Starting phenix.real_space_refine on Sat Feb 7 14:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.map" model { file = "/net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1j_48814/02_2026/9n1j_48814.cif" } resolution = 3.91 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= 0.001 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 21492 2.51 5 N 5464 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 32868 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8168 Chain: "D" Number of atoms: 8007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8168 Chain: "B" Number of atoms: 8007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8168 Chain: "C" Number of atoms: 8007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1063, 7997 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8168 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: 13.83, per 1000 atoms: 0.42 Number of scatterers: 32868 At special positions: 0 Unit cell: (134.638, 134.638, 163.548, 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 5672 8.00 N 5464 7.00 C 21492 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: 2.65 Conformation dependent library (CDL) restraints added in 2.7 seconds 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8024 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 20 sheets defined 67.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.688A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.708A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.688A pdb=" N ILE A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 224 " --> pdb=" O TRP A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.651A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.508A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.926A 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 removed outlier: 3.539A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.650A pdb=" N LEU A 391 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 474 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 566 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.855A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.521A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.577A 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: 3.976A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.621A 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 764 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 940 removed outlier: 3.688A pdb=" N GLN A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 968 removed outlier: 3.703A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 4.538A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.588A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.687A 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: 3.747A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1094 removed outlier: 3.910A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.596A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.323A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1191 removed outlier: 3.612A pdb=" N GLU A1175 " --> pdb=" O HIS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1232 removed outlier: 3.899A pdb=" N SER A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A1221 " --> pdb=" O ARG A1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.688A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.708A pdb=" N ALA D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.688A pdb=" N ILE D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 224 " --> pdb=" O TRP D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.651A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.508A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.926A 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 removed outlier: 3.540A pdb=" N ASP D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 388 through 392 removed outlier: 3.650A pdb=" N LEU D 391 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 474 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 566 Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.855A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.522A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.578A 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: 3.977A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.621A 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 764 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 940 removed outlier: 3.688A pdb=" N GLN D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.702A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.538A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.589A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.686A 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: 3.747A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1094 removed outlier: 3.910A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.596A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.323A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 removed outlier: 3.611A pdb=" N GLU D1175 " --> pdb=" O HIS D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1232 removed outlier: 3.899A pdb=" N SER D1220 " --> pdb=" O GLU D1216 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET D1221 " --> pdb=" O ARG D1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.688A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.708A pdb=" N ALA B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.688A pdb=" N ILE B 223 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 224 " --> pdb=" O TRP B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.650A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.508A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.926A 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 removed outlier: 3.539A pdb=" N ASP B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 388 through 392 removed outlier: 3.649A pdb=" N LEU B 391 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 474 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 566 Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.856A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.522A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.577A 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: 3.977A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.621A 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 764 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 940 removed outlier: 3.688A pdb=" N GLN B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 968 removed outlier: 3.703A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.539A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.588A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.687A 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: 3.746A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1094 removed outlier: 3.909A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B1094 " --> pdb=" O VAL B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.595A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.323A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.611A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 3.898A pdb=" N SER B1220 " --> pdb=" O GLU B1216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B1221 " --> pdb=" O ARG B1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.688A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.708A pdb=" N ALA C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 209 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.688A pdb=" N ILE C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.651A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.508A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.926A 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 removed outlier: 3.539A pdb=" N ASP C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.650A pdb=" N LEU C 391 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 474 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 566 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.855A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.522A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.577A 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: 3.976A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.621A 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 764 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 940 removed outlier: 3.688A pdb=" N GLN C 940 " --> pdb=" O ILE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.703A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 4.539A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.588A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.687A 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: 3.747A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1094 removed outlier: 3.910A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C1084 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C1094 " --> pdb=" O VAL C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 4.596A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.349A 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: 4.323A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 removed outlier: 3.612A pdb=" N GLU C1175 " --> pdb=" O HIS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1232 removed outlier: 3.899A pdb=" N SER C1220 " --> pdb=" O GLU C1216 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C1221 " --> pdb=" O ARG C1217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.573A 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: 6.686A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.242A 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: 7.332A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.958A 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: 6.493A 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: 8.110A pdb=" N VAL A 327 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA A 301 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1047 through 1049 Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.573A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.685A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.243A 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: 7.332A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.494A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186 removed outlier: 8.110A pdb=" N VAL D 327 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA D 301 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1047 through 1049 Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.573A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 240 removed outlier: 6.686A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.243A 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: 7.332A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 125 through 126 removed outlier: 6.493A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 184 through 186 removed outlier: 8.109A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1047 through 1049 Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.573A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.686A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.493A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 184 through 186 removed outlier: 8.110A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1047 through 1049 2061 hydrogen bonds defined for protein. 6127 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: 8.56 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5726 1.33 - 1.45: 8461 1.45 - 1.58: 19081 1.58 - 1.70: 8 1.70 - 1.83: 404 Bond restraints: 33680 Sorted by residual: bond pdb=" N VAL B 394 " pdb=" CA VAL B 394 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.22e-02 6.72e+03 1.14e+01 bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.22e-02 6.72e+03 1.09e+01 bond pdb=" N VAL C 394 " pdb=" CA VAL C 394 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.22e-02 6.72e+03 1.09e+01 bond pdb=" N VAL D 394 " pdb=" CA VAL D 394 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N VAL C1078 " pdb=" CA VAL C1078 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.65e+00 ... (remaining 33675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 43444 1.92 - 3.84: 2003 3.84 - 5.76: 368 5.76 - 7.69: 111 7.69 - 9.61: 54 Bond angle restraints: 45980 Sorted by residual: angle pdb=" C PHE A 395 " pdb=" N ARG A 396 " pdb=" CA ARG A 396 " ideal model delta sigma weight residual 123.00 114.91 8.09 1.41e+00 5.03e-01 3.29e+01 angle pdb=" C PHE B 395 " pdb=" N ARG B 396 " pdb=" CA ARG B 396 " ideal model delta sigma weight residual 123.00 114.91 8.09 1.41e+00 5.03e-01 3.29e+01 angle pdb=" C PHE D 395 " pdb=" N ARG D 396 " pdb=" CA ARG D 396 " ideal model delta sigma weight residual 123.00 114.92 8.08 1.41e+00 5.03e-01 3.28e+01 angle pdb=" C PHE C 395 " pdb=" N ARG C 396 " pdb=" CA ARG C 396 " ideal model delta sigma weight residual 123.00 114.93 8.07 1.41e+00 5.03e-01 3.27e+01 angle pdb=" CA LYS D 208 " pdb=" CB LYS D 208 " pdb=" CG LYS D 208 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 ... (remaining 45975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 19920 24.53 - 49.05: 987 49.05 - 73.58: 145 73.58 - 98.11: 8 98.11 - 122.63: 12 Dihedral angle restraints: 21072 sinusoidal: 8668 harmonic: 12404 Sorted by residual: dihedral pdb=" CA CYS A 214 " pdb=" C CYS A 214 " pdb=" N THR A 215 " pdb=" CA THR A 215 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA CYS D 214 " pdb=" C CYS D 214 " pdb=" N THR D 215 " pdb=" CA THR D 215 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA CYS C 214 " pdb=" C CYS C 214 " pdb=" N THR C 215 " pdb=" CA THR C 215 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 21069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4029 0.055 - 0.111: 1013 0.111 - 0.166: 249 0.166 - 0.221: 52 0.221 - 0.276: 25 Chirality restraints: 5368 Sorted by residual: chirality pdb=" CA ASP C 404 " pdb=" N ASP C 404 " pdb=" C ASP C 404 " pdb=" CB ASP C 404 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ASP B 404 " pdb=" N ASP B 404 " pdb=" C ASP B 404 " pdb=" CB ASP B 404 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP A 404 " pdb=" N ASP A 404 " pdb=" C ASP A 404 " pdb=" CB ASP A 404 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 5365 not shown) Planarity restraints: 5668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 854 " 0.040 2.00e-02 2.50e+03 3.75e-02 2.46e+01 pdb=" CG PHE D 854 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE D 854 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE D 854 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 854 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 854 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE D 854 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 854 " -0.040 2.00e-02 2.50e+03 3.74e-02 2.45e+01 pdb=" CG PHE C 854 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE C 854 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 854 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 854 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 854 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE C 854 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 854 " 0.040 2.00e-02 2.50e+03 3.74e-02 2.44e+01 pdb=" CG PHE A 854 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE A 854 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 854 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 854 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 854 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 854 " -0.002 2.00e-02 2.50e+03 ... (remaining 5665 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 15685 3.01 - 3.48: 35918 3.48 - 3.95: 54359 3.95 - 4.43: 61920 4.43 - 4.90: 97964 Nonbonded interactions: 265846 Sorted by model distance: nonbonded pdb=" N ASP B 404 " pdb=" O ASP B 404 " model vdw 2.533 2.496 nonbonded pdb=" N ASP D 404 " pdb=" O ASP D 404 " model vdw 2.534 2.496 nonbonded pdb=" N ASP A 404 " pdb=" O ASP A 404 " model vdw 2.534 2.496 nonbonded pdb=" N ASP C 404 " pdb=" O ASP C 404 " model vdw 2.535 2.496 nonbonded pdb=" CB GLU B 305 " pdb=" OE1 GLU B 305 " model vdw 2.544 2.752 ... (remaining 265841 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 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: 5.260 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.570 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.086 33680 Z= 0.286 Angle : 0.981 9.608 45980 Z= 0.530 Chirality : 0.056 0.276 5368 Planarity : 0.009 0.102 5668 Dihedral : 14.121 122.635 13048 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.38 % Allowed : 0.35 % Favored : 99.27 % 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: -1.60 (0.11), residues: 4208 helix: -0.76 (0.08), residues: 2656 sheet: -1.08 (0.30), residues: 328 loop : -1.35 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 357 TYR 0.040 0.003 TYR A1181 PHE 0.084 0.003 PHE D 854 TRP 0.056 0.002 TRP D 621 HIS 0.011 0.002 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00569 (33680) covalent geometry : angle 0.98129 (45980) hydrogen bonds : bond 0.16507 ( 2061) hydrogen bonds : angle 7.02393 ( 6127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 451 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8752 (mtt) cc_final: 0.8216 (mmt) REVERT: A 179 MET cc_start: 0.7823 (mmm) cc_final: 0.7283 (mmm) REVERT: A 213 ILE cc_start: 0.7041 (mt) cc_final: 0.6377 (mt) REVERT: A 255 MET cc_start: 0.6298 (mmm) cc_final: 0.5966 (mmm) REVERT: A 457 MET cc_start: 0.7731 (tpp) cc_final: 0.7219 (tpp) REVERT: A 458 LEU cc_start: 0.9093 (tp) cc_final: 0.8827 (mt) REVERT: A 701 LEU cc_start: 0.9355 (tp) cc_final: 0.9111 (tp) REVERT: A 778 MET cc_start: 0.5849 (mtp) cc_final: 0.5452 (ttt) REVERT: A 932 SER cc_start: 0.9166 (m) cc_final: 0.8814 (p) REVERT: A 951 ILE cc_start: 0.8483 (mt) cc_final: 0.8086 (mm) REVERT: A 983 MET cc_start: 0.8039 (mmm) cc_final: 0.7784 (mmm) REVERT: A 1135 MET cc_start: 0.6786 (ppp) cc_final: 0.5906 (tpt) REVERT: A 1186 ASP cc_start: 0.8328 (m-30) cc_final: 0.8062 (m-30) REVERT: A 1207 MET cc_start: 0.8327 (ttp) cc_final: 0.8106 (ttm) REVERT: D 138 MET cc_start: 0.8712 (mtt) cc_final: 0.8234 (mmt) REVERT: D 255 MET cc_start: 0.6203 (mmm) cc_final: 0.5983 (mmm) REVERT: D 457 MET cc_start: 0.7678 (tpp) cc_final: 0.7168 (tpp) REVERT: D 458 LEU cc_start: 0.9045 (tp) cc_final: 0.8778 (mt) REVERT: D 701 LEU cc_start: 0.9321 (tp) cc_final: 0.9079 (tp) REVERT: D 778 MET cc_start: 0.5834 (mtp) cc_final: 0.5436 (ttt) REVERT: D 932 SER cc_start: 0.9201 (m) cc_final: 0.8852 (p) REVERT: D 951 ILE cc_start: 0.8523 (mt) cc_final: 0.8128 (mm) REVERT: D 983 MET cc_start: 0.7995 (mmm) cc_final: 0.7770 (mmm) REVERT: D 1072 MET cc_start: 0.8290 (ttm) cc_final: 0.8053 (ttp) REVERT: D 1133 MET cc_start: 0.8735 (ptp) cc_final: 0.8521 (mtm) REVERT: D 1135 MET cc_start: 0.6636 (ppp) cc_final: 0.5340 (tpt) REVERT: D 1186 ASP cc_start: 0.8312 (m-30) cc_final: 0.8051 (m-30) REVERT: B 138 MET cc_start: 0.8708 (mtt) cc_final: 0.8245 (mmt) REVERT: B 166 LEU cc_start: 0.7622 (tp) cc_final: 0.7384 (mt) REVERT: B 242 MET cc_start: 0.3567 (tpt) cc_final: 0.1801 (ttp) REVERT: B 353 ASN cc_start: 0.6452 (p0) cc_final: 0.6084 (p0) REVERT: B 457 MET cc_start: 0.7641 (tpp) cc_final: 0.7286 (tpp) REVERT: B 458 LEU cc_start: 0.9108 (tp) cc_final: 0.8842 (mt) REVERT: B 701 LEU cc_start: 0.9302 (tp) cc_final: 0.9040 (tp) REVERT: B 778 MET cc_start: 0.5740 (mtp) cc_final: 0.5313 (ttt) REVERT: B 932 SER cc_start: 0.9129 (m) cc_final: 0.8712 (p) REVERT: B 951 ILE cc_start: 0.8619 (mt) cc_final: 0.8335 (mm) REVERT: B 1207 MET cc_start: 0.8635 (ttp) cc_final: 0.8144 (ttm) REVERT: C 138 MET cc_start: 0.8751 (mtt) cc_final: 0.8275 (mmt) REVERT: C 255 MET cc_start: 0.6167 (mmm) cc_final: 0.5959 (mmm) REVERT: C 457 MET cc_start: 0.7671 (tpp) cc_final: 0.7119 (tpp) REVERT: C 458 LEU cc_start: 0.9062 (tp) cc_final: 0.8803 (mt) REVERT: C 701 LEU cc_start: 0.9325 (tp) cc_final: 0.9103 (tp) REVERT: C 778 MET cc_start: 0.5686 (mtp) cc_final: 0.5408 (ttt) REVERT: C 932 SER cc_start: 0.9175 (m) cc_final: 0.8831 (p) REVERT: C 951 ILE cc_start: 0.8461 (mt) cc_final: 0.8120 (mm) REVERT: C 983 MET cc_start: 0.8023 (mmm) cc_final: 0.7770 (mmm) REVERT: C 1030 MET cc_start: 0.8306 (mtm) cc_final: 0.7949 (mtp) REVERT: C 1072 MET cc_start: 0.8300 (ttm) cc_final: 0.7967 (ttp) REVERT: C 1135 MET cc_start: 0.6788 (ppp) cc_final: 0.5737 (tpt) outliers start: 12 outliers final: 0 residues processed: 459 average time/residue: 0.2007 time to fit residues: 155.5293 Evaluate side-chains 284 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 955 ASN A1092 ASN ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 955 ASN D1012 ASN D1092 ASN ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 693 GLN B 955 ASN B1012 ASN ** B1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN C1012 ASN C1092 ASN ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.068255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051017 restraints weight = 306436.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052936 restraints weight = 137252.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054199 restraints weight = 80106.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.055032 restraints weight = 55104.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055515 restraints weight = 42911.945| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33680 Z= 0.180 Angle : 0.666 13.545 45980 Z= 0.340 Chirality : 0.041 0.212 5368 Planarity : 0.005 0.058 5668 Dihedral : 8.909 74.765 6252 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.60 % Allowed : 5.53 % Favored : 93.86 % 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: 0.34 (0.13), residues: 4208 helix: 0.94 (0.09), residues: 2688 sheet: -1.18 (0.32), residues: 284 loop : -0.86 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 876 TYR 0.022 0.002 TYR A1028 PHE 0.022 0.002 PHE A 866 TRP 0.033 0.002 TRP A 621 HIS 0.006 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00405 (33680) covalent geometry : angle 0.66566 (45980) hydrogen bonds : bond 0.04463 ( 2061) hydrogen bonds : angle 4.37062 ( 6127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8626 (mtt) cc_final: 0.8187 (mmt) REVERT: A 179 MET cc_start: 0.7723 (mmm) cc_final: 0.7512 (mmm) REVERT: A 213 ILE cc_start: 0.6922 (mt) cc_final: 0.6426 (mt) REVERT: A 242 MET cc_start: 0.2129 (OUTLIER) cc_final: -0.0061 (ttp) REVERT: A 457 MET cc_start: 0.7670 (tpp) cc_final: 0.7405 (tpp) REVERT: A 778 MET cc_start: 0.6006 (mtp) cc_final: 0.5602 (ttt) REVERT: A 932 SER cc_start: 0.9194 (m) cc_final: 0.8790 (p) REVERT: D 138 MET cc_start: 0.8658 (mtt) cc_final: 0.8270 (mmt) REVERT: D 242 MET cc_start: 0.3301 (tpt) cc_final: 0.0589 (ttp) REVERT: D 255 MET cc_start: 0.6415 (mmm) cc_final: 0.6119 (mmm) REVERT: D 778 MET cc_start: 0.5948 (mtp) cc_final: 0.5544 (ttt) REVERT: D 932 SER cc_start: 0.9181 (m) cc_final: 0.8795 (p) REVERT: B 242 MET cc_start: 0.4081 (tpt) cc_final: 0.1740 (ttp) REVERT: B 255 MET cc_start: 0.5695 (mmp) cc_final: 0.5290 (tpp) REVERT: B 458 LEU cc_start: 0.9132 (tp) cc_final: 0.8861 (mt) REVERT: B 625 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7345 (mtm) REVERT: B 759 LEU cc_start: 0.8534 (mm) cc_final: 0.8175 (pp) REVERT: B 778 MET cc_start: 0.5841 (mtp) cc_final: 0.5433 (ttt) REVERT: B 932 SER cc_start: 0.9203 (m) cc_final: 0.8797 (p) REVERT: B 1207 MET cc_start: 0.8519 (ttp) cc_final: 0.7809 (ttm) REVERT: C 138 MET cc_start: 0.8641 (mtt) cc_final: 0.8265 (mmt) REVERT: C 242 MET cc_start: 0.3274 (tpt) cc_final: 0.0637 (ttp) REVERT: C 255 MET cc_start: 0.6349 (mmm) cc_final: 0.6081 (mmm) REVERT: C 302 LEU cc_start: 0.8626 (tp) cc_final: 0.8332 (tp) REVERT: C 457 MET cc_start: 0.7609 (tpp) cc_final: 0.7383 (tpp) REVERT: C 778 MET cc_start: 0.5820 (mtp) cc_final: 0.5452 (ttt) REVERT: C 932 SER cc_start: 0.9208 (m) cc_final: 0.8820 (p) outliers start: 19 outliers final: 7 residues processed: 318 average time/residue: 0.1942 time to fit residues: 105.2155 Evaluate side-chains 260 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 954 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 32 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 323 optimal weight: 50.0000 chunk 61 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 122 optimal weight: 0.0030 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A1093 ASN A1176 GLN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1092 ASN D1176 GLN B 693 GLN B1092 ASN B1176 GLN C 504 HIS C 693 GLN C 955 ASN C1092 ASN C1176 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.067678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050168 restraints weight = 343538.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052159 restraints weight = 147962.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.053454 restraints weight = 84887.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054328 restraints weight = 57956.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054884 restraints weight = 44492.090| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33680 Z= 0.141 Angle : 0.601 12.662 45980 Z= 0.299 Chirality : 0.039 0.212 5368 Planarity : 0.005 0.051 5668 Dihedral : 7.639 59.640 6252 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.73 % Allowed : 7.28 % Favored : 91.98 % 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: 1.09 (0.13), residues: 4208 helix: 1.67 (0.10), residues: 2708 sheet: -1.10 (0.30), residues: 328 loop : -0.92 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 210 TYR 0.020 0.001 TYR A1028 PHE 0.021 0.002 PHE A 866 TRP 0.036 0.002 TRP D 621 HIS 0.006 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00308 (33680) covalent geometry : angle 0.60092 (45980) hydrogen bonds : bond 0.04199 ( 2061) hydrogen bonds : angle 4.11762 ( 6127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 1.379 Fit side-chains REVERT: A 138 MET cc_start: 0.8647 (mtt) cc_final: 0.8240 (mmt) REVERT: A 242 MET cc_start: 0.2330 (tpt) cc_final: 0.0460 (ttp) REVERT: A 255 MET cc_start: 0.5274 (tpp) cc_final: 0.4973 (tpp) REVERT: A 759 LEU cc_start: 0.8552 (mm) cc_final: 0.8243 (pp) REVERT: A 778 MET cc_start: 0.5950 (mtp) cc_final: 0.5371 (ttt) REVERT: A 932 SER cc_start: 0.9189 (m) cc_final: 0.8794 (p) REVERT: D 138 MET cc_start: 0.8628 (mtt) cc_final: 0.8266 (mmt) REVERT: D 242 MET cc_start: 0.3224 (tpt) cc_final: 0.0824 (ttp) REVERT: D 255 MET cc_start: 0.6450 (mmm) cc_final: 0.6075 (mmm) REVERT: D 759 LEU cc_start: 0.8585 (mm) cc_final: 0.8227 (pp) REVERT: D 778 MET cc_start: 0.5906 (mtp) cc_final: 0.5469 (ttt) REVERT: D 932 SER cc_start: 0.9183 (m) cc_final: 0.8790 (p) REVERT: D 1092 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8145 (t0) REVERT: B 138 MET cc_start: 0.8546 (mtp) cc_final: 0.8222 (mmt) REVERT: B 242 MET cc_start: 0.3861 (tpt) cc_final: 0.2017 (ttp) REVERT: B 255 MET cc_start: 0.5746 (mmp) cc_final: 0.5274 (tpp) REVERT: B 409 ILE cc_start: 0.9082 (mm) cc_final: 0.8743 (tt) REVERT: B 458 LEU cc_start: 0.9146 (tp) cc_final: 0.8878 (mt) REVERT: B 759 LEU cc_start: 0.8535 (mm) cc_final: 0.8180 (pp) REVERT: B 778 MET cc_start: 0.5847 (mtp) cc_final: 0.5438 (ttt) REVERT: B 932 SER cc_start: 0.9191 (m) cc_final: 0.8787 (p) REVERT: B 1209 MET cc_start: 0.8347 (mpp) cc_final: 0.7912 (mpp) REVERT: C 138 MET cc_start: 0.8609 (mtt) cc_final: 0.8258 (mmt) REVERT: C 242 MET cc_start: 0.3156 (tpt) cc_final: 0.0974 (ttp) REVERT: C 255 MET cc_start: 0.6471 (mmm) cc_final: 0.6105 (mmm) REVERT: C 457 MET cc_start: 0.7753 (tpp) cc_final: 0.7522 (tpp) REVERT: C 759 LEU cc_start: 0.8587 (mm) cc_final: 0.8242 (pp) REVERT: C 778 MET cc_start: 0.5832 (mtp) cc_final: 0.5366 (ttt) REVERT: C 932 SER cc_start: 0.9249 (m) cc_final: 0.8857 (p) REVERT: C 1092 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7988 (t160) outliers start: 23 outliers final: 9 residues processed: 272 average time/residue: 0.1836 time to fit residues: 87.7032 Evaluate side-chains 255 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 1092 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 1092 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 340 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 353 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN B 693 GLN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.067668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049901 restraints weight = 393888.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051977 restraints weight = 159120.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053373 restraints weight = 88588.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.054257 restraints weight = 59262.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054854 restraints weight = 45185.917| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33680 Z= 0.119 Angle : 0.550 11.489 45980 Z= 0.274 Chirality : 0.038 0.172 5368 Planarity : 0.004 0.048 5668 Dihedral : 7.388 59.716 6252 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.57 % Allowed : 8.56 % Favored : 90.87 % 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: 1.48 (0.13), residues: 4208 helix: 1.99 (0.10), residues: 2708 sheet: -1.01 (0.31), residues: 320 loop : -0.80 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.017 0.001 TYR B1028 PHE 0.019 0.001 PHE D1091 TRP 0.031 0.001 TRP C 621 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00260 (33680) covalent geometry : angle 0.55018 (45980) hydrogen bonds : bond 0.03876 ( 2061) hydrogen bonds : angle 3.96008 ( 6127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8589 (mtt) cc_final: 0.8213 (mmt) REVERT: A 242 MET cc_start: 0.1868 (OUTLIER) cc_final: 0.0229 (ttp) REVERT: A 759 LEU cc_start: 0.8535 (mm) cc_final: 0.8224 (pp) REVERT: A 778 MET cc_start: 0.5968 (mtp) cc_final: 0.5409 (ttt) REVERT: A 932 SER cc_start: 0.9157 (m) cc_final: 0.8780 (p) REVERT: D 138 MET cc_start: 0.8581 (mtt) cc_final: 0.8249 (mmt) REVERT: D 179 MET cc_start: 0.8031 (mmp) cc_final: 0.7803 (mmm) REVERT: D 242 MET cc_start: 0.3265 (tpt) cc_final: 0.1005 (ttp) REVERT: D 255 MET cc_start: 0.6445 (mmm) cc_final: 0.6000 (mmm) REVERT: D 759 LEU cc_start: 0.8575 (mm) cc_final: 0.8249 (pp) REVERT: D 778 MET cc_start: 0.5885 (mtp) cc_final: 0.5536 (ttt) REVERT: D 932 SER cc_start: 0.9163 (m) cc_final: 0.8775 (p) REVERT: D 1093 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8040 (t0) REVERT: B 138 MET cc_start: 0.8489 (mtp) cc_final: 0.8182 (mmt) REVERT: B 242 MET cc_start: 0.3749 (tpt) cc_final: 0.1859 (ttp) REVERT: B 255 MET cc_start: 0.5642 (mmp) cc_final: 0.5203 (tpp) REVERT: B 409 ILE cc_start: 0.9039 (mm) cc_final: 0.8678 (tt) REVERT: B 458 LEU cc_start: 0.9102 (tp) cc_final: 0.8886 (mt) REVERT: B 625 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: B 685 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 759 LEU cc_start: 0.8509 (mm) cc_final: 0.8169 (pp) REVERT: B 778 MET cc_start: 0.5864 (mtp) cc_final: 0.5504 (ttt) REVERT: B 932 SER cc_start: 0.9193 (m) cc_final: 0.8815 (p) REVERT: B 1133 MET cc_start: 0.8234 (mtm) cc_final: 0.7963 (mtm) REVERT: B 1209 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7288 (mmm) REVERT: C 138 MET cc_start: 0.8568 (mtt) cc_final: 0.8249 (mmt) REVERT: C 242 MET cc_start: 0.3274 (tpt) cc_final: 0.1138 (ttp) REVERT: C 255 MET cc_start: 0.6403 (mmm) cc_final: 0.5988 (mmm) REVERT: C 691 TYR cc_start: 0.8587 (t80) cc_final: 0.8297 (t80) REVERT: C 759 LEU cc_start: 0.8595 (mm) cc_final: 0.8273 (pp) REVERT: C 778 MET cc_start: 0.5816 (mtp) cc_final: 0.5382 (ttt) REVERT: C 932 SER cc_start: 0.9160 (m) cc_final: 0.8785 (p) outliers start: 18 outliers final: 5 residues processed: 267 average time/residue: 0.1792 time to fit residues: 84.6890 Evaluate side-chains 261 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 1093 ASN Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 630 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 269 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 238 optimal weight: 0.0070 chunk 224 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 332 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 345 optimal weight: 0.2980 chunk 359 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 overall best weight: 1.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.067618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.049496 restraints weight = 392796.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051828 restraints weight = 164056.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052995 restraints weight = 92976.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054464 restraints weight = 59180.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054504 restraints weight = 42924.912| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33680 Z= 0.117 Angle : 0.550 10.931 45980 Z= 0.272 Chirality : 0.038 0.226 5368 Planarity : 0.004 0.045 5668 Dihedral : 7.094 59.912 6252 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.48 % Allowed : 9.48 % Favored : 90.04 % 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: 1.76 (0.13), residues: 4208 helix: 2.21 (0.10), residues: 2704 sheet: -0.83 (0.31), residues: 320 loop : -0.71 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 210 TYR 0.017 0.001 TYR B1028 PHE 0.017 0.001 PHE A 866 TRP 0.033 0.001 TRP C 621 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00255 (33680) covalent geometry : angle 0.55018 (45980) hydrogen bonds : bond 0.03745 ( 2061) hydrogen bonds : angle 3.85115 ( 6127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 1.388 Fit side-chains REVERT: A 138 MET cc_start: 0.8645 (mtt) cc_final: 0.8270 (mmt) REVERT: A 242 MET cc_start: 0.1958 (OUTLIER) cc_final: 0.0625 (mtt) REVERT: A 255 MET cc_start: 0.5319 (tpp) cc_final: 0.5061 (tpp) REVERT: A 685 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8274 (mt-10) REVERT: A 691 TYR cc_start: 0.8587 (t80) cc_final: 0.8242 (t80) REVERT: A 759 LEU cc_start: 0.8566 (mm) cc_final: 0.8222 (pp) REVERT: A 778 MET cc_start: 0.5866 (mtp) cc_final: 0.5397 (ttt) REVERT: A 932 SER cc_start: 0.9153 (m) cc_final: 0.8777 (p) REVERT: D 138 MET cc_start: 0.8622 (mtt) cc_final: 0.8277 (mmt) REVERT: D 179 MET cc_start: 0.8117 (mmp) cc_final: 0.7550 (mmm) REVERT: D 242 MET cc_start: 0.3408 (tpt) cc_final: 0.1133 (ttp) REVERT: D 691 TYR cc_start: 0.8621 (t80) cc_final: 0.8252 (t80) REVERT: D 759 LEU cc_start: 0.8534 (mm) cc_final: 0.8198 (pp) REVERT: D 778 MET cc_start: 0.5871 (mtp) cc_final: 0.5490 (ttp) REVERT: D 932 SER cc_start: 0.9158 (m) cc_final: 0.8765 (p) REVERT: B 138 MET cc_start: 0.8498 (mtp) cc_final: 0.8231 (mmt) REVERT: B 242 MET cc_start: 0.3729 (tpt) cc_final: 0.1966 (ttp) REVERT: B 255 MET cc_start: 0.5660 (mmp) cc_final: 0.5086 (tpp) REVERT: B 458 LEU cc_start: 0.9110 (tp) cc_final: 0.8873 (mt) REVERT: B 685 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 691 TYR cc_start: 0.8566 (t80) cc_final: 0.8179 (t80) REVERT: B 759 LEU cc_start: 0.8494 (mm) cc_final: 0.8159 (pp) REVERT: B 778 MET cc_start: 0.5858 (mtp) cc_final: 0.5505 (ttt) REVERT: B 932 SER cc_start: 0.9190 (m) cc_final: 0.8787 (p) REVERT: B 1133 MET cc_start: 0.8164 (mtm) cc_final: 0.7884 (mtm) REVERT: B 1209 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7202 (mmm) REVERT: C 138 MET cc_start: 0.8620 (mtt) cc_final: 0.8283 (mmt) REVERT: C 242 MET cc_start: 0.3425 (tpt) cc_final: 0.1374 (ttp) REVERT: C 255 MET cc_start: 0.6568 (mmm) cc_final: 0.6036 (mmm) REVERT: C 691 TYR cc_start: 0.8605 (t80) cc_final: 0.8271 (t80) REVERT: C 759 LEU cc_start: 0.8569 (mm) cc_final: 0.8237 (pp) REVERT: C 778 MET cc_start: 0.5765 (mtp) cc_final: 0.5430 (ttt) REVERT: C 932 SER cc_start: 0.9159 (m) cc_final: 0.8778 (p) outliers start: 15 outliers final: 3 residues processed: 271 average time/residue: 0.1859 time to fit residues: 88.4323 Evaluate side-chains 255 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 630 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 69 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 410 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1176 GLN B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.067244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050038 restraints weight = 293164.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051889 restraints weight = 133502.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053092 restraints weight = 79234.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053893 restraints weight = 55357.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.054423 restraints weight = 43522.661| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33680 Z= 0.116 Angle : 0.537 9.968 45980 Z= 0.268 Chirality : 0.038 0.234 5368 Planarity : 0.004 0.044 5668 Dihedral : 6.953 59.584 6252 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.54 % Allowed : 10.31 % Favored : 89.15 % 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: 1.91 (0.13), residues: 4208 helix: 2.34 (0.10), residues: 2680 sheet: -0.70 (0.32), residues: 320 loop : -0.66 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 210 TYR 0.016 0.001 TYR B1028 PHE 0.016 0.001 PHE D1001 TRP 0.061 0.002 TRP B 431 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00254 (33680) covalent geometry : angle 0.53679 (45980) hydrogen bonds : bond 0.03697 ( 2061) hydrogen bonds : angle 3.83135 ( 6127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 1.398 Fit side-chains REVERT: A 138 MET cc_start: 0.8617 (mtt) cc_final: 0.8257 (mmt) REVERT: A 242 MET cc_start: 0.1804 (OUTLIER) cc_final: 0.0626 (mtt) REVERT: A 691 TYR cc_start: 0.8563 (t80) cc_final: 0.8234 (t80) REVERT: A 759 LEU cc_start: 0.8564 (mm) cc_final: 0.8223 (pp) REVERT: A 778 MET cc_start: 0.5927 (mtp) cc_final: 0.5430 (ttt) REVERT: A 932 SER cc_start: 0.9163 (m) cc_final: 0.8781 (p) REVERT: D 138 MET cc_start: 0.8598 (mtt) cc_final: 0.8269 (mmt) REVERT: D 179 MET cc_start: 0.8131 (mmp) cc_final: 0.7661 (mmm) REVERT: D 242 MET cc_start: 0.3266 (tpt) cc_final: 0.0933 (ttp) REVERT: D 625 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6802 (mtm) REVERT: D 691 TYR cc_start: 0.8612 (t80) cc_final: 0.8258 (t80) REVERT: D 759 LEU cc_start: 0.8542 (mm) cc_final: 0.8206 (pp) REVERT: D 778 MET cc_start: 0.5833 (mtp) cc_final: 0.5452 (ttt) REVERT: D 932 SER cc_start: 0.9166 (m) cc_final: 0.8772 (p) REVERT: B 138 MET cc_start: 0.8492 (mtp) cc_final: 0.8246 (mmt) REVERT: B 242 MET cc_start: 0.3452 (tpt) cc_final: 0.1838 (ttp) REVERT: B 255 MET cc_start: 0.5607 (mmp) cc_final: 0.5104 (tpp) REVERT: B 458 LEU cc_start: 0.9100 (tp) cc_final: 0.8877 (mt) REVERT: B 691 TYR cc_start: 0.8574 (t80) cc_final: 0.8177 (t80) REVERT: B 734 MET cc_start: 0.8675 (ppp) cc_final: 0.8418 (ppp) REVERT: B 759 LEU cc_start: 0.8480 (mm) cc_final: 0.8161 (pp) REVERT: B 778 MET cc_start: 0.5785 (mtp) cc_final: 0.5512 (ttt) REVERT: B 932 SER cc_start: 0.9191 (m) cc_final: 0.8784 (p) REVERT: B 1133 MET cc_start: 0.8142 (mtm) cc_final: 0.7874 (mtm) REVERT: B 1209 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: C 138 MET cc_start: 0.8590 (mtt) cc_final: 0.8268 (mmt) REVERT: C 179 MET cc_start: 0.8229 (mmm) cc_final: 0.7571 (mmm) REVERT: C 242 MET cc_start: 0.3348 (tpt) cc_final: 0.1239 (ttp) REVERT: C 691 TYR cc_start: 0.8606 (t80) cc_final: 0.8282 (t80) REVERT: C 759 LEU cc_start: 0.8603 (mm) cc_final: 0.8282 (pp) REVERT: C 778 MET cc_start: 0.5752 (mtp) cc_final: 0.5397 (ttt) REVERT: C 932 SER cc_start: 0.9167 (m) cc_final: 0.8787 (p) outliers start: 17 outliers final: 7 residues processed: 266 average time/residue: 0.1868 time to fit residues: 87.7652 Evaluate side-chains 256 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 642 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 60 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 220 optimal weight: 30.0000 chunk 7 optimal weight: 0.1980 chunk 286 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 358 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 HIS D 693 GLN B 504 HIS B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN C1171 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.065962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047986 restraints weight = 429702.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050005 restraints weight = 169948.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051369 restraints weight = 94963.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052255 restraints weight = 63768.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052848 restraints weight = 48607.568| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33680 Z= 0.177 Angle : 0.624 9.832 45980 Z= 0.310 Chirality : 0.040 0.234 5368 Planarity : 0.004 0.041 5668 Dihedral : 6.995 58.705 6252 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.83 % Allowed : 10.59 % Favored : 88.58 % 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: 1.65 (0.13), residues: 4208 helix: 2.13 (0.10), residues: 2700 sheet: -0.65 (0.32), residues: 320 loop : -0.85 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 210 TYR 0.018 0.002 TYR B1028 PHE 0.022 0.002 PHE D 866 TRP 0.040 0.002 TRP B 431 HIS 0.006 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00394 (33680) covalent geometry : angle 0.62445 (45980) hydrogen bonds : bond 0.04181 ( 2061) hydrogen bonds : angle 4.07320 ( 6127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 1.366 Fit side-chains REVERT: A 138 MET cc_start: 0.8732 (mtt) cc_final: 0.8340 (mmt) REVERT: A 179 MET cc_start: 0.7345 (mmm) cc_final: 0.7052 (mmm) REVERT: A 242 MET cc_start: 0.2228 (OUTLIER) cc_final: 0.0972 (mtt) REVERT: A 759 LEU cc_start: 0.8605 (mm) cc_final: 0.8219 (pp) REVERT: A 778 MET cc_start: 0.6135 (mtp) cc_final: 0.5455 (ttt) REVERT: A 932 SER cc_start: 0.9223 (m) cc_final: 0.8829 (p) REVERT: A 978 MET cc_start: 0.8704 (mpp) cc_final: 0.8502 (mpp) REVERT: D 138 MET cc_start: 0.8727 (mtt) cc_final: 0.8337 (mmt) REVERT: D 242 MET cc_start: 0.3439 (tpt) cc_final: 0.1231 (ttp) REVERT: D 778 MET cc_start: 0.6019 (mtp) cc_final: 0.5516 (ttt) REVERT: D 932 SER cc_start: 0.9236 (m) cc_final: 0.8838 (p) REVERT: B 138 MET cc_start: 0.8553 (mtp) cc_final: 0.8307 (mmt) REVERT: B 242 MET cc_start: 0.3711 (tpt) cc_final: 0.2379 (ttp) REVERT: B 255 MET cc_start: 0.5774 (mmp) cc_final: 0.5247 (tpp) REVERT: B 345 TYR cc_start: 0.7724 (m-80) cc_final: 0.7315 (m-80) REVERT: B 458 LEU cc_start: 0.9158 (tp) cc_final: 0.8891 (mt) REVERT: B 778 MET cc_start: 0.6062 (mtp) cc_final: 0.5647 (ttt) REVERT: B 932 SER cc_start: 0.9251 (m) cc_final: 0.8854 (p) REVERT: B 978 MET cc_start: 0.8684 (mpp) cc_final: 0.8471 (mpp) REVERT: B 1209 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7273 (mmm) REVERT: C 138 MET cc_start: 0.8720 (mtt) cc_final: 0.8345 (mmt) REVERT: C 179 MET cc_start: 0.8156 (mmm) cc_final: 0.7846 (mmm) REVERT: C 242 MET cc_start: 0.3407 (tpt) cc_final: 0.1057 (ttm) REVERT: C 255 MET cc_start: 0.6465 (mmm) cc_final: 0.5853 (tpp) REVERT: C 778 MET cc_start: 0.5938 (mtp) cc_final: 0.5405 (ttt) REVERT: C 932 SER cc_start: 0.9217 (m) cc_final: 0.8827 (p) REVERT: C 978 MET cc_start: 0.8688 (mpp) cc_final: 0.8483 (mpp) outliers start: 26 outliers final: 10 residues processed: 258 average time/residue: 0.1831 time to fit residues: 82.4452 Evaluate side-chains 249 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 642 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 60 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 375 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 126 optimal weight: 40.0000 chunk 164 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** 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 = 0.3611 r_free = 0.3611 target = 0.065762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.048408 restraints weight = 337575.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050271 restraints weight = 146425.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051492 restraints weight = 85091.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.052292 restraints weight = 58751.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052841 restraints weight = 45854.069| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33680 Z= 0.169 Angle : 0.605 12.014 45980 Z= 0.301 Chirality : 0.039 0.238 5368 Planarity : 0.004 0.042 5668 Dihedral : 6.685 59.600 6252 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 11.23 % Favored : 88.10 % 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: 1.59 (0.13), residues: 4208 helix: 2.12 (0.10), residues: 2672 sheet: -0.49 (0.32), residues: 316 loop : -0.94 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 210 TYR 0.018 0.002 TYR B1028 PHE 0.019 0.002 PHE A1001 TRP 0.042 0.002 TRP B 431 HIS 0.005 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00378 (33680) covalent geometry : angle 0.60545 (45980) hydrogen bonds : bond 0.04091 ( 2061) hydrogen bonds : angle 4.08511 ( 6127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 1.270 Fit side-chains REVERT: A 138 MET cc_start: 0.8691 (mtt) cc_final: 0.8333 (mmt) REVERT: A 179 MET cc_start: 0.7411 (mmm) cc_final: 0.7127 (mmm) REVERT: A 242 MET cc_start: 0.2203 (OUTLIER) cc_final: 0.0547 (ttm) REVERT: A 458 LEU cc_start: 0.9247 (tp) cc_final: 0.8934 (mt) REVERT: A 778 MET cc_start: 0.6220 (mtp) cc_final: 0.5577 (ttt) REVERT: A 932 SER cc_start: 0.9217 (m) cc_final: 0.8818 (p) REVERT: A 978 MET cc_start: 0.8668 (mpp) cc_final: 0.8449 (mpp) REVERT: D 138 MET cc_start: 0.8732 (mtt) cc_final: 0.8359 (mmt) REVERT: D 179 MET cc_start: 0.7721 (mmm) cc_final: 0.7253 (mmm) REVERT: D 242 MET cc_start: 0.3360 (tpt) cc_final: 0.1285 (ttt) REVERT: D 255 MET cc_start: 0.6353 (mmm) cc_final: 0.5822 (tpp) REVERT: D 691 TYR cc_start: 0.8752 (t80) cc_final: 0.8408 (t80) REVERT: D 778 MET cc_start: 0.5914 (mtp) cc_final: 0.5356 (ttt) REVERT: D 932 SER cc_start: 0.9244 (m) cc_final: 0.8846 (p) REVERT: B 138 MET cc_start: 0.8542 (mtp) cc_final: 0.8307 (mmt) REVERT: B 242 MET cc_start: 0.3726 (tpt) cc_final: 0.2690 (ttt) REVERT: B 255 MET cc_start: 0.5825 (mmp) cc_final: 0.5320 (tpp) REVERT: B 345 TYR cc_start: 0.7805 (m-80) cc_final: 0.7412 (m-80) REVERT: B 458 LEU cc_start: 0.9156 (tp) cc_final: 0.8919 (mt) REVERT: B 778 MET cc_start: 0.6092 (mtp) cc_final: 0.5687 (ttt) REVERT: B 932 SER cc_start: 0.9262 (m) cc_final: 0.8863 (p) REVERT: B 978 MET cc_start: 0.8666 (mpp) cc_final: 0.8451 (mpp) REVERT: B 1209 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7213 (mmm) REVERT: C 138 MET cc_start: 0.8696 (mtt) cc_final: 0.8362 (mmt) REVERT: C 179 MET cc_start: 0.8174 (mmm) cc_final: 0.7880 (mmm) REVERT: C 242 MET cc_start: 0.3393 (tpt) cc_final: 0.1645 (ttt) REVERT: C 431 TRP cc_start: 0.7458 (m-90) cc_final: 0.7230 (m-90) REVERT: C 691 TYR cc_start: 0.8777 (t80) cc_final: 0.8452 (t80) REVERT: C 778 MET cc_start: 0.5951 (mtp) cc_final: 0.5340 (ttt) REVERT: C 932 SER cc_start: 0.9234 (m) cc_final: 0.8847 (p) REVERT: C 978 MET cc_start: 0.8683 (mpp) cc_final: 0.8464 (mpp) outliers start: 21 outliers final: 13 residues processed: 252 average time/residue: 0.1862 time to fit residues: 82.1296 Evaluate side-chains 252 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 642 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 186 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 246 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 256 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1171 HIS B 343 HIS B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.065019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047450 restraints weight = 379900.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049357 restraints weight = 159130.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050631 restraints weight = 90852.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051455 restraints weight = 61777.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052002 restraints weight = 47773.102| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33680 Z= 0.232 Angle : 0.701 10.611 45980 Z= 0.350 Chirality : 0.042 0.225 5368 Planarity : 0.005 0.041 5668 Dihedral : 6.744 57.751 6252 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.83 % Allowed : 11.51 % Favored : 87.66 % 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: 1.11 (0.13), residues: 4208 helix: 1.73 (0.10), residues: 2704 sheet: -0.71 (0.33), residues: 312 loop : -1.16 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 210 TYR 0.019 0.002 TYR B1028 PHE 0.024 0.002 PHE B 866 TRP 0.043 0.002 TRP B 431 HIS 0.007 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00515 (33680) covalent geometry : angle 0.70084 (45980) hydrogen bonds : bond 0.04585 ( 2061) hydrogen bonds : angle 4.39308 ( 6127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 1.293 Fit side-chains REVERT: A 138 MET cc_start: 0.8735 (mtt) cc_final: 0.8363 (mmt) REVERT: A 149 LEU cc_start: 0.8421 (tt) cc_final: 0.8215 (tp) REVERT: A 242 MET cc_start: 0.2581 (OUTLIER) cc_final: 0.1113 (ttm) REVERT: A 458 LEU cc_start: 0.9230 (tp) cc_final: 0.8906 (mt) REVERT: A 778 MET cc_start: 0.6343 (mtp) cc_final: 0.5621 (ttt) REVERT: A 932 SER cc_start: 0.9252 (m) cc_final: 0.8827 (p) REVERT: A 978 MET cc_start: 0.8786 (mpp) cc_final: 0.8555 (mpp) REVERT: D 138 MET cc_start: 0.8726 (mtt) cc_final: 0.8383 (mmt) REVERT: D 149 LEU cc_start: 0.8441 (tt) cc_final: 0.8202 (tp) REVERT: D 179 MET cc_start: 0.7804 (mmm) cc_final: 0.7388 (mmm) REVERT: D 242 MET cc_start: 0.3587 (tpt) cc_final: 0.1789 (ttt) REVERT: D 778 MET cc_start: 0.6186 (mtp) cc_final: 0.5520 (ttt) REVERT: D 932 SER cc_start: 0.9262 (m) cc_final: 0.8833 (p) REVERT: D 1172 ASP cc_start: 0.8414 (t0) cc_final: 0.8106 (t0) REVERT: B 138 MET cc_start: 0.8579 (mtp) cc_final: 0.8325 (mmt) REVERT: B 242 MET cc_start: 0.3942 (tpt) cc_final: 0.3147 (ttt) REVERT: B 255 MET cc_start: 0.5736 (mmp) cc_final: 0.5314 (tpp) REVERT: B 345 TYR cc_start: 0.7826 (m-80) cc_final: 0.7447 (m-80) REVERT: B 458 LEU cc_start: 0.9155 (tp) cc_final: 0.8908 (mt) REVERT: B 778 MET cc_start: 0.6175 (mtp) cc_final: 0.5759 (ttp) REVERT: B 932 SER cc_start: 0.9236 (m) cc_final: 0.8837 (p) REVERT: B 978 MET cc_start: 0.8749 (mpp) cc_final: 0.8524 (mpp) REVERT: B 1209 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7204 (mmm) REVERT: C 138 MET cc_start: 0.8732 (mtt) cc_final: 0.8399 (mmt) REVERT: C 179 MET cc_start: 0.8105 (mmm) cc_final: 0.7592 (mmm) REVERT: C 242 MET cc_start: 0.3363 (tpt) cc_final: 0.1943 (ttt) REVERT: C 255 MET cc_start: 0.6419 (mmm) cc_final: 0.5867 (tpp) REVERT: C 778 MET cc_start: 0.6201 (mtp) cc_final: 0.5477 (ttt) REVERT: C 932 SER cc_start: 0.9248 (m) cc_final: 0.8834 (p) REVERT: C 978 MET cc_start: 0.8774 (mpp) cc_final: 0.8548 (mpp) outliers start: 26 outliers final: 19 residues processed: 253 average time/residue: 0.1846 time to fit residues: 80.5791 Evaluate side-chains 252 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 642 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 4 optimal weight: 0.9980 chunk 281 optimal weight: 10.0000 chunk 115 optimal weight: 40.0000 chunk 220 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.065389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.047890 restraints weight = 363576.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049783 restraints weight = 153315.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.051053 restraints weight = 87941.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051886 restraints weight = 59985.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052427 restraints weight = 46428.892| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33680 Z= 0.174 Angle : 0.635 11.339 45980 Z= 0.313 Chirality : 0.040 0.229 5368 Planarity : 0.004 0.042 5668 Dihedral : 6.585 59.401 6252 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.70 % Allowed : 11.74 % Favored : 87.56 % 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: 1.33 (0.13), residues: 4208 helix: 1.92 (0.10), residues: 2684 sheet: -0.75 (0.31), residues: 340 loop : -1.04 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 210 TYR 0.017 0.002 TYR B1028 PHE 0.018 0.002 PHE B 866 TRP 0.040 0.002 TRP B 431 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00388 (33680) covalent geometry : angle 0.63506 (45980) hydrogen bonds : bond 0.04258 ( 2061) hydrogen bonds : angle 4.20430 ( 6127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.605 Fit side-chains REVERT: A 138 MET cc_start: 0.8699 (mtt) cc_final: 0.8338 (mmt) REVERT: A 149 LEU cc_start: 0.8339 (tt) cc_final: 0.8122 (tp) REVERT: A 242 MET cc_start: 0.2522 (OUTLIER) cc_final: 0.1084 (ttm) REVERT: A 458 LEU cc_start: 0.9221 (tp) cc_final: 0.8923 (mt) REVERT: A 778 MET cc_start: 0.6281 (mtp) cc_final: 0.5679 (ttt) REVERT: A 932 SER cc_start: 0.9264 (m) cc_final: 0.8859 (p) REVERT: A 978 MET cc_start: 0.8716 (mpp) cc_final: 0.8479 (mpp) REVERT: A 999 MET cc_start: 0.8427 (ttm) cc_final: 0.8164 (ttm) REVERT: D 138 MET cc_start: 0.8676 (mtt) cc_final: 0.8344 (mmt) REVERT: D 149 LEU cc_start: 0.8464 (tt) cc_final: 0.8226 (tp) REVERT: D 179 MET cc_start: 0.7839 (mmm) cc_final: 0.7326 (mmm) REVERT: D 242 MET cc_start: 0.3647 (tpt) cc_final: 0.1952 (ttt) REVERT: D 255 MET cc_start: 0.6439 (mmm) cc_final: 0.5859 (tpp) REVERT: D 778 MET cc_start: 0.6103 (mtp) cc_final: 0.5502 (ttt) REVERT: D 932 SER cc_start: 0.9280 (m) cc_final: 0.8881 (p) REVERT: D 999 MET cc_start: 0.8443 (ttm) cc_final: 0.8184 (ttm) REVERT: D 1172 ASP cc_start: 0.8372 (t0) cc_final: 0.8089 (t0) REVERT: B 138 MET cc_start: 0.8548 (mtp) cc_final: 0.8302 (mmt) REVERT: B 242 MET cc_start: 0.3911 (tpt) cc_final: 0.3232 (ttt) REVERT: B 255 MET cc_start: 0.5833 (mmp) cc_final: 0.5483 (tpt) REVERT: B 345 TYR cc_start: 0.7806 (m-80) cc_final: 0.7462 (m-80) REVERT: B 458 LEU cc_start: 0.9126 (tp) cc_final: 0.8896 (mt) REVERT: B 778 MET cc_start: 0.6063 (mtp) cc_final: 0.5624 (ttp) REVERT: B 932 SER cc_start: 0.9227 (m) cc_final: 0.8827 (p) REVERT: B 978 MET cc_start: 0.8712 (mpp) cc_final: 0.8475 (mpp) REVERT: B 1133 MET cc_start: 0.8202 (mtm) cc_final: 0.7932 (mtm) REVERT: B 1209 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7220 (mmm) REVERT: C 138 MET cc_start: 0.8703 (mtt) cc_final: 0.8371 (mmt) REVERT: C 179 MET cc_start: 0.8166 (mmm) cc_final: 0.7905 (mmm) REVERT: C 242 MET cc_start: 0.3408 (tpt) cc_final: 0.2054 (ttt) REVERT: C 255 MET cc_start: 0.6382 (mmm) cc_final: 0.5674 (tpp) REVERT: C 431 TRP cc_start: 0.7617 (m-90) cc_final: 0.7396 (m-90) REVERT: C 778 MET cc_start: 0.6127 (mtp) cc_final: 0.5571 (ttt) REVERT: C 932 SER cc_start: 0.9275 (m) cc_final: 0.8878 (p) REVERT: C 978 MET cc_start: 0.8716 (mpp) cc_final: 0.8487 (mpp) REVERT: C 999 MET cc_start: 0.8440 (ttm) cc_final: 0.8174 (ttm) outliers start: 22 outliers final: 16 residues processed: 253 average time/residue: 0.1873 time to fit residues: 82.5708 Evaluate side-chains 258 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 642 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 132 optimal weight: 0.0980 chunk 62 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 370 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 235 optimal weight: 0.0000 chunk 340 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 5 optimal weight: 40.0000 overall best weight: 2.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.065935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.048248 restraints weight = 397306.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050695 restraints weight = 167204.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052214 restraints weight = 84528.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052685 restraints weight = 50265.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.052757 restraints weight = 47133.253| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33680 Z= 0.127 Angle : 0.590 12.105 45980 Z= 0.288 Chirality : 0.038 0.212 5368 Planarity : 0.004 0.042 5668 Dihedral : 6.350 59.391 6252 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.57 % Allowed : 11.90 % Favored : 87.53 % 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: 1.66 (0.13), residues: 4208 helix: 2.21 (0.10), residues: 2672 sheet: -0.64 (0.31), residues: 344 loop : -0.96 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 210 TYR 0.015 0.001 TYR B1028 PHE 0.018 0.001 PHE A1001 TRP 0.043 0.002 TRP D 431 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00281 (33680) covalent geometry : angle 0.59030 (45980) hydrogen bonds : bond 0.03961 ( 2061) hydrogen bonds : angle 3.97492 ( 6127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5792.73 seconds wall clock time: 101 minutes 7.61 seconds (6067.61 seconds total)