 475 MET cc_start: 0.7710 (mpp) cc_final: 0.5974 (ttm) REVERT: E 848 MET cc_start: 0.0785 (pmm) cc_final: -0.0490 (pmm) REVERT: E 917 MET cc_start: -0.2921 (mtt) cc_final: -0.3123 (mtt) REVERT: E 1157 MET cc_start: 0.3411 (ppp) cc_final: 0.2870 (ptm) REVERT: F 431 MET cc_start: 0.4179 (mmm) cc_final: 0.3759 (ptm) REVERT: F 622 MET cc_start: 0.4206 (mpp) cc_final: 0.3904 (mpp) REVERT: F 848 MET cc_start: 0.1051 (pmm) cc_final: 0.0576 (pmm) REVERT: G 155 LEU cc_start: 0.9140 (mt) cc_final: 0.8926 (tt) REVERT: G 431 MET cc_start: 0.4990 (mmm) cc_final: 0.4152 (ppp) REVERT: G 530 MET cc_start: -0.0135 (ptp) cc_final: -0.0924 (ptm) REVERT: G 1157 MET cc_start: 0.3161 (ppp) cc_final: 0.2670 (ptt) REVERT: V 69 MET cc_start: 0.8484 (mmp) cc_final: 0.8023 (mmm) REVERT: Z 273 ASN cc_start: 0.7561 (t0) cc_final: 0.7118 (t0) REVERT: Z 274 ILE cc_start: 0.8203 (tt) cc_final: 0.7977 (tt) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.4731 time to fit residues: 448.9822 Evaluate side-chains 426 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 552 optimal weight: 40.0000 chunk 495 optimal weight: 9.9990 chunk 275 optimal weight: 0.0030 chunk 169 optimal weight: 20.0000 chunk 334 optimal weight: 50.0000 chunk 264 optimal weight: 30.0000 chunk 512 optimal weight: 8.9990 chunk 198 optimal weight: 50.0000 chunk 311 optimal weight: 20.0000 chunk 381 optimal weight: 40.0000 chunk 593 optimal weight: 9.9990 overall best weight: 9.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 455 GLN A 468 GLN A 519 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS C 108 GLN C 195 GLN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1081 GLN F 108 GLN F 821 HIS ** F 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 113 GLN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 821 HIS ** G1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 51822 Z= 0.236 Angle : 0.674 16.143 70659 Z= 0.340 Chirality : 0.044 0.204 8142 Planarity : 0.006 0.066 9235 Dihedral : 5.037 33.277 7178 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.08 % Favored : 92.61 % Rotamer: Outliers : 0.99 % Allowed : 9.81 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 6510 helix: -0.31 (0.11), residues: 1976 sheet: -1.25 (0.16), residues: 965 loop : -1.55 (0.10), residues: 3569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 276 HIS 0.010 0.001 HIS E1376 PHE 0.019 0.002 PHE Z 258 TYR 0.018 0.002 TYR V 270 ARG 0.015 0.001 ARG F 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 462 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.7833 (tpt) cc_final: 0.7584 (tpt) REVERT: A 622 MET cc_start: 0.4718 (mpp) cc_final: 0.3939 (mmm) REVERT: A 848 MET cc_start: 0.1061 (pmm) cc_final: 0.0254 (pmm) REVERT: A 1055 LEU cc_start: 0.9073 (mt) cc_final: 0.8662 (pp) REVERT: A 1134 LEU cc_start: 0.8348 (tp) cc_final: 0.8024 (tp) REVERT: A 1209 MET cc_start: 0.5900 (tpt) cc_final: 0.5503 (tpt) REVERT: C 848 MET cc_start: 0.0673 (pmm) cc_final: -0.0059 (pmm) REVERT: C 1209 MET cc_start: 0.6271 (tpt) cc_final: 0.5538 (tpt) REVERT: E 421 MET cc_start: 0.7945 (tpt) cc_final: 0.7696 (tpt) REVERT: E 423 MET cc_start: 0.8075 (tpt) cc_final: 0.7481 (tmm) REVERT: E 429 ASN cc_start: 0.6698 (t0) cc_final: 0.6274 (t0) REVERT: E 465 ILE cc_start: 0.7811 (pt) cc_final: 0.7582 (pt) REVERT: E 823 ARG cc_start: 0.5610 (mmm-85) cc_final: 0.5376 (mmm-85) REVERT: E 848 MET cc_start: 0.1036 (pmm) cc_final: 0.0108 (pmm) REVERT: E 917 MET cc_start: -0.2755 (mtt) cc_final: -0.3013 (mtt) REVERT: E 1055 LEU cc_start: 0.8918 (mt) cc_final: 0.8552 (pp) REVERT: E 1134 LEU cc_start: 0.8183 (mt) cc_final: 0.7856 (tp) REVERT: E 1157 MET cc_start: 0.2901 (ppp) cc_final: 0.2601 (ptm) REVERT: E 1209 MET cc_start: 0.6015 (tpt) cc_final: 0.5318 (tpt) REVERT: E 1363 ARG cc_start: 0.8519 (tpm170) cc_final: 0.8255 (tpp-160) REVERT: F 108 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: F 242 MET cc_start: 0.7035 (tpp) cc_final: 0.6732 (tpp) REVERT: F 423 MET cc_start: 0.7818 (tmm) cc_final: 0.7479 (tmm) REVERT: F 530 MET cc_start: 0.1298 (ptm) cc_final: 0.0981 (ptm) REVERT: F 848 MET cc_start: 0.1222 (pmm) cc_final: 0.0711 (pmm) REVERT: F 959 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4637 (mtp) REVERT: F 1055 LEU cc_start: 0.9071 (mt) cc_final: 0.8558 (pp) REVERT: F 1209 MET cc_start: 0.5865 (tpt) cc_final: 0.5258 (tpt) REVERT: G 255 ILE cc_start: 0.8934 (tp) cc_final: 0.8728 (mm) REVERT: G 429 ASN cc_start: 0.6756 (t0) cc_final: 0.6431 (t0) REVERT: G 431 MET cc_start: 0.4762 (mmm) cc_final: 0.4465 (mmm) REVERT: G 1055 LEU cc_start: 0.9211 (mt) cc_final: 0.8785 (pp) REVERT: R 4 MET cc_start: 0.6926 (mmt) cc_final: 0.6611 (mmt) REVERT: R 69 MET cc_start: 0.7720 (tpt) cc_final: 0.7400 (tpt) REVERT: V 69 MET cc_start: 0.8700 (mmp) cc_final: 0.8327 (mmm) REVERT: Z 273 ASN cc_start: 0.7684 (t0) cc_final: 0.7340 (t0) REVERT: Z 279 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7627 (ttmt) outliers start: 53 outliers final: 26 residues processed: 493 average time/residue: 0.4730 time to fit residues: 399.2159 Evaluate side-chains 418 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 390 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 1354 LEU Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 959 MET Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 1366 HIS Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 330 optimal weight: 30.0000 chunk 184 optimal weight: 40.0000 chunk 494 optimal weight: 7.9990 chunk 404 optimal weight: 50.0000 chunk 163 optimal weight: 50.0000 chunk 594 optimal weight: 0.4980 chunk 642 optimal weight: 10.0000 chunk 529 optimal weight: 7.9990 chunk 590 optimal weight: 7.9990 chunk 202 optimal weight: 50.0000 chunk 477 optimal weight: 20.0000 overall best weight: 6.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1143 ASN ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS G1102 HIS ** G1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51822 Z= 0.189 Angle : 0.624 11.357 70659 Z= 0.308 Chirality : 0.043 0.230 8142 Planarity : 0.005 0.060 9235 Dihedral : 4.704 28.916 7178 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.77 % Favored : 92.93 % Rotamer: Outliers : 1.44 % Allowed : 12.14 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 6510 helix: 0.11 (0.12), residues: 1974 sheet: -1.12 (0.16), residues: 989 loop : -1.41 (0.11), residues: 3547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 276 HIS 0.008 0.001 HIS A1102 PHE 0.020 0.001 PHE G1050 TYR 0.015 0.001 TYR R 270 ARG 0.005 0.000 ARG Z 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 848 MET cc_start: 0.0976 (pmm) cc_final: 0.0332 (pmm) REVERT: A 1055 LEU cc_start: 0.9213 (mt) cc_final: 0.8945 (pp) REVERT: A 1134 LEU cc_start: 0.8234 (tp) cc_final: 0.7931 (tp) REVERT: A 1209 MET cc_start: 0.5626 (tpt) cc_final: 0.5423 (tpt) REVERT: C 848 MET cc_start: 0.0956 (pmm) cc_final: 0.0034 (pmm) REVERT: C 1209 MET cc_start: 0.5466 (tpt) cc_final: 0.4835 (tpt) REVERT: E 423 MET cc_start: 0.7868 (tpt) cc_final: 0.7449 (tmm) REVERT: E 848 MET cc_start: 0.1181 (pmm) cc_final: 0.0303 (pmm) REVERT: E 958 MET cc_start: 0.4138 (ptt) cc_final: 0.3790 (ptt) REVERT: E 1055 LEU cc_start: 0.9045 (mt) cc_final: 0.8714 (pp) REVERT: E 1134 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7964 (tp) REVERT: E 1209 MET cc_start: 0.5764 (tpt) cc_final: 0.5221 (tpt) REVERT: F 421 MET cc_start: 0.7919 (tpt) cc_final: 0.7481 (tpp) REVERT: F 530 MET cc_start: 0.0695 (ptm) cc_final: 0.0351 (ptm) REVERT: F 531 MET cc_start: 0.5055 (mmm) cc_final: 0.4581 (mmm) REVERT: F 622 MET cc_start: 0.4718 (mmm) cc_final: 0.3613 (mpp) REVERT: F 848 MET cc_start: 0.1322 (pmm) cc_final: 0.0833 (pmm) REVERT: F 1055 LEU cc_start: 0.9160 (mt) cc_final: 0.8671 (pp) REVERT: F 1121 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8834 (pp) REVERT: F 1366 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5653 (m90) REVERT: G 470 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7988 (m) REVERT: G 1055 LEU cc_start: 0.9155 (mt) cc_final: 0.8854 (pp) REVERT: R 207 LEU cc_start: 0.6481 (tt) cc_final: 0.5599 (tp) REVERT: V 69 MET cc_start: 0.8559 (mmp) cc_final: 0.8203 (mmm) REVERT: V 285 ASP cc_start: 0.7061 (t70) cc_final: 0.6368 (t70) REVERT: Z 273 ASN cc_start: 0.7704 (t0) cc_final: 0.7400 (t0) outliers start: 77 outliers final: 46 residues processed: 479 average time/residue: 0.4826 time to fit residues: 398.1886 Evaluate side-chains 434 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 384 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 1102 HIS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 1102 HIS Chi-restraints excluded: chain E residue 1134 LEU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 1102 HIS Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1366 HIS Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 1366 HIS Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 316 ASP Chi-restraints excluded: chain Z residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 587 optimal weight: 20.0000 chunk 447 optimal weight: 50.0000 chunk 308 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 283 optimal weight: 50.0000 chunk 399 optimal weight: 9.9990 chunk 597 optimal weight: 50.0000 chunk 632 optimal weight: 50.0000 chunk 311 optimal weight: 8.9990 chunk 565 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN F 305 GLN ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 GLN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 51822 Z= 0.190 Angle : 0.616 10.578 70659 Z= 0.303 Chirality : 0.042 0.166 8142 Planarity : 0.005 0.057 9235 Dihedral : 4.574 24.372 7178 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer: Outliers : 1.94 % Allowed : 13.60 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 6510 helix: 0.31 (0.12), residues: 2009 sheet: -0.87 (0.17), residues: 943 loop : -1.45 (0.11), residues: 3558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 276 HIS 0.015 0.001 HIS A1102 PHE 0.020 0.001 PHE E 634 TYR 0.016 0.001 TYR R 270 ARG 0.005 0.000 ARG G1363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 418 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.7899 (tpt) cc_final: 0.7649 (tpt) REVERT: A 524 MET cc_start: 0.3702 (tmm) cc_final: 0.3097 (tmm) REVERT: A 848 MET cc_start: 0.1231 (pmm) cc_final: 0.0470 (pmm) REVERT: A 920 MET cc_start: 0.4826 (mmp) cc_final: 0.3193 (mtt) REVERT: A 1055 LEU cc_start: 0.9149 (mt) cc_final: 0.8912 (pp) REVERT: A 1134 LEU cc_start: 0.8277 (tp) cc_final: 0.7904 (tp) REVERT: A 1209 MET cc_start: 0.5655 (tpt) cc_final: 0.5405 (tpt) REVERT: C 848 MET cc_start: 0.1657 (pmm) cc_final: 0.0816 (pmm) REVERT: C 1157 MET cc_start: 0.2805 (ptt) cc_final: 0.2166 (ptm) REVERT: C 1209 MET cc_start: 0.5148 (tpt) cc_final: 0.4464 (tpt) REVERT: E 232 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8038 (m) REVERT: E 423 MET cc_start: 0.7781 (tpt) cc_final: 0.7424 (tmm) REVERT: E 429 ASN cc_start: 0.6918 (t0) cc_final: 0.6710 (t0) REVERT: E 465 ILE cc_start: 0.8002 (pt) cc_final: 0.7777 (pt) REVERT: E 848 MET cc_start: 0.1378 (pmm) cc_final: 0.0624 (pmm) REVERT: E 924 THR cc_start: -0.2138 (OUTLIER) cc_final: -0.2416 (t) REVERT: E 1055 LEU cc_start: 0.8985 (mt) cc_final: 0.8688 (pp) REVERT: E 1209 MET cc_start: 0.5600 (tpt) cc_final: 0.5114 (tpt) REVERT: F 421 MET cc_start: 0.7845 (tpt) cc_final: 0.7305 (tpp) REVERT: F 530 MET cc_start: 0.1242 (ptm) cc_final: 0.0973 (ptm) REVERT: F 622 MET cc_start: 0.4833 (mmm) cc_final: 0.4270 (mpp) REVERT: F 848 MET cc_start: 0.1695 (pmm) cc_final: 0.1121 (pmm) REVERT: F 1055 LEU cc_start: 0.9086 (mt) cc_final: 0.8686 (pp) REVERT: F 1121 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8898 (pp) REVERT: F 1366 HIS cc_start: 0.6006 (OUTLIER) cc_final: 0.5575 (m90) REVERT: G 412 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8004 (mm) REVERT: G 470 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8017 (m) REVERT: G 958 MET cc_start: 0.4121 (ptt) cc_final: 0.3453 (tmm) REVERT: G 1055 LEU cc_start: 0.9112 (mt) cc_final: 0.8856 (pp) REVERT: G 1157 MET cc_start: 0.2486 (ptt) cc_final: 0.2101 (ptt) REVERT: R 207 LEU cc_start: 0.6484 (tt) cc_final: 0.5477 (tp) REVERT: V 69 MET cc_start: 0.8525 (mmp) cc_final: 0.8258 (mmt) REVERT: Z 273 ASN cc_start: 0.7903 (t0) cc_final: 0.7683 (t0) outliers start: 104 outliers final: 59 residues processed: 493 average time/residue: 0.4790 time to fit residues: 406.7838 Evaluate side-chains 451 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 386 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1102 HIS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1102 HIS Chi-restraints excluded: chain E residue 1354 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1102 HIS Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1366 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1155 VAL Chi-restraints excluded: chain G residue 1366 HIS Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 316 ASP Chi-restraints excluded: chain Z residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 526 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 470 optimal weight: 30.0000 chunk 260 optimal weight: 50.0000 chunk 539 optimal weight: 40.0000 chunk 436 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 322 optimal weight: 50.0000 chunk 567 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 129 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN A 447 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN C 519 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 ASN C 656 ASN C 821 HIS ** C 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN E 519 GLN ** E 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 ASN E 821 HIS ** E 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN F 519 GLN ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 GLN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 298 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 51822 Z= 0.495 Angle : 0.873 11.068 70659 Z= 0.447 Chirality : 0.049 0.287 8142 Planarity : 0.007 0.170 9235 Dihedral : 5.776 25.996 7178 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.41 % Favored : 89.46 % Rotamer: Outliers : 3.15 % Allowed : 15.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6510 helix: -0.49 (0.11), residues: 2103 sheet: -1.45 (0.16), residues: 967 loop : -1.82 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 527 HIS 0.012 0.002 HIS A 122 PHE 0.034 0.003 PHE R 137 TYR 0.023 0.003 TYR R 270 ARG 0.044 0.001 ARG E1363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 380 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: A 242 MET cc_start: 0.7629 (tpp) cc_final: 0.7428 (tpp) REVERT: A 271 MET cc_start: 0.8107 (tmm) cc_final: 0.7768 (tmm) REVERT: A 465 ILE cc_start: 0.7910 (pt) cc_final: 0.7587 (pt) REVERT: A 524 MET cc_start: 0.3884 (tmm) cc_final: 0.3241 (tmm) REVERT: A 848 MET cc_start: 0.2226 (pmm) cc_final: 0.1583 (pmm) REVERT: A 1134 LEU cc_start: 0.8697 (tp) cc_final: 0.8325 (tp) REVERT: A 1209 MET cc_start: 0.5310 (tpt) cc_final: 0.5039 (tpt) REVERT: C 412 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8280 (mm) REVERT: C 848 MET cc_start: 0.2386 (pmm) cc_final: 0.1622 (pmm) REVERT: C 1209 MET cc_start: 0.5736 (tpt) cc_final: 0.5367 (tpt) REVERT: E 412 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8373 (mm) REVERT: E 465 ILE cc_start: 0.8251 (pt) cc_final: 0.7926 (pt) REVERT: E 848 MET cc_start: 0.2874 (pmm) cc_final: 0.2136 (pmm) REVERT: E 924 THR cc_start: -0.2043 (OUTLIER) cc_final: -0.2323 (t) REVERT: E 1157 MET cc_start: 0.2194 (ptt) cc_final: 0.1602 (ptt) REVERT: E 1209 MET cc_start: 0.5799 (tpt) cc_final: 0.5234 (tpt) REVERT: F 242 MET cc_start: 0.7648 (tpp) cc_final: 0.7407 (tpp) REVERT: F 412 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8477 (mm) REVERT: F 421 MET cc_start: 0.8192 (tpt) cc_final: 0.7647 (tpp) REVERT: F 465 ILE cc_start: 0.8039 (pt) cc_final: 0.7758 (pt) REVERT: F 848 MET cc_start: 0.2464 (pmm) cc_final: 0.1891 (pmm) REVERT: F 1055 LEU cc_start: 0.9279 (mt) cc_final: 0.8885 (pp) REVERT: F 1082 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7602 (tp) REVERT: F 1121 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8980 (pp) REVERT: F 1134 LEU cc_start: 0.8498 (tp) cc_final: 0.8173 (tp) REVERT: F 1209 MET cc_start: 0.6318 (tpt) cc_final: 0.6008 (mmp) REVERT: G 412 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8610 (mm) REVERT: G 460 TYR cc_start: 0.7709 (m-80) cc_final: 0.7229 (m-10) REVERT: G 465 ILE cc_start: 0.8426 (pt) cc_final: 0.8105 (pt) REVERT: G 470 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8029 (m) REVERT: G 524 MET cc_start: 0.4076 (tmm) cc_final: 0.3806 (tmm) REVERT: G 920 MET cc_start: 0.3548 (mpp) cc_final: 0.3164 (mpp) REVERT: G 1055 LEU cc_start: 0.9254 (mt) cc_final: 0.8953 (pp) REVERT: R 287 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (pp) REVERT: Z 450 MET cc_start: 0.7357 (tpp) cc_final: 0.7109 (tpp) outliers start: 169 outliers final: 99 residues processed: 514 average time/residue: 0.4728 time to fit residues: 417.1326 Evaluate side-chains 459 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 350 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1100 HIS Chi-restraints excluded: chain C residue 1102 HIS Chi-restraints excluded: chain C residue 1354 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 450 ARG Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1100 HIS Chi-restraints excluded: chain E residue 1102 HIS Chi-restraints excluded: chain E residue 1354 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1102 HIS Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain F residue 1354 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1198 ARG Chi-restraints excluded: chain G residue 1361 MET Chi-restraints excluded: chain G residue 1366 HIS Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain V residue 297 VAL Chi-restraints excluded: chain Z residue 131 PHE Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 438 THR Chi-restraints excluded: chain Z residue 458 VAL Chi-restraints excluded: chain Z residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 212 optimal weight: 7.9990 chunk 569 optimal weight: 7.9990 chunk 124 optimal weight: 50.0000 chunk 371 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 632 optimal weight: 50.0000 chunk 525 optimal weight: 50.0000 chunk 292 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 209 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 267 GLN A 305 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 HIS A1102 HIS C 122 HIS ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 ASN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 305 GLN ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 895 ASN ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 ASN ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1064 HIS G 122 HIS G 305 GLN G 429 ASN G 480 HIS ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 ASN ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1064 HIS G1366 HIS ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51822 Z= 0.197 Angle : 0.669 14.745 70659 Z= 0.327 Chirality : 0.044 0.315 8142 Planarity : 0.005 0.061 9235 Dihedral : 5.008 23.071 7178 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 1.92 % Allowed : 17.79 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.10), residues: 6510 helix: 0.09 (0.11), residues: 2033 sheet: -1.32 (0.16), residues: 959 loop : -1.58 (0.11), residues: 3518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 276 HIS 0.006 0.001 HIS C 651 PHE 0.015 0.001 PHE Z 255 TYR 0.017 0.001 TYR R 270 ARG 0.007 0.000 ARG F1076 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 441 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7801 (tmm) cc_final: 0.7519 (tmm) REVERT: A 848 MET cc_start: 0.2194 (pmm) cc_final: 0.1421 (pmm) REVERT: A 1082 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7806 (tp) REVERT: A 1134 LEU cc_start: 0.8433 (tp) cc_final: 0.8154 (tp) REVERT: C 421 MET cc_start: 0.8316 (tpt) cc_final: 0.8113 (tpt) REVERT: C 460 TYR cc_start: 0.7933 (m-80) cc_final: 0.7689 (m-10) REVERT: C 520 MET cc_start: 0.6610 (mmm) cc_final: 0.6295 (mpp) REVERT: C 848 MET cc_start: 0.2573 (pmm) cc_final: 0.1771 (pmm) REVERT: E 412 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8245 (mm) REVERT: E 465 ILE cc_start: 0.8326 (pt) cc_final: 0.7947 (pt) REVERT: E 848 MET cc_start: 0.2198 (pmm) cc_final: 0.1637 (pmm) REVERT: E 924 THR cc_start: -0.2272 (OUTLIER) cc_final: -0.2550 (t) REVERT: E 1209 MET cc_start: 0.5341 (tpt) cc_final: 0.5056 (tpt) REVERT: F 271 MET cc_start: 0.8304 (tmm) cc_final: 0.7871 (tmm) REVERT: F 421 MET cc_start: 0.8126 (tpt) cc_final: 0.7623 (tpp) REVERT: F 429 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7529 (t0) REVERT: F 465 ILE cc_start: 0.7674 (pt) cc_final: 0.7366 (pt) REVERT: F 584 MET cc_start: 0.6430 (tpt) cc_final: 0.5703 (tmm) REVERT: F 848 MET cc_start: 0.2402 (pmm) cc_final: 0.1695 (pmm) REVERT: F 1055 LEU cc_start: 0.9222 (mt) cc_final: 0.8834 (pp) REVERT: F 1082 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7689 (tp) REVERT: F 1121 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8936 (pp) REVERT: F 1209 MET cc_start: 0.6505 (tpt) cc_final: 0.6240 (mmp) REVERT: G 470 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8002 (m) REVERT: G 634 PHE cc_start: 0.6235 (m-80) cc_final: 0.5886 (m-10) REVERT: G 848 MET cc_start: 0.1981 (pmm) cc_final: 0.1325 (pmm) REVERT: G 920 MET cc_start: 0.3570 (mpp) cc_final: 0.3144 (mpp) REVERT: G 1055 LEU cc_start: 0.9149 (mt) cc_final: 0.8900 (pp) REVERT: G 1075 ASP cc_start: 0.6359 (t0) cc_final: 0.6056 (t0) REVERT: R 69 MET cc_start: 0.7713 (tpt) cc_final: 0.7468 (tpt) REVERT: R 287 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8150 (pp) REVERT: V 69 MET cc_start: 0.8996 (mmm) cc_final: 0.8746 (mmm) REVERT: V 82 LYS cc_start: 0.7883 (pttm) cc_final: 0.7658 (pttm) REVERT: Z 174 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: Z 273 ASN cc_start: 0.7993 (t0) cc_final: 0.7718 (t0) REVERT: Z 446 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6405 (m-10) REVERT: Z 450 MET cc_start: 0.7905 (tpp) cc_final: 0.7656 (tpp) outliers start: 103 outliers final: 61 residues processed: 521 average time/residue: 0.4791 time to fit residues: 425.5335 Evaluate side-chains 460 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 389 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1102 HIS Chi-restraints excluded: chain C residue 1129 CYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 878 GLU Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1102 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 915 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1139 THR Chi-restraints excluded: chain G residue 1155 VAL Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 139 LEU Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 174 GLN Chi-restraints excluded: chain Z residue 231 MET Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Chi-restraints excluded: chain Z residue 456 TYR Chi-restraints excluded: chain Z residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 610 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 360 optimal weight: 30.0000 chunk 462 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 532 optimal weight: 40.0000 chunk 353 optimal weight: 10.0000 chunk 630 optimal weight: 0.0030 chunk 394 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 291 optimal weight: 10.0000 overall best weight: 7.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 51822 Z= 0.205 Angle : 0.664 12.960 70659 Z= 0.322 Chirality : 0.044 0.417 8142 Planarity : 0.005 0.070 9235 Dihedral : 4.800 22.659 7178 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.40 % Favored : 91.47 % Rotamer: Outliers : 2.18 % Allowed : 18.15 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 6510 helix: 0.22 (0.12), residues: 2045 sheet: -1.27 (0.16), residues: 960 loop : -1.49 (0.11), residues: 3505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP V 276 HIS 0.010 0.001 HIS A1102 PHE 0.020 0.001 PHE E 634 TYR 0.018 0.001 TYR R 270 ARG 0.009 0.000 ARG A1363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 416 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7874 (tmm) cc_final: 0.7577 (tmm) REVERT: A 421 MET cc_start: 0.8085 (tpt) cc_final: 0.7712 (tpt) REVERT: A 524 MET cc_start: 0.4351 (tmm) cc_final: 0.3518 (tmm) REVERT: A 789 MET cc_start: 0.1921 (mmt) cc_final: 0.1677 (mmp) REVERT: A 848 MET cc_start: 0.2222 (pmm) cc_final: 0.1505 (pmm) REVERT: A 1134 LEU cc_start: 0.8568 (tp) cc_final: 0.8211 (tp) REVERT: C 412 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8372 (mm) REVERT: C 452 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 460 TYR cc_start: 0.7994 (m-80) cc_final: 0.7618 (m-10) REVERT: C 789 MET cc_start: 0.3804 (mmp) cc_final: 0.3569 (mmp) REVERT: C 848 MET cc_start: 0.2545 (pmm) cc_final: 0.1690 (pmm) REVERT: E 412 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 421 MET cc_start: 0.8205 (tpt) cc_final: 0.7929 (tpt) REVERT: E 465 ILE cc_start: 0.8248 (pt) cc_final: 0.7861 (pt) REVERT: E 848 MET cc_start: 0.2294 (pmm) cc_final: 0.1835 (pmm) REVERT: E 924 THR cc_start: -0.2254 (OUTLIER) cc_final: -0.2519 (t) REVERT: E 1055 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9008 (pp) REVERT: F 271 MET cc_start: 0.8379 (tmm) cc_final: 0.7919 (tmm) REVERT: F 305 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8057 (pp30) REVERT: F 421 MET cc_start: 0.8181 (tpt) cc_final: 0.7712 (tpp) REVERT: F 465 ILE cc_start: 0.7736 (pt) cc_final: 0.7440 (pt) REVERT: F 531 MET cc_start: 0.4777 (mmm) cc_final: 0.4552 (mmm) REVERT: F 584 MET cc_start: 0.6456 (tpt) cc_final: 0.5723 (tmm) REVERT: F 848 MET cc_start: 0.2351 (pmm) cc_final: 0.1626 (pmm) REVERT: F 1055 LEU cc_start: 0.9217 (mt) cc_final: 0.8827 (pp) REVERT: F 1082 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7836 (tp) REVERT: F 1121 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8927 (pp) REVERT: F 1209 MET cc_start: 0.6506 (tpt) cc_final: 0.6291 (mmp) REVERT: G 394 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7730 (tp) REVERT: G 412 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8325 (mm) REVERT: G 470 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (m) REVERT: G 524 MET cc_start: 0.4075 (tmm) cc_final: 0.3623 (tmm) REVERT: G 848 MET cc_start: 0.1928 (pmm) cc_final: 0.1356 (pmm) REVERT: G 920 MET cc_start: 0.3730 (mpp) cc_final: 0.3344 (mpp) REVERT: G 1055 LEU cc_start: 0.9156 (mt) cc_final: 0.8893 (pp) REVERT: R 287 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8202 (pp) REVERT: V 69 MET cc_start: 0.8939 (mmm) cc_final: 0.8642 (mmm) REVERT: Z 174 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: Z 273 ASN cc_start: 0.8010 (t0) cc_final: 0.7737 (t0) REVERT: Z 446 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6399 (m-10) REVERT: Z 450 MET cc_start: 0.7932 (tpp) cc_final: 0.7614 (tpp) outliers start: 117 outliers final: 68 residues processed: 507 average time/residue: 0.4706 time to fit residues: 410.1959 Evaluate side-chains 476 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 394 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1129 CYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1102 HIS Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 878 GLU Chi-restraints excluded: chain G residue 915 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1139 THR Chi-restraints excluded: chain G residue 1155 VAL Chi-restraints excluded: chain G residue 1198 ARG Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 174 GLN Chi-restraints excluded: chain Z residue 231 MET Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Chi-restraints excluded: chain Z residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 389 optimal weight: 3.9990 chunk 251 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 189 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 40.0000 chunk 400 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 311 optimal weight: 0.7980 chunk 58 optimal weight: 50.0000 chunk 495 optimal weight: 50.0000 overall best weight: 5.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1100 HIS ** E1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 713 HIS ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 472 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 51822 Z= 0.186 Angle : 0.668 13.753 70659 Z= 0.320 Chirality : 0.044 0.418 8142 Planarity : 0.005 0.059 9235 Dihedral : 4.650 22.230 7178 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.53 % Favored : 92.33 % Rotamer: Outliers : 1.98 % Allowed : 18.59 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 6510 helix: 0.32 (0.12), residues: 2044 sheet: -1.20 (0.17), residues: 958 loop : -1.42 (0.11), residues: 3508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 276 HIS 0.013 0.001 HIS E1100 PHE 0.022 0.001 PHE E 634 TYR 0.020 0.001 TYR G 503 ARG 0.010 0.000 ARG G1363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 426 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8106 (tpt) cc_final: 0.7693 (tpt) REVERT: A 524 MET cc_start: 0.4571 (tmm) cc_final: 0.3797 (tmm) REVERT: A 848 MET cc_start: 0.2078 (pmm) cc_final: 0.1435 (pmm) REVERT: A 1134 LEU cc_start: 0.8526 (tp) cc_final: 0.8237 (tp) REVERT: C 452 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: C 460 TYR cc_start: 0.8018 (m-80) cc_final: 0.7615 (m-10) REVERT: C 848 MET cc_start: 0.2663 (pmm) cc_final: 0.1956 (pmm) REVERT: E 305 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8170 (pp30) REVERT: E 412 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8218 (mm) REVERT: E 421 MET cc_start: 0.8218 (tpt) cc_final: 0.7904 (tpt) REVERT: E 465 ILE cc_start: 0.8219 (pt) cc_final: 0.7819 (pt) REVERT: E 848 MET cc_start: 0.2255 (pmm) cc_final: 0.1799 (pmm) REVERT: E 924 THR cc_start: -0.2262 (OUTLIER) cc_final: -0.2521 (t) REVERT: E 1055 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9077 (pp) REVERT: F 271 MET cc_start: 0.8359 (tmm) cc_final: 0.7825 (tmm) REVERT: F 421 MET cc_start: 0.8104 (tpt) cc_final: 0.7644 (tpp) REVERT: F 465 ILE cc_start: 0.7736 (pt) cc_final: 0.7436 (pt) REVERT: F 531 MET cc_start: 0.4703 (mmm) cc_final: 0.4423 (mmm) REVERT: F 848 MET cc_start: 0.2317 (pmm) cc_final: 0.1648 (pmm) REVERT: F 1055 LEU cc_start: 0.9196 (mt) cc_final: 0.8816 (pp) REVERT: F 1082 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7702 (tp) REVERT: F 1121 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8905 (pp) REVERT: G 429 ASN cc_start: 0.8048 (m-40) cc_final: 0.7755 (t0) REVERT: G 470 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7994 (m) REVERT: G 524 MET cc_start: 0.4086 (tmm) cc_final: 0.3634 (tmm) REVERT: G 645 MET cc_start: 0.5476 (mmp) cc_final: 0.4639 (mmp) REVERT: G 920 MET cc_start: 0.3138 (mpp) cc_final: 0.2801 (mpp) REVERT: G 1055 LEU cc_start: 0.9146 (mt) cc_final: 0.8889 (pp) REVERT: G 1361 MET cc_start: 0.8195 (ptt) cc_final: 0.7962 (ptt) REVERT: R 225 LEU cc_start: 0.3310 (OUTLIER) cc_final: 0.2993 (mp) REVERT: R 287 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8275 (pp) REVERT: V 65 GLU cc_start: 0.8109 (tp30) cc_final: 0.7907 (tp30) REVERT: V 69 MET cc_start: 0.8927 (mmm) cc_final: 0.8648 (mmm) REVERT: V 276 TRP cc_start: 0.8192 (t-100) cc_final: 0.7774 (t-100) REVERT: Z 273 ASN cc_start: 0.7995 (t0) cc_final: 0.7688 (t0) REVERT: Z 446 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: Z 450 MET cc_start: 0.7952 (tpp) cc_final: 0.7679 (tpp) outliers start: 106 outliers final: 70 residues processed: 510 average time/residue: 0.4800 time to fit residues: 422.3606 Evaluate side-chains 483 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 402 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1129 CYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 878 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1139 THR Chi-restraints excluded: chain G residue 1155 VAL Chi-restraints excluded: chain G residue 1198 ARG Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 231 MET Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Chi-restraints excluded: chain Z residue 458 VAL Chi-restraints excluded: chain Z residue 472 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 573 optimal weight: 10.0000 chunk 603 optimal weight: 20.0000 chunk 550 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 255 optimal weight: 30.0000 chunk 461 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 530 optimal weight: 20.0000 chunk 555 optimal weight: 10.0000 chunk 585 optimal weight: 40.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 GLN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 51822 Z= 0.238 Angle : 0.694 13.365 70659 Z= 0.336 Chirality : 0.044 0.430 8142 Planarity : 0.005 0.054 9235 Dihedral : 4.720 26.493 7178 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.65 % Favored : 91.23 % Rotamer: Outliers : 1.79 % Allowed : 18.97 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 6510 helix: 0.42 (0.12), residues: 2009 sheet: -1.16 (0.17), residues: 920 loop : -1.44 (0.11), residues: 3581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 276 HIS 0.013 0.001 HIS A1102 PHE 0.032 0.001 PHE E 634 TYR 0.018 0.001 TYR R 270 ARG 0.010 0.001 ARG G1363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 402 time to evaluate : 4.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8124 (tpt) cc_final: 0.7874 (tpt) REVERT: A 524 MET cc_start: 0.4601 (tmm) cc_final: 0.3821 (tmm) REVERT: A 848 MET cc_start: 0.2150 (pmm) cc_final: 0.1520 (pmm) REVERT: A 1134 LEU cc_start: 0.8499 (tp) cc_final: 0.8234 (tp) REVERT: C 412 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (mm) REVERT: C 452 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: C 460 TYR cc_start: 0.8078 (m-80) cc_final: 0.7763 (m-10) REVERT: C 848 MET cc_start: 0.2334 (pmm) cc_final: 0.1528 (pmm) REVERT: E 412 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 421 MET cc_start: 0.8230 (tpt) cc_final: 0.8026 (tpt) REVERT: E 465 ILE cc_start: 0.8285 (pt) cc_final: 0.7896 (pt) REVERT: E 848 MET cc_start: 0.2329 (pmm) cc_final: 0.1904 (pmm) REVERT: E 924 THR cc_start: -0.2112 (OUTLIER) cc_final: -0.2381 (t) REVERT: E 1055 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9067 (pp) REVERT: F 271 MET cc_start: 0.8488 (tmm) cc_final: 0.7940 (tmm) REVERT: F 412 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (mm) REVERT: F 421 MET cc_start: 0.8153 (tpt) cc_final: 0.7689 (tpp) REVERT: F 465 ILE cc_start: 0.8051 (pt) cc_final: 0.7783 (pt) REVERT: F 531 MET cc_start: 0.4746 (mmm) cc_final: 0.4413 (mmm) REVERT: F 584 MET cc_start: 0.6524 (tpt) cc_final: 0.5758 (tmm) REVERT: F 848 MET cc_start: 0.2347 (pmm) cc_final: 0.1680 (pmm) REVERT: F 959 MET cc_start: 0.3790 (mpp) cc_final: 0.2927 (mpp) REVERT: F 1055 LEU cc_start: 0.9193 (mt) cc_final: 0.8819 (pp) REVERT: F 1082 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7657 (tp) REVERT: F 1121 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8929 (pp) REVERT: G 394 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7742 (tp) REVERT: G 470 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7912 (m) REVERT: G 524 MET cc_start: 0.4415 (tmm) cc_final: 0.4133 (tmm) REVERT: G 1055 LEU cc_start: 0.9158 (mt) cc_final: 0.8911 (pp) REVERT: R 225 LEU cc_start: 0.3376 (OUTLIER) cc_final: 0.3049 (mp) REVERT: R 287 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8238 (pp) REVERT: V 276 TRP cc_start: 0.8195 (t-100) cc_final: 0.7794 (t-100) REVERT: Z 136 GLU cc_start: 0.5055 (mp0) cc_final: 0.4778 (mp0) REVERT: Z 273 ASN cc_start: 0.8037 (t0) cc_final: 0.7758 (t0) REVERT: Z 446 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: Z 450 MET cc_start: 0.7787 (tpp) cc_final: 0.7474 (tpp) outliers start: 96 outliers final: 72 residues processed: 470 average time/residue: 0.4815 time to fit residues: 390.8694 Evaluate side-chains 479 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 394 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1129 CYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 878 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 959 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1139 THR Chi-restraints excluded: chain G residue 1155 VAL Chi-restraints excluded: chain G residue 1198 ARG Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 231 MET Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Chi-restraints excluded: chain Z residue 458 VAL Chi-restraints excluded: chain Z residue 472 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 385 optimal weight: 10.0000 chunk 621 optimal weight: 40.0000 chunk 379 optimal weight: 30.0000 chunk 294 optimal weight: 50.0000 chunk 431 optimal weight: 40.0000 chunk 651 optimal weight: 40.0000 chunk 599 optimal weight: 50.0000 chunk 518 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 400 optimal weight: 50.0000 chunk 318 optimal weight: 40.0000 overall best weight: 32.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 195 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN C 902 HIS ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 122 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 902 HIS E1018 HIS ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 902 HIS ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 902 HIS ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 270 ASN ** Z 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 51822 Z= 0.625 Angle : 1.072 13.365 70659 Z= 0.550 Chirality : 0.056 0.523 8142 Planarity : 0.009 0.101 9235 Dihedral : 6.609 25.487 7178 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.67 % Favored : 87.14 % Rotamer: Outliers : 2.05 % Allowed : 19.23 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.10), residues: 6510 helix: -1.20 (0.10), residues: 2127 sheet: -1.99 (0.16), residues: 888 loop : -2.19 (0.10), residues: 3495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP F 527 HIS 0.050 0.003 HIS A1102 PHE 0.046 0.004 PHE C 244 TYR 0.031 0.004 TYR C 833 ARG 0.015 0.002 ARG G 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13020 Ramachandran restraints generated. 6510 Oldfield, 0 Emsley, 6510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 359 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.5058 (tmm) cc_final: 0.4186 (tmm) REVERT: A 848 MET cc_start: 0.3537 (pmm) cc_final: 0.3056 (pmm) REVERT: A 1134 LEU cc_start: 0.8853 (tp) cc_final: 0.8548 (tp) REVERT: A 1157 MET cc_start: 0.3567 (ptt) cc_final: 0.3222 (ptm) REVERT: C 412 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8768 (mm) REVERT: C 414 ASN cc_start: 0.7332 (t0) cc_final: 0.6952 (t0) REVERT: C 848 MET cc_start: 0.3683 (pmm) cc_final: 0.2865 (pmm) REVERT: C 920 MET cc_start: 0.4806 (OUTLIER) cc_final: 0.4458 (mtp) REVERT: E 412 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8691 (mm) REVERT: E 414 ASN cc_start: 0.7997 (m-40) cc_final: 0.7681 (t0) REVERT: E 848 MET cc_start: 0.3840 (pmm) cc_final: 0.3599 (pmm) REVERT: E 924 THR cc_start: -0.1903 (OUTLIER) cc_final: -0.2148 (t) REVERT: F 645 MET cc_start: 0.6291 (mmp) cc_final: 0.5885 (mmp) REVERT: F 823 ARG cc_start: 0.4459 (mmm160) cc_final: 0.3293 (mmm160) REVERT: F 848 MET cc_start: 0.3901 (pmm) cc_final: 0.3167 (pmm) REVERT: F 1121 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8995 (pp) REVERT: G 262 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7613 (ttm) REVERT: G 470 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7955 (m) REVERT: G 524 MET cc_start: 0.4415 (tmm) cc_final: 0.4191 (tmm) REVERT: R 4 MET cc_start: 0.8108 (mmt) cc_final: 0.7525 (mmt) REVERT: R 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8393 (pp) REVERT: Z 446 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: Z 450 MET cc_start: 0.8054 (tpp) cc_final: 0.7741 (tpp) outliers start: 110 outliers final: 81 residues processed: 445 average time/residue: 0.4944 time to fit residues: 378.7753 Evaluate side-chains 420 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 330 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 924 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1129 CYS Chi-restraints excluded: chain C residue 1139 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 258 TYR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1121 LEU Chi-restraints excluded: chain F residue 1139 THR Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 673 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1102 HIS Chi-restraints excluded: chain G residue 1139 THR Chi-restraints excluded: chain G residue 1381 LEU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 139 LEU Chi-restraints excluded: chain V residue 283 LEU Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 131 PHE Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 231 MET Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Chi-restraints excluded: chain Z residue 458 VAL Chi-restraints excluded: chain Z residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 412 optimal weight: 4.9990 chunk 552 optimal weight: 50.0000 chunk 158 optimal weight: 30.0000 chunk 478 optimal weight: 7.9990 chunk 76 optimal weight: 50.0000 chunk 144 optimal weight: 30.0000 chunk 519 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 533 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 468 GLN A 501 GLN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 892 ASN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1143 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 ASN E1057 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1058 GLN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 472 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.103379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.081514 restraints weight = 322039.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081978 restraints weight = 246606.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081976 restraints weight = 178913.381| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 51822 Z= 0.241 Angle : 0.763 13.447 70659 Z= 0.372 Chirality : 0.047 0.460 8142 Planarity : 0.005 0.064 9235 Dihedral : 5.466 23.964 7178 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 91.00 % Rotamer: Outliers : 1.49 % Allowed : 20.18 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.10), residues: 6510 helix: -0.32 (0.11), residues: 2007 sheet: -1.58 (0.16), residues: 968 loop : -1.83 (0.11), residues: 3535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP V 276 HIS 0.009 0.001 HIS A1102 PHE 0.037 0.001 PHE E 634 TYR 0.021 0.002 TYR C 975 ARG 0.010 0.001 ARG G1363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7924.09 seconds wall clock time: 141 minutes 39.81 seconds (8499.81 seconds total)