Starting phenix.real_space_refine on Sat Feb 7 14:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1h_48812/02_2026/9n1h_48812.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 240 5.16 5 C 21540 2.51 5 N 5456 2.21 5 O 5668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32904 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8016 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 Conformer: "B" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 bond proxies already assigned to first conformer: 8179 Chain: "D" Number of atoms: 8016 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 Conformer: "B" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 bond proxies already assigned to first conformer: 8179 Chain: "B" Number of atoms: 8016 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 Conformer: "B" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 bond proxies already assigned to first conformer: 8179 Chain: "C" Number of atoms: 8016 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 Conformer: "B" Number of residues, atoms: 1060, 8006 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1016} Chain breaks: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 bond proxies already assigned to first conformer: 8179 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS A 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS A 674 " occ=0.56 residue: pdb=" N AHIS D 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.56 residue: pdb=" N AHIS B 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.56 residue: pdb=" N AHIS C 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS C 674 " occ=0.56 Time building chain proxies: 13.76, per 1000 atoms: 0.42 Number of scatterers: 32904 At special positions: 0 Unit cell: (157.766, 157.766, 158.592, 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 240 16.00 O 5668 8.00 N 5456 7.00 C 21540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.96 Conformation dependent library (CDL) restraints added in 2.9 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 16 sheets defined 67.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.717A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.609A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.610A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.660A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.207A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.983A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.742A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.839A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.590A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.658A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.664A pdb=" N GLY A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 4.400A pdb=" N LEU A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 847 through 872 Processing helix chain 'A' and resid 879 through 902 Processing helix chain 'A' and resid 907 through 917 Processing helix chain 'A' and resid 918 through 939 Processing helix chain 'A' and resid 943 through 968 removed outlier: 3.701A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 4.587A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.630A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Proline residue: A1027 - end of helix Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.701A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1094 removed outlier: 3.953A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.699A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1126 No H-bonds generated for 'chain 'A' and resid 1124 through 1126' Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 4.242A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1232 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.717A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.609A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.610A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.661A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 4.207A pdb=" N ILE D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.983A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 441 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 476 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 501 through 514 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 564 Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.742A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.839A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.589A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 723 through 728 removed outlier: 3.658A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.664A pdb=" N GLY D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 761 through 767 removed outlier: 4.401A pdb=" N LEU D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 846 Processing helix chain 'D' and resid 847 through 872 Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 917 Processing helix chain 'D' and resid 918 through 939 Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.701A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.586A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.630A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Proline residue: D1027 - end of helix Processing helix chain 'D' and resid 1031 through 1033 No H-bonds generated for 'chain 'D' and resid 1031 through 1033' Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.702A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1094 removed outlier: 3.953A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.700A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1126 No H-bonds generated for 'chain 'D' and resid 1124 through 1126' Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 4.242A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' and resid 1192 through 1232 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.717A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.609A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.610A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.660A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 4.207A pdb=" N ILE B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.982A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.742A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.840A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.590A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.658A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.664A pdb=" N GLY B 742 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 760 Processing helix chain 'B' and resid 761 through 767 removed outlier: 4.400A pdb=" N LEU B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 847 through 872 Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 917 Processing helix chain 'B' and resid 918 through 939 Processing helix chain 'B' and resid 943 through 968 removed outlier: 3.701A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.587A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.631A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.701A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1094 removed outlier: 3.953A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.699A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1126 No H-bonds generated for 'chain 'B' and resid 1124 through 1126' Processing helix chain 'B' and resid 1127 through 1145 removed outlier: 4.242A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 Processing helix chain 'B' and resid 1192 through 1232 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.716A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.608A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 209 Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.610A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.661A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 4.207A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.983A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 476 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 501 through 514 Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 564 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.741A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.838A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.590A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.658A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.664A pdb=" N GLY C 742 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.400A pdb=" N LEU C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 846 Processing helix chain 'C' and resid 847 through 872 Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 917 Processing helix chain 'C' and resid 918 through 939 Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.702A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 4.587A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.631A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Proline residue: C1027 - end of helix Processing helix chain 'C' and resid 1031 through 1033 No H-bonds generated for 'chain 'C' and resid 1031 through 1033' Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.701A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1094 removed outlier: 3.952A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL C1084 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 4.699A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1126 No H-bonds generated for 'chain 'C' and resid 1124 through 1126' Processing helix chain 'C' and resid 1127 through 1145 removed outlier: 4.242A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1232 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.555A pdb=" N GLN A 99 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.670A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 6.391A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.439A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.555A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.670A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.390A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 186 removed outlier: 6.439A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.555A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 240 removed outlier: 6.670A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 125 through 126 removed outlier: 6.391A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.439A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE B 395 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.555A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.671A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.390A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.439A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) 2093 hydrogen bonds defined for protein. 6211 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: 6.90 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5624 1.32 - 1.45: 8505 1.45 - 1.57: 19183 1.57 - 1.69: 8 1.69 - 1.82: 404 Bond restraints: 33724 Sorted by residual: bond pdb=" N PHE A 442 " pdb=" CA PHE A 442 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.15e-02 7.56e+03 7.85e+00 bond pdb=" N PHE B 442 " pdb=" CA PHE B 442 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.15e-02 7.56e+03 7.77e+00 bond pdb=" N PHE D 442 " pdb=" CA PHE D 442 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.15e-02 7.56e+03 7.70e+00 bond pdb=" N PHE C 442 " pdb=" CA PHE C 442 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.15e-02 7.56e+03 7.70e+00 bond pdb=" N SER D 478 " pdb=" CA SER D 478 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.51e+00 ... (remaining 33719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 44310 2.31 - 4.62: 1361 4.62 - 6.93: 233 6.93 - 9.24: 96 9.24 - 11.55: 28 Bond angle restraints: 46028 Sorted by residual: angle pdb=" N GLU B1184 " pdb=" CA GLU B1184 " pdb=" C GLU B1184 " ideal model delta sigma weight residual 111.69 102.71 8.98 1.23e+00 6.61e-01 5.33e+01 angle pdb=" N GLU A1184 " pdb=" CA GLU A1184 " pdb=" C GLU A1184 " ideal model delta sigma weight residual 111.69 102.72 8.97 1.23e+00 6.61e-01 5.31e+01 angle pdb=" N GLU D1184 " pdb=" CA GLU D1184 " pdb=" C GLU D1184 " ideal model delta sigma weight residual 111.69 102.75 8.94 1.23e+00 6.61e-01 5.28e+01 angle pdb=" N GLU C1184 " pdb=" CA GLU C1184 " pdb=" C GLU C1184 " ideal model delta sigma weight residual 111.69 102.76 8.93 1.23e+00 6.61e-01 5.27e+01 angle pdb=" C PHE B1182 " pdb=" N ARG B1183 " pdb=" CA ARG B1183 " ideal model delta sigma weight residual 122.56 111.01 11.55 1.72e+00 3.38e-01 4.51e+01 ... (remaining 46023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 19396 24.44 - 48.88: 1452 48.88 - 73.31: 220 73.31 - 97.75: 12 97.75 - 122.19: 12 Dihedral angle restraints: 21092 sinusoidal: 8724 harmonic: 12368 Sorted by residual: dihedral pdb=" CBC Y01 D1404 " pdb=" CAR Y01 D1404 " pdb=" CAT Y01 D1404 " pdb=" CBH Y01 D1404 " ideal model delta sinusoidal sigma weight residual -57.13 65.06 -122.19 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CBC Y01 C1404 " pdb=" CAR Y01 C1404 " pdb=" CAT Y01 C1404 " pdb=" CBH Y01 C1404 " ideal model delta sinusoidal sigma weight residual -57.13 65.03 -122.16 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CBC Y01 A1403 " pdb=" CAR Y01 A1403 " pdb=" CAT Y01 A1403 " pdb=" CBH Y01 A1403 " ideal model delta sinusoidal sigma weight residual -57.13 65.03 -122.16 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 21089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4929 0.096 - 0.191: 419 0.191 - 0.287: 12 0.287 - 0.383: 4 0.383 - 0.478: 4 Chirality restraints: 5368 Sorted by residual: chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU D 483 " pdb=" CB LEU D 483 " pdb=" CD1 LEU D 483 " pdb=" CD2 LEU D 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 5365 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D1183 " 0.025 2.00e-02 2.50e+03 5.12e-02 2.63e+01 pdb=" C ARG D1183 " -0.089 2.00e-02 2.50e+03 pdb=" O ARG D1183 " 0.034 2.00e-02 2.50e+03 pdb=" N GLU D1184 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1183 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C ARG B1183 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG B1183 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU B1184 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1183 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.62e+01 pdb=" C ARG A1183 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A1183 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A1184 " -0.030 2.00e-02 2.50e+03 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 14548 2.99 - 3.46: 35829 3.46 - 3.94: 54407 3.94 - 4.42: 61950 4.42 - 4.90: 99889 Nonbonded interactions: 266623 Sorted by model distance: nonbonded pdb=" O PHE D1182 " pdb=" CA ARG D1183 " model vdw 2.507 2.776 nonbonded pdb=" O PHE A1182 " pdb=" CA ARG A1183 " model vdw 2.508 2.776 nonbonded pdb=" O PHE B1182 " pdb=" CA ARG B1183 " model vdw 2.508 2.776 nonbonded pdb=" O PHE C1182 " pdb=" CA ARG C1183 " model vdw 2.509 2.776 nonbonded pdb=" CA ASP B 406 " pdb=" OD1 ASP B 406 " model vdw 2.577 2.776 ... (remaining 266618 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.500 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.006 0.095 33724 Z= 0.297 Angle : 1.007 11.551 46028 Z= 0.549 Chirality : 0.055 0.478 5368 Planarity : 0.008 0.100 5664 Dihedral : 16.454 122.189 13092 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.91 % Allowed : 20.46 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 4196 helix: -0.17 (0.09), residues: 2628 sheet: -0.78 (0.33), residues: 280 loop : -1.20 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG D 210 TYR 0.040 0.002 TYR B 503 PHE 0.027 0.003 PHE D 634 TRP 0.019 0.002 TRP D 431 HIS 0.004 0.001 HIS C 480 Details of bonding type rmsd covalent geometry : bond 0.00626 (33724) covalent geometry : angle 1.00696 (46028) hydrogen bonds : bond 0.13049 ( 2093) hydrogen bonds : angle 5.91159 ( 6211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 573 time to evaluate : 1.364 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 121 MET cc_start: 0.8545 (mmm) cc_final: 0.8155 (mmp) REVERT: A 175 ILE cc_start: 0.9264 (mm) cc_final: 0.8834 (pt) REVERT: A 329 CYS cc_start: 0.8958 (m) cc_final: 0.8266 (t) REVERT: A 358 ASP cc_start: 0.8924 (m-30) cc_final: 0.8659 (p0) REVERT: A 386 MET cc_start: 0.7301 (mmt) cc_final: 0.6929 (mmt) REVERT: A 397 MET cc_start: 0.7606 (mmm) cc_final: 0.7234 (tpp) REVERT: A 459 ASP cc_start: 0.8459 (m-30) cc_final: 0.8075 (m-30) REVERT: A 489 GLU cc_start: 0.8081 (pt0) cc_final: 0.7595 (mp0) REVERT: A 503 TYR cc_start: 0.8014 (t80) cc_final: 0.7789 (t80) REVERT: A 510 LYS cc_start: 0.9312 (mmtp) cc_final: 0.8857 (tptt) REVERT: A 778 MET cc_start: 0.5921 (mtp) cc_final: 0.5593 (tpp) REVERT: A 1166 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8607 (mm-30) REVERT: A 1179 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8595 (mt-10) REVERT: A 1180 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8260 (tp30) REVERT: D 121 MET cc_start: 0.8435 (mmm) cc_final: 0.8167 (mmp) REVERT: D 209 SER cc_start: 0.8753 (t) cc_final: 0.8524 (m) REVERT: D 329 CYS cc_start: 0.8637 (m) cc_final: 0.8097 (t) REVERT: D 337 ASP cc_start: 0.9307 (m-30) cc_final: 0.9035 (m-30) REVERT: D 358 ASP cc_start: 0.8907 (m-30) cc_final: 0.8547 (p0) REVERT: D 397 MET cc_start: 0.7802 (mmm) cc_final: 0.7492 (tpp) REVERT: D 407 LEU cc_start: 0.9089 (mt) cc_final: 0.8618 (pt) REVERT: D 411 THR cc_start: 0.9071 (p) cc_final: 0.8831 (p) REVERT: D 459 ASP cc_start: 0.8475 (m-30) cc_final: 0.8089 (m-30) REVERT: D 489 GLU cc_start: 0.8194 (pt0) cc_final: 0.7720 (mp0) REVERT: D 510 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.8859 (tptt) REVERT: D 557 ARG cc_start: 0.8283 (mmp-170) cc_final: 0.7987 (tpp80) REVERT: D 778 MET cc_start: 0.6044 (mtp) cc_final: 0.5441 (tpt) REVERT: D 1179 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8624 (mt-10) REVERT: B 121 MET cc_start: 0.8543 (mmm) cc_final: 0.8156 (mmp) REVERT: B 329 CYS cc_start: 0.8997 (m) cc_final: 0.8289 (t) REVERT: B 358 ASP cc_start: 0.8924 (m-30) cc_final: 0.8705 (p0) REVERT: B 386 MET cc_start: 0.7318 (mmt) cc_final: 0.7002 (mmt) REVERT: B 397 MET cc_start: 0.7701 (mmm) cc_final: 0.7356 (tpp) REVERT: B 459 ASP cc_start: 0.8523 (m-30) cc_final: 0.8137 (m-30) REVERT: B 489 GLU cc_start: 0.8137 (pt0) cc_final: 0.7632 (mp0) REVERT: B 503 TYR cc_start: 0.7998 (t80) cc_final: 0.7775 (t80) REVERT: B 510 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8863 (tptt) REVERT: B 778 MET cc_start: 0.5939 (mtp) cc_final: 0.5623 (tpp) REVERT: B 1166 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8578 (mm-30) REVERT: B 1179 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8576 (mt-10) REVERT: C 121 MET cc_start: 0.8423 (mmm) cc_final: 0.8160 (mmp) REVERT: C 127 PHE cc_start: 0.9028 (p90) cc_final: 0.8679 (p90) REVERT: C 329 CYS cc_start: 0.8613 (m) cc_final: 0.8089 (t) REVERT: C 337 ASP cc_start: 0.9322 (m-30) cc_final: 0.9047 (m-30) REVERT: C 358 ASP cc_start: 0.8908 (m-30) cc_final: 0.8537 (p0) REVERT: C 397 MET cc_start: 0.7786 (mmm) cc_final: 0.7473 (tpp) REVERT: C 407 LEU cc_start: 0.9094 (mt) cc_final: 0.8630 (pt) REVERT: C 411 THR cc_start: 0.9075 (p) cc_final: 0.8827 (p) REVERT: C 459 ASP cc_start: 0.8475 (m-30) cc_final: 0.8089 (m-30) REVERT: C 489 GLU cc_start: 0.8190 (pt0) cc_final: 0.7710 (mp0) REVERT: C 510 LYS cc_start: 0.9417 (mmtp) cc_final: 0.8858 (tptt) REVERT: C 557 ARG cc_start: 0.8288 (mmp-170) cc_final: 0.7992 (tpp80) REVERT: C 778 MET cc_start: 0.6034 (mtp) cc_final: 0.5435 (tpt) REVERT: C 1179 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8690 (mt-10) outliers start: 29 outliers final: 0 residues processed: 583 average time/residue: 0.2306 time to fit residues: 214.9388 Evaluate side-chains 471 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 510 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 343 HIS A 446 GLN A 637 HIS A 696 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN D 279 GLN D 446 GLN D 637 HIS D 696 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1092 ASN B 279 GLN B 446 GLN B 637 HIS B 696 GLN B 867 ASN B1092 ASN C 279 GLN C 446 GLN C 637 HIS C 696 GLN C 749 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.111324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078129 restraints weight = 153286.222| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.69 r_work: 0.3070 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33724 Z= 0.182 Angle : 0.613 9.208 46028 Z= 0.317 Chirality : 0.041 0.238 5368 Planarity : 0.005 0.065 5664 Dihedral : 8.705 64.624 6240 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.11 % Allowed : 19.36 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.13), residues: 4196 helix: 1.52 (0.10), residues: 2632 sheet: -0.55 (0.32), residues: 284 loop : -0.83 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1203 TYR 0.016 0.001 TYR C 958 PHE 0.015 0.002 PHE C 611 TRP 0.028 0.002 TRP C 31 HIS 0.004 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00410 (33724) covalent geometry : angle 0.61325 (46028) hydrogen bonds : bond 0.04620 ( 2093) hydrogen bonds : angle 4.28897 ( 6211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 455 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8268 (mmp) REVERT: A 329 CYS cc_start: 0.9191 (m) cc_final: 0.8550 (t) REVERT: A 358 ASP cc_start: 0.9030 (m-30) cc_final: 0.8746 (p0) REVERT: A 397 MET cc_start: 0.7901 (mmm) cc_final: 0.7052 (tpt) REVERT: A 459 ASP cc_start: 0.8841 (m-30) cc_final: 0.8471 (m-30) REVERT: A 510 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8970 (tptt) REVERT: A 685 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8710 (mt-10) REVERT: A 778 MET cc_start: 0.5921 (mtp) cc_final: 0.5504 (tpt) REVERT: A 919 TYR cc_start: 0.6481 (m-10) cc_final: 0.6121 (p90) REVERT: A 1166 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 1180 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8282 (tp30) REVERT: D 31 TRP cc_start: 0.7786 (t60) cc_final: 0.7520 (t60) REVERT: D 121 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8344 (mmp) REVERT: D 329 CYS cc_start: 0.9269 (m) cc_final: 0.8469 (t) REVERT: D 337 ASP cc_start: 0.9458 (m-30) cc_final: 0.9156 (m-30) REVERT: D 358 ASP cc_start: 0.8997 (m-30) cc_final: 0.8665 (p0) REVERT: D 397 MET cc_start: 0.7909 (mmm) cc_final: 0.7254 (tpt) REVERT: D 459 ASP cc_start: 0.8855 (m-30) cc_final: 0.8480 (m-30) REVERT: D 778 MET cc_start: 0.5945 (mtp) cc_final: 0.5666 (mtp) REVERT: D 1180 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8142 (tp30) REVERT: B 121 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8261 (mmp) REVERT: B 329 CYS cc_start: 0.9206 (m) cc_final: 0.8564 (t) REVERT: B 358 ASP cc_start: 0.9026 (m-30) cc_final: 0.8791 (p0) REVERT: B 386 MET cc_start: 0.7378 (mmt) cc_final: 0.7052 (mmt) REVERT: B 397 MET cc_start: 0.7906 (mmm) cc_final: 0.7342 (tpt) REVERT: B 459 ASP cc_start: 0.8859 (m-30) cc_final: 0.8477 (m-30) REVERT: B 510 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9044 (tptt) REVERT: B 685 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 778 MET cc_start: 0.5925 (mtp) cc_final: 0.5515 (tpt) REVERT: B 919 TYR cc_start: 0.6500 (m-10) cc_final: 0.6069 (p90) REVERT: B 1166 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 1180 GLU cc_start: 0.8826 (tp30) cc_final: 0.8595 (tp30) REVERT: C 31 TRP cc_start: 0.7792 (t60) cc_final: 0.7529 (t60) REVERT: C 121 MET cc_start: 0.8577 (mmm) cc_final: 0.8297 (mmp) REVERT: C 329 CYS cc_start: 0.9298 (m) cc_final: 0.8500 (t) REVERT: C 337 ASP cc_start: 0.9468 (m-30) cc_final: 0.9171 (m-30) REVERT: C 358 ASP cc_start: 0.8998 (m-30) cc_final: 0.8667 (p0) REVERT: C 397 MET cc_start: 0.7853 (mmm) cc_final: 0.7222 (tpt) REVERT: C 459 ASP cc_start: 0.8870 (m-30) cc_final: 0.8509 (m-30) REVERT: C 510 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9209 (mmtp) REVERT: C 778 MET cc_start: 0.5967 (mtp) cc_final: 0.5693 (mtp) REVERT: C 1180 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8126 (tp30) outliers start: 67 outliers final: 27 residues processed: 503 average time/residue: 0.2113 time to fit residues: 175.8125 Evaluate side-chains 459 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 427 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 410 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 396 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 296 optimal weight: 0.6980 chunk 251 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1092 ASN A1093 ASN D 343 HIS D 955 ASN D1092 ASN D1093 ASN B 343 HIS B 955 ASN B1093 ASN C 343 HIS C 749 ASN C 955 ASN C1092 ASN C1093 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.111941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079475 restraints weight = 167599.499| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.18 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33724 Z= 0.112 Angle : 0.543 10.020 46028 Z= 0.276 Chirality : 0.039 0.254 5368 Planarity : 0.004 0.056 5664 Dihedral : 7.829 58.658 6236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 20.52 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.13), residues: 4196 helix: 2.01 (0.10), residues: 2664 sheet: -0.58 (0.32), residues: 280 loop : -0.64 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.016 0.001 TYR B 958 PHE 0.014 0.001 PHE C 36 TRP 0.013 0.001 TRP A 740 HIS 0.007 0.000 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00242 (33724) covalent geometry : angle 0.54297 (46028) hydrogen bonds : bond 0.04088 ( 2093) hydrogen bonds : angle 4.05766 ( 6211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 468 time to evaluate : 1.304 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 121 MET cc_start: 0.8426 (mmm) cc_final: 0.8079 (mmp) REVERT: A 208 LYS cc_start: 0.7930 (pttm) cc_final: 0.7599 (pttm) REVERT: A 329 CYS cc_start: 0.9282 (m) cc_final: 0.8547 (t) REVERT: A 358 ASP cc_start: 0.8917 (m-30) cc_final: 0.8682 (p0) REVERT: A 386 MET cc_start: 0.7431 (mmt) cc_final: 0.7184 (mmt) REVERT: A 397 MET cc_start: 0.7847 (mmm) cc_final: 0.7045 (tpt) REVERT: A 459 ASP cc_start: 0.8701 (m-30) cc_final: 0.8333 (m-30) REVERT: A 510 LYS cc_start: 0.9359 (mmtp) cc_final: 0.8987 (tptt) REVERT: A 685 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 778 MET cc_start: 0.5685 (mtp) cc_final: 0.5397 (mtp) REVERT: A 1166 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8681 (mm-30) REVERT: D 31 TRP cc_start: 0.7834 (t60) cc_final: 0.7572 (t60) REVERT: D 121 MET cc_start: 0.8439 (mmm) cc_final: 0.8164 (mmp) REVERT: D 329 CYS cc_start: 0.9237 (m) cc_final: 0.8455 (t) REVERT: D 337 ASP cc_start: 0.9485 (m-30) cc_final: 0.9192 (m-30) REVERT: D 358 ASP cc_start: 0.8920 (m-30) cc_final: 0.8630 (p0) REVERT: D 397 MET cc_start: 0.8026 (mmm) cc_final: 0.7225 (tpt) REVERT: D 403 GLN cc_start: 0.8282 (mp10) cc_final: 0.8017 (mp10) REVERT: D 459 ASP cc_start: 0.8698 (m-30) cc_final: 0.8337 (m-30) REVERT: D 685 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8117 (mt-10) REVERT: D 778 MET cc_start: 0.5675 (mtp) cc_final: 0.5392 (mtp) REVERT: D 886 ILE cc_start: 0.8909 (mt) cc_final: 0.8549 (mt) REVERT: D 1180 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7624 (tp30) REVERT: B 121 MET cc_start: 0.8414 (mmm) cc_final: 0.8057 (mmp) REVERT: B 208 LYS cc_start: 0.8088 (pttm) cc_final: 0.7713 (pttm) REVERT: B 329 CYS cc_start: 0.9239 (m) cc_final: 0.8230 (p) REVERT: B 386 MET cc_start: 0.7589 (mmt) cc_final: 0.7334 (mmt) REVERT: B 397 MET cc_start: 0.7792 (mmm) cc_final: 0.6989 (tpt) REVERT: B 459 ASP cc_start: 0.8694 (m-30) cc_final: 0.8329 (m-30) REVERT: B 510 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9057 (tptt) REVERT: B 685 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 778 MET cc_start: 0.5680 (mtp) cc_final: 0.5392 (mtp) REVERT: B 1166 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8677 (mm-30) REVERT: B 1179 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8347 (mt-10) REVERT: B 1180 GLU cc_start: 0.8341 (tp30) cc_final: 0.7985 (tp30) REVERT: C 31 TRP cc_start: 0.7855 (t60) cc_final: 0.7590 (t60) REVERT: C 121 MET cc_start: 0.8406 (mmm) cc_final: 0.8143 (mmp) REVERT: C 329 CYS cc_start: 0.9263 (m) cc_final: 0.8472 (t) REVERT: C 337 ASP cc_start: 0.9497 (m-30) cc_final: 0.9198 (m-30) REVERT: C 358 ASP cc_start: 0.8924 (m-30) cc_final: 0.8637 (p0) REVERT: C 397 MET cc_start: 0.7995 (mmm) cc_final: 0.7197 (tpt) REVERT: C 403 GLN cc_start: 0.8260 (mp10) cc_final: 0.7996 (mp10) REVERT: C 459 ASP cc_start: 0.8696 (m-30) cc_final: 0.8338 (m-30) REVERT: C 510 LYS cc_start: 0.9410 (mmtp) cc_final: 0.8954 (tptt) REVERT: C 685 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8057 (mt-10) REVERT: C 778 MET cc_start: 0.5760 (mtp) cc_final: 0.5475 (mtp) REVERT: C 886 ILE cc_start: 0.8913 (mt) cc_final: 0.8556 (mt) REVERT: C 1180 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7641 (tp30) outliers start: 56 outliers final: 29 residues processed: 514 average time/residue: 0.1922 time to fit residues: 165.0337 Evaluate side-chains 475 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 445 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.122 > 50: distance: 39 - 61: 9.186 distance: 43 - 66: 8.560 distance: 53 - 61: 11.482 distance: 61 - 62: 16.629 distance: 62 - 63: 14.457 distance: 62 - 65: 23.912 distance: 63 - 64: 25.033 distance: 63 - 66: 5.459 distance: 66 - 67: 7.547 distance: 67 - 68: 13.101 distance: 67 - 70: 8.174 distance: 68 - 69: 13.188 distance: 68 - 71: 6.964 distance: 71 - 72: 3.796 distance: 72 - 73: 4.900 distance: 72 - 75: 5.491 distance: 73 - 74: 11.211 distance: 81 - 82: 9.265 distance: 82 - 83: 5.734 distance: 82 - 85: 4.298 distance: 83 - 84: 18.182 distance: 83 - 86: 21.862 distance: 87 - 90: 9.438 distance: 88 - 89: 7.329 distance: 88 - 91: 15.243 distance: 91 - 92: 10.377 distance: 92 - 93: 8.675 distance: 92 - 95: 12.416 distance: 93 - 94: 9.633 distance: 93 - 99: 13.923 distance: 95 - 96: 13.743 distance: 96 - 97: 6.841 distance: 96 - 98: 6.436 distance: 99 - 100: 11.672 distance: 100 - 101: 7.091 distance: 100 - 103: 13.265 distance: 101 - 102: 20.286 distance: 101 - 109: 16.900 distance: 103 - 104: 8.885 distance: 104 - 105: 9.031 distance: 104 - 106: 9.506 distance: 105 - 107: 6.731 distance: 106 - 108: 6.575 distance: 107 - 108: 10.471 distance: 109 - 110: 3.082 distance: 110 - 111: 5.863 distance: 110 - 113: 9.500 distance: 111 - 112: 9.701 distance: 111 - 120: 16.535 distance: 113 - 114: 7.045 distance: 114 - 115: 14.203 distance: 114 - 116: 11.593 distance: 115 - 117: 9.959 distance: 116 - 118: 6.343 distance: 117 - 119: 9.429 distance: 118 - 119: 12.574 distance: 120 - 121: 5.543 distance: 120 - 126: 16.526 distance: 121 - 122: 10.287 distance: 121 - 124: 22.128 distance: 122 - 123: 17.108 distance: 122 - 127: 9.903 distance: 124 - 125: 6.476 distance: 125 - 126: 12.838