Starting phenix.real_space_refine on Wed Jan 15 09:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa2_38192/01_2025/8xa2_38192_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa2_38192/01_2025/8xa2_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_38192/01_2025/8xa2_38192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa2_38192/01_2025/8xa2_38192.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa2_38192/01_2025/8xa2_38192_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa2_38192/01_2025/8xa2_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 20.41, per 1000 atoms: 0.40 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: 8.84 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: 4.82 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: 17.71 Time building geometry restraints manager: 10.52 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: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 81.630 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.280 ------------------------------------------------------------------------------- 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 : 4.149 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: 0.4717 time to fit residues: 448.1477 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 : 4.159 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.110540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.089363 restraints weight = 321177.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.089146 restraints weight = 277339.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.088859 restraints weight = 217691.066| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 4.161 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: 0.8337 (tpt) cc_final: 0.8010 (tpt) REVERT: A 475 MET cc_start: 0.8069 (mpp) cc_final: 0.7677 (mmm) REVERT: A 622 MET cc_start: 0.5302 (mpp) cc_final: 0.4587 (mmm) REVERT: A 848 MET cc_start: -0.0873 (pmm) cc_final: -0.1198 (pmm) REVERT: A 1055 LEU cc_start: 0.9401 (mt) cc_final: 0.8992 (pp) REVERT: A 1134 LEU cc_start: 0.8834 (tp) cc_final: 0.8563 (tp) REVERT: A 1209 MET cc_start: 0.6212 (tpt) cc_final: 0.5650 (tpt) REVERT: C 423 MET cc_start: 0.8162 (tmm) cc_final: 0.7888 (tmm) REVERT: C 848 MET cc_start: -0.1293 (pmm) cc_final: -0.1640 (pmm) REVERT: C 1209 MET cc_start: 0.6403 (tpt) cc_final: 0.5628 (tpt) REVERT: E 242 MET cc_start: 0.7873 (mmm) cc_final: 0.7448 (tpp) REVERT: E 421 MET cc_start: 0.8273 (tpt) cc_final: 0.7979 (tpt) REVERT: E 423 MET cc_start: 0.8190 (tpt) cc_final: 0.7424 (tmm) REVERT: E 429 ASN cc_start: 0.7618 (t0) cc_final: 0.7197 (t0) REVERT: E 475 MET cc_start: 0.8004 (mpp) cc_final: 0.7694 (mmm) REVERT: E 634 PHE cc_start: 0.7199 (m-80) cc_final: 0.6789 (m-10) REVERT: E 848 MET cc_start: -0.0981 (pmm) cc_final: -0.1388 (pmm) REVERT: E 1055 LEU cc_start: 0.9270 (mt) cc_final: 0.8910 (pp) REVERT: E 1134 LEU cc_start: 0.8890 (mt) cc_final: 0.8595 (tp) REVERT: E 1209 MET cc_start: 0.6394 (tpt) cc_final: 0.5643 (tpt) REVERT: E 1363 ARG cc_start: 0.9140 (tpm170) cc_final: 0.8789 (tpp-160) REVERT: F 108 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: F 242 MET cc_start: 0.7679 (tpp) cc_final: 0.7324 (tpp) REVERT: F 423 MET cc_start: 0.7941 (tmm) cc_final: 0.7493 (tmm) REVERT: F 959 MET cc_start: 0.4536 (OUTLIER) cc_final: 0.3884 (mtp) REVERT: F 1055 LEU cc_start: 0.9301 (mt) cc_final: 0.8845 (pp) REVERT: F 1209 MET cc_start: 0.6190 (tpt) cc_final: 0.5445 (tpt) REVERT: G 155 LEU cc_start: 0.9355 (mt) cc_final: 0.9150 (tt) REVERT: G 255 ILE cc_start: 0.9331 (tp) cc_final: 0.9098 (mm) REVERT: G 429 ASN cc_start: 0.7863 (t0) cc_final: 0.7494 (t0) REVERT: G 1055 LEU cc_start: 0.9490 (mt) cc_final: 0.9169 (pp) REVERT: R 4 MET cc_start: 0.7161 (mmt) cc_final: 0.6809 (mmt) REVERT: R 69 MET cc_start: 0.7806 (tpt) cc_final: 0.7549 (tpt) REVERT: V 69 MET cc_start: 0.8933 (mmp) cc_final: 0.8539 (mmm) REVERT: Z 273 ASN cc_start: 0.8583 (t0) cc_final: 0.8323 (t0) REVERT: Z 279 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8225 (ttmt) REVERT: Z 348 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7389 (pp30) outliers start: 53 outliers final: 26 residues processed: 493 average time/residue: 0.4787 time to fit residues: 406.7391 Evaluate side-chains 421 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 4.170 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Z residue 348 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 16 optimal weight: 7.9990 chunk 492 optimal weight: 0.0270 chunk 450 optimal weight: 40.0000 chunk 482 optimal weight: 20.0000 chunk 647 optimal weight: 50.0000 chunk 651 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 477 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 559 optimal weight: 9.9990 overall best weight: 8.2048 ------------------------------------------------------------------------------- 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 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** A 713 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1143 ASN ** E 267 GLN ** 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** E 713 HIS ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN G 519 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.109659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.088539 restraints weight = 324818.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.088590 restraints weight = 271856.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.088453 restraints weight = 196915.842| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51822 Z= 0.204 Angle : 0.630 11.814 70659 Z= 0.312 Chirality : 0.043 0.234 8142 Planarity : 0.005 0.061 9235 Dihedral : 4.749 28.716 7178 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.97 % Favored : 92.73 % Rotamer: Outliers : 1.53 % Allowed : 12.14 % Favored : 86.33 % 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: -1.36 (0.10), residues: 6510 helix: 0.10 (0.12), residues: 1974 sheet: -1.11 (0.16), residues: 982 loop : -1.43 (0.11), residues: 3554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP V 276 HIS 0.007 0.001 HIS A1102 PHE 0.022 0.001 PHE G1050 TYR 0.015 0.001 TYR R 270 ARG 0.007 0.000 ARG F 450 *********************** 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 505 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 423 time to evaluate : 4.258 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 266 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7682 (t) REVERT: A 475 MET cc_start: 0.8127 (mpp) cc_final: 0.7909 (mmm) REVERT: A 848 MET cc_start: -0.0487 (pmm) cc_final: -0.0761 (pmm) REVERT: A 1055 LEU cc_start: 0.9496 (mt) cc_final: 0.9168 (pp) REVERT: A 1134 LEU cc_start: 0.8621 (tp) cc_final: 0.8338 (tp) REVERT: A 1209 MET cc_start: 0.5842 (tpt) cc_final: 0.5453 (tpt) REVERT: C 848 MET cc_start: -0.0590 (pmm) cc_final: -0.1050 (pmm) REVERT: C 1209 MET cc_start: 0.5617 (tpt) cc_final: 0.4900 (tpt) REVERT: E 242 MET cc_start: 0.7773 (mmm) cc_final: 0.7552 (tpp) REVERT: E 423 MET cc_start: 0.8043 (tpt) cc_final: 0.7530 (tmm) REVERT: E 475 MET cc_start: 0.7924 (mpp) cc_final: 0.7657 (mmm) REVERT: E 531 MET cc_start: 0.4410 (mmp) cc_final: 0.4135 (mmm) REVERT: E 634 PHE cc_start: 0.7173 (m-80) cc_final: 0.6724 (m-10) REVERT: E 848 MET cc_start: -0.0624 (pmm) cc_final: -0.1142 (pmm) REVERT: E 1055 LEU cc_start: 0.9298 (mt) cc_final: 0.9010 (pp) REVERT: E 1209 MET cc_start: 0.6261 (tpt) cc_final: 0.5527 (tpt) REVERT: F 421 MET cc_start: 0.8427 (tpt) cc_final: 0.7986 (tpp) REVERT: F 423 MET cc_start: 0.7937 (tmm) cc_final: 0.7682 (tmm) REVERT: F 531 MET cc_start: 0.5434 (mmm) cc_final: 0.5171 (mmm) REVERT: F 622 MET cc_start: 0.5289 (mmm) cc_final: 0.4700 (mpp) REVERT: F 1055 LEU cc_start: 0.9346 (mt) cc_final: 0.8902 (pp) REVERT: F 1121 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9057 (pp) REVERT: G 470 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8297 (m) REVERT: G 848 MET cc_start: -0.0667 (pmm) cc_final: -0.0901 (pmm) REVERT: G 1055 LEU cc_start: 0.9380 (mt) cc_final: 0.9135 (pp) REVERT: R 4 MET cc_start: 0.7242 (mmp) cc_final: 0.6677 (mmt) REVERT: R 207 LEU cc_start: 0.7302 (tt) cc_final: 0.6524 (tp) REVERT: V 69 MET cc_start: 0.8746 (mmp) cc_final: 0.8405 (mmm) REVERT: V 285 ASP cc_start: 0.8150 (t70) cc_final: 0.7476 (t70) REVERT: Z 273 ASN cc_start: 0.8544 (t0) cc_final: 0.8279 (t0) REVERT: Z 450 MET cc_start: 0.8066 (tpp) cc_final: 0.7818 (tpp) outliers start: 82 outliers final: 47 residues processed: 472 average time/residue: 0.4715 time to fit residues: 383.3662 Evaluate side-chains 431 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 381 time to evaluate : 4.125 ------------------------------------------------------------------------------- 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 266 THR 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 213 ILE Chi-restraints excluded: chain E residue 258 TYR 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 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 G residue 125 ASP 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 1102 HIS 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 65 optimal weight: 6.9990 chunk 419 optimal weight: 10.0000 chunk 306 optimal weight: 50.0000 chunk 537 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 50.0000 chunk 222 optimal weight: 50.0000 chunk 465 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 GLN ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.086796 restraints weight = 324714.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.086913 restraints weight = 256305.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.087031 restraints weight = 189736.617| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 51822 Z= 0.207 Angle : 0.627 11.086 70659 Z= 0.311 Chirality : 0.043 0.151 8142 Planarity : 0.005 0.058 9235 Dihedral : 4.656 24.887 7178 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.33 % Favored : 92.43 % Rotamer: Outliers : 2.03 % Allowed : 13.71 % Favored : 84.26 % 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: -1.24 (0.10), residues: 6510 helix: 0.28 (0.12), residues: 2009 sheet: -0.88 (0.17), residues: 938 loop : -1.48 (0.11), residues: 3563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 276 HIS 0.024 0.001 HIS G1102 PHE 0.019 0.001 PHE C1050 TYR 0.017 0.001 TYR R 270 ARG 0.008 0.000 ARG Z 234 *********************** 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 530 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 421 time to evaluate : 4.296 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 421 MET cc_start: 0.8349 (tpt) cc_final: 0.8024 (tpt) REVERT: A 475 MET cc_start: 0.8135 (mpp) cc_final: 0.7845 (mmm) REVERT: A 524 MET cc_start: 0.3696 (tmm) cc_final: 0.3181 (tmm) REVERT: A 848 MET cc_start: -0.0529 (pmm) cc_final: -0.0902 (pmm) REVERT: A 920 MET cc_start: 0.4848 (mmp) cc_final: 0.3160 (mtt) REVERT: A 1055 LEU cc_start: 0.9486 (mt) cc_final: 0.9163 (pp) REVERT: A 1134 LEU cc_start: 0.8697 (tp) cc_final: 0.8355 (tp) REVERT: A 1209 MET cc_start: 0.5879 (tpt) cc_final: 0.5480 (tpt) REVERT: C 848 MET cc_start: -0.0046 (pmm) cc_final: -0.0524 (pmm) REVERT: C 1157 MET cc_start: 0.3055 (ptt) cc_final: 0.2452 (ptm) REVERT: C 1209 MET cc_start: 0.5357 (tpt) cc_final: 0.4617 (tpt) REVERT: E 232 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7934 (m) REVERT: E 245 MET cc_start: 0.8331 (mmm) cc_final: 0.8080 (mmm) REVERT: E 253 ARG cc_start: 0.8597 (mmp80) cc_final: 0.8352 (mmp80) REVERT: E 423 MET cc_start: 0.8058 (tpt) cc_final: 0.7558 (tmm) REVERT: E 429 ASN cc_start: 0.7974 (t0) cc_final: 0.7651 (t0) REVERT: E 531 MET cc_start: 0.4391 (mmp) cc_final: 0.3786 (mmm) REVERT: E 634 PHE cc_start: 0.7181 (m-80) cc_final: 0.6759 (m-10) REVERT: E 848 MET cc_start: -0.0315 (pmm) cc_final: -0.0796 (pmm) REVERT: E 924 THR cc_start: -0.2421 (OUTLIER) cc_final: -0.2719 (t) REVERT: E 1055 LEU cc_start: 0.9345 (mt) cc_final: 0.9067 (pp) REVERT: E 1209 MET cc_start: 0.6151 (tpt) cc_final: 0.5424 (tpt) REVERT: E 1363 ARG cc_start: 0.9137 (tpm170) cc_final: 0.8663 (tpm170) REVERT: F 421 MET cc_start: 0.8280 (tpt) cc_final: 0.7777 (tpp) REVERT: F 622 MET cc_start: 0.5476 (mmm) cc_final: 0.4953 (mpp) REVERT: F 726 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6566 (mm) REVERT: F 1055 LEU cc_start: 0.9286 (mt) cc_final: 0.8921 (pp) REVERT: F 1121 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9062 (pp) REVERT: F 1134 LEU cc_start: 0.8147 (tt) cc_final: 0.7911 (tp) REVERT: F 1209 MET cc_start: 0.5790 (tpt) cc_final: 0.5469 (tpt) REVERT: G 186 ASP cc_start: 0.7985 (p0) cc_final: 0.7743 (p0) REVERT: G 412 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8431 (mm) REVERT: G 470 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8302 (m) REVERT: G 848 MET cc_start: -0.0652 (pmm) cc_final: -0.0977 (pmm) REVERT: G 1157 MET cc_start: 0.3733 (ptt) cc_final: 0.3203 (ptt) REVERT: R 4 MET cc_start: 0.7599 (mmp) cc_final: 0.6909 (mmt) REVERT: R 15 GLU cc_start: 0.9038 (pm20) cc_final: 0.8790 (mp0) REVERT: R 207 LEU cc_start: 0.7209 (tt) cc_final: 0.6386 (tp) REVERT: Z 254 ARG cc_start: 0.6805 (ptt-90) cc_final: 0.6565 (ptp90) REVERT: Z 273 ASN cc_start: 0.8643 (t0) cc_final: 0.8408 (t0) REVERT: Z 450 MET cc_start: 0.8299 (tpp) cc_final: 0.7959 (tpp) outliers start: 109 outliers final: 63 residues processed: 502 average time/residue: 0.4700 time to fit residues: 406.3361 Evaluate side-chains 460 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 391 time to evaluate : 4.153 ------------------------------------------------------------------------------- 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 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 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 386 ILE 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 213 ILE Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 266 THR 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 115 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 201 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 726 ILE 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 1155 VAL Chi-restraints excluded: chain G residue 155 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 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 74 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 326 VAL Chi-restraints excluded: chain Z residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 43 optimal weight: 50.0000 chunk 322 optimal weight: 20.0000 chunk 361 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 621 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 412 optimal weight: 40.0000 chunk 247 optimal weight: 40.0000 chunk 304 optimal weight: 30.0000 chunk 297 optimal weight: 50.0000 chunk 176 optimal weight: 30.0000 overall best weight: 16.7996 ------------------------------------------------------------------------------- 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 305 GLN ** 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** ** 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 C 108 GLN 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 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 HIS C 895 ASN ** C1057 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 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 ** E1057 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 653 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 ASN ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 129 HIS ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 GLN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN G 895 ASN ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1102 HIS ** 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** V 101 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.104933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.082863 restraints weight = 327088.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.083175 restraints weight = 260081.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.083142 restraints weight = 183868.400| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 51822 Z= 0.361 Angle : 0.756 16.339 70659 Z= 0.380 Chirality : 0.046 0.251 8142 Planarity : 0.006 0.089 9235 Dihedral : 5.214 24.860 7178 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.80 % Favored : 90.08 % Rotamer: Outliers : 2.85 % Allowed : 16.04 % Favored : 81.11 % 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: -1.62 (0.10), residues: 6510 helix: -0.04 (0.11), residues: 2050 sheet: -1.35 (0.16), residues: 962 loop : -1.64 (0.11), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 468 HIS 0.009 0.002 HIS R 39 PHE 0.028 0.002 PHE R 137 TYR 0.020 0.002 TYR R 270 ARG 0.020 0.001 ARG Z 352 *********************** 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 560 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 407 time to evaluate : 4.266 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 108 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: A 242 MET cc_start: 0.8171 (tpp) cc_final: 0.7821 (tpp) REVERT: A 271 MET cc_start: 0.8078 (tmm) cc_final: 0.7696 (tmm) REVERT: A 285 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 465 ILE cc_start: 0.8550 (pt) cc_final: 0.8336 (pt) REVERT: A 524 MET cc_start: 0.3731 (tmm) cc_final: 0.3144 (tmm) REVERT: A 543 THR cc_start: 0.8893 (t) cc_final: 0.8671 (p) REVERT: A 848 MET cc_start: 0.0650 (pmm) cc_final: 0.0213 (pmm) REVERT: A 1082 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 1134 LEU cc_start: 0.8926 (tp) cc_final: 0.8629 (tp) REVERT: A 1209 MET cc_start: 0.5657 (tpt) cc_final: 0.5035 (tpt) REVERT: C 412 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8259 (mm) REVERT: C 543 THR cc_start: 0.8876 (t) cc_final: 0.8646 (p) REVERT: C 848 MET cc_start: 0.0656 (pmm) cc_final: 0.0205 (pmm) REVERT: C 1209 MET cc_start: 0.6018 (tpt) cc_final: 0.5658 (tpt) REVERT: E 253 ARG cc_start: 0.8612 (mmp80) cc_final: 0.8382 (mmp80) REVERT: E 386 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8491 (pt) REVERT: E 634 PHE cc_start: 0.6958 (m-80) cc_final: 0.6676 (m-10) REVERT: E 848 MET cc_start: 0.0893 (pmm) cc_final: 0.0355 (pmm) REVERT: E 924 THR cc_start: -0.2160 (OUTLIER) cc_final: -0.2437 (t) REVERT: E 1157 MET cc_start: 0.3167 (ptt) cc_final: 0.2455 (ptt) REVERT: E 1209 MET cc_start: 0.6208 (tpt) cc_final: 0.5541 (tpt) REVERT: E 1363 ARG cc_start: 0.9094 (tpm170) cc_final: 0.8401 (tpm170) REVERT: F 412 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8625 (mm) REVERT: F 414 ASN cc_start: 0.7699 (m-40) cc_final: 0.7279 (t0) REVERT: F 421 MET cc_start: 0.8364 (tpt) cc_final: 0.7970 (tpp) REVERT: F 531 MET cc_start: 0.4896 (mpp) cc_final: 0.4621 (mpp) REVERT: F 920 MET cc_start: 0.3968 (mpp) cc_final: 0.3738 (mpp) REVERT: F 1055 LEU cc_start: 0.9373 (mt) cc_final: 0.9075 (pp) REVERT: F 1121 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9089 (pp) REVERT: F 1366 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7340 (m90) REVERT: G 394 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8549 (tp) REVERT: G 412 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8697 (mm) REVERT: G 920 MET cc_start: 0.2764 (mpp) cc_final: 0.2453 (mpp) REVERT: R 4 MET cc_start: 0.8121 (mmp) cc_final: 0.7425 (mmt) REVERT: R 219 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8170 (tt) REVERT: V 69 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8650 (mmm) REVERT: V 82 LYS cc_start: 0.8713 (pttm) cc_final: 0.8509 (pttm) REVERT: Z 450 MET cc_start: 0.8360 (tpp) cc_final: 0.7992 (tpp) outliers start: 153 outliers final: 84 residues processed: 523 average time/residue: 0.4850 time to fit residues: 432.9195 Evaluate side-chains 476 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 379 time to evaluate : 4.188 ------------------------------------------------------------------------------- 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 266 THR 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 979 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain C residue 194 ASP 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 397 LEU Chi-restraints excluded: chain C residue 412 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 C residue 1129 CYS Chi-restraints excluded: chain C residue 1354 LEU 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 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 386 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 VAL 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 F residue 155 LEU Chi-restraints excluded: chain F residue 181 LEU 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 412 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 848 MET Chi-restraints excluded: chain F residue 915 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 1198 ARG 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 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 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE 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 209 PHE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 69 MET 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 285 ASP Chi-restraints excluded: chain V residue 292 ILE 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 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 73 optimal weight: 20.0000 chunk 384 optimal weight: 50.0000 chunk 328 optimal weight: 20.0000 chunk 406 optimal weight: 30.0000 chunk 239 optimal weight: 0.9990 chunk 594 optimal weight: 0.0370 chunk 599 optimal weight: 50.0000 chunk 227 optimal weight: 40.0000 chunk 9 optimal weight: 30.0000 chunk 493 optimal weight: 0.5980 chunk 448 optimal weight: 30.0000 overall best weight: 8.3268 ------------------------------------------------------------------------------- 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** A 895 ASN ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 HIS A1102 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1376 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 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** ** G 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1064 HIS G1102 HIS G1366 HIS ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.106229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.083817 restraints weight = 323059.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.084515 restraints weight = 244951.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.084522 restraints weight = 164723.317| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51822 Z= 0.214 Angle : 0.660 13.650 70659 Z= 0.323 Chirality : 0.043 0.278 8142 Planarity : 0.005 0.054 9235 Dihedral : 4.847 24.706 7178 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.45 % Favored : 92.41 % Rotamer: Outliers : 2.01 % Allowed : 17.62 % Favored : 80.36 % 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: -1.38 (0.11), residues: 6510 helix: 0.21 (0.11), residues: 2055 sheet: -1.29 (0.16), residues: 954 loop : -1.50 (0.11), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 276 HIS 0.008 0.001 HIS A1102 PHE 0.015 0.001 PHE Z 350 TYR 0.017 0.001 TYR R 270 ARG 0.007 0.000 ARG Z 230 *********************** 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 533 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 425 time to evaluate : 4.273 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 271 MET cc_start: 0.8008 (tmm) cc_final: 0.7748 (tmm) REVERT: A 285 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9012 (p) REVERT: A 421 MET cc_start: 0.8416 (tpt) cc_final: 0.8128 (tpt) REVERT: A 848 MET cc_start: 0.0641 (pmm) cc_final: 0.0168 (pmm) REVERT: A 920 MET cc_start: 0.5127 (mmp) cc_final: 0.4825 (mmm) REVERT: A 1134 LEU cc_start: 0.8921 (tp) cc_final: 0.8638 (tp) REVERT: A 1209 MET cc_start: 0.5525 (tpt) cc_final: 0.5072 (tpt) REVERT: C 460 TYR cc_start: 0.8600 (m-80) cc_final: 0.8261 (m-10) REVERT: C 543 THR cc_start: 0.8828 (t) cc_final: 0.8570 (p) REVERT: C 848 MET cc_start: 0.0915 (pmm) cc_final: 0.0468 (pmm) REVERT: C 1209 MET cc_start: 0.6110 (tpt) cc_final: 0.5821 (tpt) REVERT: E 186 ASP cc_start: 0.7618 (p0) cc_final: 0.7370 (p0) REVERT: E 253 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8422 (mmp80) REVERT: E 386 ILE cc_start: 0.8894 (tt) cc_final: 0.8518 (pt) REVERT: E 421 MET cc_start: 0.8545 (tpt) cc_final: 0.8210 (tpt) REVERT: E 423 MET cc_start: 0.7852 (tpt) cc_final: 0.7282 (tmm) REVERT: E 634 PHE cc_start: 0.6958 (m-80) cc_final: 0.6672 (m-10) REVERT: E 848 MET cc_start: 0.0361 (pmm) cc_final: -0.0035 (pmm) REVERT: E 924 THR cc_start: -0.2131 (OUTLIER) cc_final: -0.2422 (t) REVERT: E 1209 MET cc_start: 0.5535 (tpt) cc_final: 0.5006 (tpt) REVERT: E 1363 ARG cc_start: 0.9078 (tpm170) cc_final: 0.8401 (tpm170) REVERT: F 271 MET cc_start: 0.8213 (tmm) cc_final: 0.7839 (tmm) REVERT: F 414 ASN cc_start: 0.7764 (m-40) cc_final: 0.7437 (t0) REVERT: F 421 MET cc_start: 0.8426 (tpt) cc_final: 0.8044 (tpp) REVERT: F 531 MET cc_start: 0.4770 (mpp) cc_final: 0.4477 (mpp) REVERT: F 622 MET cc_start: 0.5790 (mpp) cc_final: 0.5488 (mpp) REVERT: F 959 MET cc_start: 0.3956 (mtt) cc_final: 0.3253 (mpp) REVERT: F 1055 LEU cc_start: 0.9360 (mt) cc_final: 0.9033 (pp) REVERT: F 1082 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8425 (tp) REVERT: F 1121 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9055 (pp) REVERT: F 1209 MET cc_start: 0.5647 (tpt) cc_final: 0.5080 (tpt) REVERT: G 186 ASP cc_start: 0.7839 (p0) cc_final: 0.7580 (p0) REVERT: G 245 MET cc_start: 0.8488 (tpp) cc_final: 0.8177 (tpt) REVERT: G 848 MET cc_start: 0.0385 (pmm) cc_final: -0.0041 (pmm) REVERT: G 920 MET cc_start: 0.2566 (mpp) cc_final: 0.2225 (mpp) REVERT: G 1055 LEU cc_start: 0.9475 (mm) cc_final: 0.9187 (pp) REVERT: G 1361 MET cc_start: 0.8365 (ptt) cc_final: 0.8146 (ptt) REVERT: R 67 TYR cc_start: 0.8439 (m-80) cc_final: 0.7978 (m-80) REVERT: V 8 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8457 (mp) REVERT: V 82 LYS cc_start: 0.8682 (pttm) cc_final: 0.8414 (pttm) REVERT: Z 174 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: Z 446 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6803 (m-10) REVERT: Z 450 MET cc_start: 0.8342 (tpp) cc_final: 0.7996 (tpp) outliers start: 108 outliers final: 67 residues processed: 508 average time/residue: 0.4710 time to fit residues: 412.2034 Evaluate side-chains 463 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 389 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 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 878 GLU Chi-restraints excluded: chain A residue 959 MET 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 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 397 LEU 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 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 407 VAL 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 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 288 VAL Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 915 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 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 272 VAL Chi-restraints excluded: chain G residue 407 VAL 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 115 LEU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 8 ILE Chi-restraints excluded: chain V residue 60 THR 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 287 THR Chi-restraints excluded: chain Z residue 312 HIS Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 446 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 429 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 619 optimal weight: 40.0000 chunk 298 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 289 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 217 optimal weight: 50.0000 chunk 589 optimal weight: 9.9990 overall best weight: 7.9590 ------------------------------------------------------------------------------- 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 ** C 137 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 455 GLN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** 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 ** 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 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** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1102 HIS ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.106184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.083746 restraints weight = 323141.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.084451 restraints weight = 245189.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.084406 restraints weight = 172248.478| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 51822 Z= 0.211 Angle : 0.658 12.761 70659 Z= 0.320 Chirality : 0.044 0.405 8142 Planarity : 0.005 0.053 9235 Dihedral : 4.717 23.896 7178 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.48 % Favored : 91.40 % Rotamer: Outliers : 2.29 % Allowed : 18.20 % Favored : 79.50 % 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: -1.26 (0.11), residues: 6510 helix: 0.32 (0.12), residues: 2045 sheet: -1.21 (0.16), residues: 960 loop : -1.43 (0.11), residues: 3505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 172 HIS 0.011 0.001 HIS E1102 PHE 0.017 0.001 PHE C 452 TYR 0.018 0.001 TYR R 270 ARG 0.006 0.000 ARG F1198 *********************** 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 536 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 413 time to evaluate : 4.238 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 242 MET cc_start: 0.8047 (tpp) cc_final: 0.7683 (tpp) REVERT: A 285 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9023 (p) REVERT: A 524 MET cc_start: 0.4369 (tmm) cc_final: 0.3674 (tmm) REVERT: A 543 THR cc_start: 0.9048 (t) cc_final: 0.8833 (p) REVERT: A 848 MET cc_start: 0.0525 (pmm) cc_final: 0.0069 (pmm) REVERT: A 920 MET cc_start: 0.4980 (mmp) cc_final: 0.3352 (mtt) REVERT: A 1134 LEU cc_start: 0.8950 (tp) cc_final: 0.8668 (tp) REVERT: A 1209 MET cc_start: 0.5698 (tpt) cc_final: 0.5151 (tpt) REVERT: C 412 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (mm) REVERT: C 460 TYR cc_start: 0.8674 (m-80) cc_final: 0.8315 (m-10) REVERT: C 543 THR cc_start: 0.8866 (t) cc_final: 0.8638 (p) REVERT: C 848 MET cc_start: 0.0821 (pmm) cc_final: 0.0349 (pmm) REVERT: E 186 ASP cc_start: 0.7604 (p0) cc_final: 0.7348 (p0) REVERT: E 253 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8367 (mmp80) REVERT: E 386 ILE cc_start: 0.8888 (tt) cc_final: 0.8581 (pt) REVERT: E 421 MET cc_start: 0.8586 (tpt) cc_final: 0.8314 (tpt) REVERT: E 634 PHE cc_start: 0.6944 (m-80) cc_final: 0.6682 (m-10) REVERT: E 848 MET cc_start: 0.0458 (pmm) cc_final: 0.0116 (pmm) REVERT: E 924 THR cc_start: -0.2079 (OUTLIER) cc_final: -0.2356 (t) REVERT: E 1157 MET cc_start: 0.3638 (ptm) cc_final: 0.3427 (ptt) REVERT: E 1209 MET cc_start: 0.5614 (tpt) cc_final: 0.5127 (tpt) REVERT: E 1363 ARG cc_start: 0.9159 (tpm170) cc_final: 0.8574 (tpm170) REVERT: F 242 MET cc_start: 0.7567 (tpp) cc_final: 0.7313 (tpp) REVERT: F 271 MET cc_start: 0.8303 (tmm) cc_final: 0.7817 (tmm) REVERT: F 305 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8266 (pp30) REVERT: F 412 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8856 (mm) REVERT: F 414 ASN cc_start: 0.7717 (m-40) cc_final: 0.7412 (t0) REVERT: F 421 MET cc_start: 0.8395 (tpt) cc_final: 0.8008 (tpp) REVERT: F 531 MET cc_start: 0.4756 (mpp) cc_final: 0.4486 (mpp) REVERT: F 959 MET cc_start: 0.3910 (mtt) cc_final: 0.3141 (mpp) REVERT: F 1055 LEU cc_start: 0.9352 (mt) cc_final: 0.9044 (pp) REVERT: F 1082 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8536 (tp) REVERT: F 1121 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9074 (pp) REVERT: F 1209 MET cc_start: 0.5838 (tpt) cc_final: 0.5603 (mmp) REVERT: F 1366 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7406 (m90) REVERT: G 394 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8154 (tp) REVERT: G 412 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8569 (mm) REVERT: G 524 MET cc_start: 0.4214 (tmm) cc_final: 0.3914 (tmm) REVERT: G 848 MET cc_start: 0.0118 (pmm) cc_final: -0.0191 (pmm) REVERT: G 920 MET cc_start: 0.2716 (mpp) cc_final: 0.2398 (mpp) REVERT: G 1055 LEU cc_start: 0.9530 (mm) cc_final: 0.9258 (pp) REVERT: G 1086 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: R 67 TYR cc_start: 0.8455 (m-80) cc_final: 0.8067 (m-80) REVERT: V 8 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8492 (mp) REVERT: V 82 LYS cc_start: 0.8681 (pttm) cc_final: 0.8468 (pttm) REVERT: Z 243 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8529 (mtp85) REVERT: Z 446 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: Z 450 MET cc_start: 0.8382 (tpp) cc_final: 0.7998 (tpp) outliers start: 123 outliers final: 78 residues processed: 509 average time/residue: 0.4757 time to fit residues: 416.4700 Evaluate side-chains 485 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 393 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 288 VAL 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 878 GLU 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 270 VAL Chi-restraints excluded: chain C residue 272 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 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 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 407 VAL Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1099 VAL 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 288 VAL Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 915 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 F residue 1366 HIS Chi-restraints excluded: chain G residue 155 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 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 490 LEU 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 915 GLU Chi-restraints excluded: chain G residue 924 THR Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 1086 GLU 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 208 MET Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 8 ILE 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 292 ILE Chi-restraints excluded: chain Z residue 243 ARG 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 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 124 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 452 optimal weight: 50.0000 chunk 163 optimal weight: 40.0000 chunk 531 optimal weight: 0.0980 chunk 66 optimal weight: 30.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 305 GLN C 455 GLN C 614 GLN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 653 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 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** V 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.106982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.085176 restraints weight = 320684.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.085540 restraints weight = 247155.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.085512 restraints weight = 174813.766| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 51822 Z= 0.172 Angle : 0.659 13.920 70659 Z= 0.314 Chirality : 0.044 0.411 8142 Planarity : 0.004 0.053 9235 Dihedral : 4.556 24.959 7178 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.54 % Favored : 92.33 % Rotamer: Outliers : 1.86 % Allowed : 18.76 % Favored : 79.37 % 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: -1.13 (0.11), residues: 6510 helix: 0.41 (0.12), residues: 2045 sheet: -1.09 (0.17), residues: 953 loop : -1.36 (0.11), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 276 HIS 0.017 0.001 HIS A1102 PHE 0.018 0.001 PHE E 452 TYR 0.017 0.001 TYR R 270 ARG 0.008 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: 100 poor density : 432 time to evaluate : 4.289 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 242 MET cc_start: 0.8014 (tpp) cc_final: 0.7679 (tpp) REVERT: A 421 MET cc_start: 0.8328 (tpt) cc_final: 0.7922 (tpt) REVERT: A 429 ASN cc_start: 0.8930 (m-40) cc_final: 0.8692 (p0) REVERT: A 524 MET cc_start: 0.4612 (tmm) cc_final: 0.3907 (tmm) REVERT: A 848 MET cc_start: 0.0420 (pmm) cc_final: 0.0015 (pmm) REVERT: A 920 MET cc_start: 0.5013 (mmp) cc_final: 0.4644 (mmm) REVERT: A 1086 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: A 1134 LEU cc_start: 0.8931 (tp) cc_final: 0.8701 (tp) REVERT: C 460 TYR cc_start: 0.8612 (m-80) cc_final: 0.8216 (m-10) REVERT: C 543 THR cc_start: 0.8832 (t) cc_final: 0.8572 (p) REVERT: C 848 MET cc_start: 0.0902 (pmm) cc_final: 0.0526 (pmm) REVERT: C 1209 MET cc_start: 0.5239 (mmm) cc_final: 0.5038 (mmp) REVERT: E 386 ILE cc_start: 0.8883 (tt) cc_final: 0.8596 (pt) REVERT: E 421 MET cc_start: 0.8582 (tpt) cc_final: 0.8329 (tpt) REVERT: E 475 MET cc_start: 0.7510 (mmm) cc_final: 0.6479 (mmm) REVERT: E 634 PHE cc_start: 0.6887 (m-80) cc_final: 0.6624 (m-10) REVERT: E 848 MET cc_start: 0.0488 (pmm) cc_final: 0.0164 (pmm) REVERT: E 924 THR cc_start: -0.2128 (OUTLIER) cc_final: -0.2414 (t) REVERT: E 1363 ARG cc_start: 0.9121 (tpm170) cc_final: 0.8534 (tpm170) REVERT: F 305 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8126 (pp30) REVERT: F 412 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8890 (mm) REVERT: F 414 ASN cc_start: 0.7924 (m-40) cc_final: 0.7653 (t0) REVERT: F 421 MET cc_start: 0.8419 (tpt) cc_final: 0.8119 (tpp) REVERT: F 531 MET cc_start: 0.4931 (mpp) cc_final: 0.4643 (mpp) REVERT: F 959 MET cc_start: 0.3748 (mtt) cc_final: 0.2906 (mpp) REVERT: F 1055 LEU cc_start: 0.9330 (mt) cc_final: 0.9009 (pp) REVERT: F 1082 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8382 (tp) REVERT: F 1121 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9023 (pp) REVERT: F 1209 MET cc_start: 0.6052 (tpt) cc_final: 0.5471 (mmp) REVERT: G 394 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8201 (tp) REVERT: G 421 MET cc_start: 0.8728 (tpt) cc_final: 0.8172 (tpt) REVERT: G 524 MET cc_start: 0.4299 (tmm) cc_final: 0.4027 (tmm) REVERT: G 848 MET cc_start: 0.0167 (pmm) cc_final: -0.0115 (pmm) REVERT: G 920 MET cc_start: 0.2673 (mpp) cc_final: 0.2322 (mpp) REVERT: G 1086 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: G 1157 MET cc_start: 0.3111 (ptt) cc_final: 0.2735 (ptt) REVERT: R 67 TYR cc_start: 0.8256 (m-80) cc_final: 0.7849 (m-80) REVERT: V 8 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8304 (mp) REVERT: Z 243 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8571 (mmm-85) REVERT: Z 450 MET cc_start: 0.8338 (tpp) cc_final: 0.7956 (tpp) outliers start: 100 outliers final: 67 residues processed: 512 average time/residue: 0.4779 time to fit residues: 421.7942 Evaluate side-chains 483 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 406 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 270 VAL 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 878 GLU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 397 LEU 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 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 407 VAL Chi-restraints excluded: chain E residue 924 THR Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1099 VAL 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 288 VAL Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 915 GLU 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 125 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 194 ASP 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 305 GLN Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 407 VAL 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 1086 GLU 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 R residue 115 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain V residue 8 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 88 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 243 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 1 optimal weight: 5.9990 chunk 554 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 497 optimal weight: 50.0000 chunk 447 optimal weight: 50.0000 chunk 611 optimal weight: 0.9980 chunk 568 optimal weight: 30.0000 chunk 503 optimal weight: 7.9990 chunk 434 optimal weight: 0.1980 overall best weight: 4.6386 ------------------------------------------------------------------------------- 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** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN C 614 GLN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** 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 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** ** G1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.106821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085015 restraints weight = 320551.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.085419 restraints weight = 249179.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085335 restraints weight = 179267.238| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51822 Z= 0.175 Angle : 0.668 14.398 70659 Z= 0.316 Chirality : 0.044 0.413 8142 Planarity : 0.004 0.052 9235 Dihedral : 4.487 25.904 7178 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 1.79 % Allowed : 19.12 % Favored : 79.09 % 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: -1.08 (0.11), residues: 6510 helix: 0.47 (0.12), residues: 2045 sheet: -1.14 (0.17), residues: 968 loop : -1.31 (0.11), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 276 HIS 0.005 0.001 HIS F 651 PHE 0.021 0.001 PHE C 452 TYR 0.017 0.001 TYR G 503 ARG 0.009 0.000 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 514 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 418 time to evaluate : 4.244 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 242 MET cc_start: 0.7946 (tpp) cc_final: 0.7586 (tpp) REVERT: A 421 MET cc_start: 0.8316 (tpt) cc_final: 0.7983 (tpt) REVERT: A 429 ASN cc_start: 0.8926 (m-40) cc_final: 0.8673 (p0) REVERT: A 524 MET cc_start: 0.4606 (tmm) cc_final: 0.3904 (tmm) REVERT: A 848 MET cc_start: 0.0279 (pmm) cc_final: -0.0089 (pmm) REVERT: A 1086 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: C 412 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 460 TYR cc_start: 0.8607 (m-80) cc_final: 0.8230 (m-10) REVERT: C 520 MET cc_start: 0.6432 (mmm) cc_final: 0.6201 (mpp) REVERT: C 543 THR cc_start: 0.8858 (t) cc_final: 0.8596 (p) REVERT: C 848 MET cc_start: 0.1173 (pmm) cc_final: 0.0702 (pmm) REVERT: C 1209 MET cc_start: 0.5340 (mmm) cc_final: 0.5132 (mmp) REVERT: E 386 ILE cc_start: 0.8959 (tt) cc_final: 0.8639 (pt) REVERT: E 475 MET cc_start: 0.7523 (mmm) cc_final: 0.6530 (mmm) REVERT: E 634 PHE cc_start: 0.6962 (m-80) cc_final: 0.6729 (m-10) REVERT: E 848 MET cc_start: 0.0513 (pmm) cc_final: 0.0178 (pmm) REVERT: E 1363 ARG cc_start: 0.9143 (tpm170) cc_final: 0.8540 (tpm170) REVERT: F 137 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8047 (t-90) REVERT: F 305 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: F 412 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8956 (mm) REVERT: F 414 ASN cc_start: 0.7982 (m-40) cc_final: 0.7679 (t0) REVERT: F 421 MET cc_start: 0.8374 (tpt) cc_final: 0.7963 (tpp) REVERT: F 531 MET cc_start: 0.5136 (mpp) cc_final: 0.4846 (mpp) REVERT: F 959 MET cc_start: 0.3736 (mtt) cc_final: 0.2877 (mpp) REVERT: F 1055 LEU cc_start: 0.9320 (mt) cc_final: 0.9005 (pp) REVERT: F 1082 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8398 (tp) REVERT: F 1121 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9118 (pp) REVERT: F 1209 MET cc_start: 0.6079 (tpt) cc_final: 0.5556 (mmp) REVERT: G 394 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8201 (tp) REVERT: G 412 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8592 (mm) REVERT: G 421 MET cc_start: 0.8815 (tpt) cc_final: 0.8396 (tpp) REVERT: G 524 MET cc_start: 0.4309 (tmm) cc_final: 0.4036 (tmm) REVERT: G 531 MET cc_start: 0.4099 (mmm) cc_final: 0.3662 (mmm) REVERT: G 848 MET cc_start: 0.0138 (pmm) cc_final: -0.0175 (pmm) REVERT: G 1055 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9262 (pp) REVERT: G 1086 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: G 1157 MET cc_start: 0.3140 (ptt) cc_final: 0.2739 (ptt) REVERT: R 67 TYR cc_start: 0.8326 (m-80) cc_final: 0.7936 (m-80) REVERT: R 225 LEU cc_start: 0.3214 (OUTLIER) cc_final: 0.2800 (mp) REVERT: V 8 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8302 (mp) REVERT: Z 450 MET cc_start: 0.8370 (tpp) cc_final: 0.7977 (tpp) outliers start: 96 outliers final: 70 residues processed: 494 average time/residue: 0.4706 time to fit residues: 402.0656 Evaluate side-chains 488 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 405 time to evaluate : 4.249 ------------------------------------------------------------------------------- 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 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 1086 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL 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 1102 HIS 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 407 VAL Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 915 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 1139 THR Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 194 ASP 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 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE 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 1055 LEU Chi-restraints excluded: chain G residue 1086 GLU 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 R residue 115 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain V residue 8 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 74 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 548 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 467 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 156 optimal weight: 50.0000 chunk 584 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 392 optimal weight: 8.9990 chunk 453 optimal weight: 9.9990 chunk 319 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 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 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** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 653 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 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** V 101 ASN ** Z 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.084459 restraints weight = 325389.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.084590 restraints weight = 260914.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084535 restraints weight = 188171.688| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 51822 Z= 0.200 Angle : 0.679 14.203 70659 Z= 0.322 Chirality : 0.044 0.418 8142 Planarity : 0.005 0.052 9235 Dihedral : 4.505 26.975 7178 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 1.79 % Allowed : 19.10 % Favored : 79.11 % 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: -1.05 (0.11), residues: 6510 helix: 0.51 (0.12), residues: 2050 sheet: -1.15 (0.17), residues: 949 loop : -1.30 (0.11), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 276 HIS 0.005 0.001 HIS F 651 PHE 0.015 0.001 PHE Z 255 TYR 0.017 0.001 TYR R 270 ARG 0.009 0.000 ARG G1363 ********************** 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 504 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 408 time to evaluate : 4.235 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 242 MET cc_start: 0.7957 (tpp) cc_final: 0.7612 (tpp) REVERT: A 421 MET cc_start: 0.8326 (tpt) cc_final: 0.8007 (tpt) REVERT: A 524 MET cc_start: 0.4623 (tmm) cc_final: 0.3925 (tmm) REVERT: A 543 THR cc_start: 0.8993 (t) cc_final: 0.8770 (p) REVERT: A 848 MET cc_start: 0.0253 (pmm) cc_final: -0.0071 (pmm) REVERT: A 1086 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: C 412 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (mm) REVERT: C 452 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: C 460 TYR cc_start: 0.8668 (m-80) cc_final: 0.8271 (m-10) REVERT: C 520 MET cc_start: 0.6471 (mmm) cc_final: 0.6252 (mpp) REVERT: C 543 THR cc_start: 0.8874 (t) cc_final: 0.8606 (p) REVERT: C 848 MET cc_start: 0.0892 (pmm) cc_final: 0.0450 (pmm) REVERT: E 386 ILE cc_start: 0.8873 (tt) cc_final: 0.8580 (pt) REVERT: E 475 MET cc_start: 0.7471 (mmm) cc_final: 0.6545 (mmm) REVERT: E 634 PHE cc_start: 0.6959 (m-80) cc_final: 0.6747 (m-10) REVERT: E 848 MET cc_start: 0.0717 (pmm) cc_final: 0.0386 (pmm) REVERT: E 1363 ARG cc_start: 0.9166 (tpm170) cc_final: 0.8574 (tpm170) REVERT: F 137 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.8045 (t70) REVERT: F 412 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8921 (mm) REVERT: F 414 ASN cc_start: 0.7963 (m-40) cc_final: 0.7684 (t0) REVERT: F 421 MET cc_start: 0.8350 (tpt) cc_final: 0.7904 (tpp) REVERT: F 531 MET cc_start: 0.5000 (mpp) cc_final: 0.4780 (mpp) REVERT: F 959 MET cc_start: 0.3415 (mtt) cc_final: 0.2400 (mpp) REVERT: F 1055 LEU cc_start: 0.9325 (mt) cc_final: 0.9024 (pp) REVERT: F 1082 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8385 (tp) REVERT: F 1121 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9121 (pp) REVERT: F 1198 ARG cc_start: -0.0152 (OUTLIER) cc_final: -0.0526 (ptp-170) REVERT: F 1209 MET cc_start: 0.5994 (tpt) cc_final: 0.5471 (mmp) REVERT: G 394 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8075 (tp) REVERT: G 412 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8602 (mm) REVERT: G 421 MET cc_start: 0.8819 (tpt) cc_final: 0.8383 (tpp) REVERT: G 524 MET cc_start: 0.4141 (tmm) cc_final: 0.3893 (tmm) REVERT: G 531 MET cc_start: 0.4529 (mmm) cc_final: 0.4104 (mmm) REVERT: G 645 MET cc_start: 0.5629 (mmp) cc_final: 0.5302 (mmp) REVERT: G 848 MET cc_start: 0.0195 (pmm) cc_final: -0.0078 (pmm) REVERT: G 1055 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9221 (pp) REVERT: G 1086 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: G 1157 MET cc_start: 0.3343 (ptt) cc_final: 0.2950 (ptt) REVERT: G 1363 ARG cc_start: 0.9235 (mtp85) cc_final: 0.8965 (ttp80) REVERT: R 67 TYR cc_start: 0.8308 (m-80) cc_final: 0.7907 (m-80) REVERT: R 225 LEU cc_start: 0.3230 (OUTLIER) cc_final: 0.2796 (mp) REVERT: V 8 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8299 (mp) REVERT: Z 243 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8618 (mmm-85) REVERT: Z 309 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8679 (mmtm) REVERT: Z 446 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: Z 450 MET cc_start: 0.8447 (tpp) cc_final: 0.8040 (tpp) outliers start: 96 outliers final: 74 residues processed: 483 average time/residue: 0.4749 time to fit residues: 395.1856 Evaluate side-chains 490 residues out of total 5540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 400 time to evaluate : 4.208 ------------------------------------------------------------------------------- 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 1086 GLU Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 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 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 1102 HIS 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 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 407 VAL Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 878 GLU Chi-restraints excluded: chain F residue 915 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 1139 THR Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1198 ARG Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 194 ASP 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 394 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 412 ILE 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 1055 LEU Chi-restraints excluded: chain G residue 1086 GLU 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 R residue 115 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain V residue 8 ILE 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 88 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain Z residue 243 ARG 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 446 TYR Chi-restraints excluded: chain Z residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 626 optimal weight: 0.4980 chunk 332 optimal weight: 0.7980 chunk 187 optimal weight: 50.0000 chunk 162 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 275 optimal weight: 40.0000 chunk 71 optimal weight: 0.0980 chunk 442 optimal weight: 4.9990 chunk 252 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 627 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 519 GLN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 HIS C 305 GLN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 HIS ** E1376 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 519 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1064 HIS 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.107539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.085790 restraints weight = 321665.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086457 restraints weight = 249252.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.086366 restraints weight = 170712.303| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 51822 Z= 0.159 Angle : 0.674 15.127 70659 Z= 0.314 Chirality : 0.044 0.406 8142 Planarity : 0.004 0.052 9235 Dihedral : 4.308 28.005 7178 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.91 % Favored : 92.96 % Rotamer: Outliers : 1.36 % Allowed : 19.53 % Favored : 79.11 % 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: -0.88 (0.11), residues: 6510 helix: 0.61 (0.12), residues: 2037 sheet: -0.87 (0.17), residues: 962 loop : -1.22 (0.11), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 276 HIS 0.006 0.001 HIS C 248 PHE 0.017 0.001 PHE Z 255 TYR 0.016 0.001 TYR R 270 ARG 0.008 0.000 ARG G1363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12370.65 seconds wall clock time: 216 minutes 34.17 seconds (12994.17 seconds total)