Starting phenix.real_space_refine on Sat Feb 7 14:48:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.map" model { file = "/net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1g_48811/02_2026/9n1g_48811.cif" } resolution = 2.62 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 248 5.16 5 C 21676 2.51 5 N 5508 2.21 5 O 5708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33140 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 Conformer: "B" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 bond proxies already assigned to first conformer: 8222 Chain: "D" Number of atoms: 8075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 Conformer: "B" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 bond proxies already assigned to first conformer: 8222 Chain: "B" Number of atoms: 8075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 Conformer: "B" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 bond proxies already assigned to first conformer: 8222 Chain: "C" Number of atoms: 8075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 Conformer: "B" Number of residues, atoms: 1068, 8057 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 769 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 397 bond proxies already assigned to first conformer: 8222 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 245 Unusual residues: {'Y01': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 8 residue: pdb=" N AHIS A 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS A 674 " occ=0.56 residue: pdb=" N AMET A 988 " occ=0.53 ... (14 atoms not shown) pdb=" CE BMET A 988 " occ=0.47 residue: pdb=" N AHIS D 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.56 residue: pdb=" N AMET D 988 " occ=0.53 ... (14 atoms not shown) pdb=" CE BMET D 988 " occ=0.47 residue: pdb=" N AHIS B 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.56 residue: pdb=" N AMET B 988 " occ=0.53 ... (14 atoms not shown) pdb=" CE BMET B 988 " occ=0.47 residue: pdb=" N AHIS C 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS C 674 " occ=0.56 residue: pdb=" N AMET C 988 " occ=0.53 ... (14 atoms not shown) pdb=" CE BMET C 988 " occ=0.47 Time building chain proxies: 14.74, per 1000 atoms: 0.44 Number of scatterers: 33140 At special positions: 0 Unit cell: (136.29, 136.29, 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 248 16.00 O 5708 8.00 N 5508 7.00 C 21676 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: 2.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 20 sheets defined 66.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.745A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.520A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.603A pdb=" N ILE A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.622A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.523A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.112A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.944A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.736A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.645A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.606A 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: 3.569A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 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 939 Processing helix chain 'A' and resid 943 through 968 removed outlier: 3.702A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 4.498A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.516A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.723A 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: 3.635A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1093 removed outlier: 3.911A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.607A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.388A 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: 4.342A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1232 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.745A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.520A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.604A pdb=" N ILE D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.621A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.523A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 4.111A pdb=" N ILE D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.944A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 501 through 514 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 564 Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.737A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.645A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.606A 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: 3.569A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 741 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 939 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: 4.624A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.497A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.516A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.723A 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: 3.635A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1093 removed outlier: 3.911A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.607A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.387A 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: 4.342A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' and resid 1192 through 1232 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.745A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.520A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.603A pdb=" N ILE B 223 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.622A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.523A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 4.112A pdb=" N ILE B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.944A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.737A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.645A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.606A 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: 3.569A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 741 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 939 Processing helix chain 'B' and resid 943 through 968 removed outlier: 3.702A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.498A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.516A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.724A 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: 3.634A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1093 removed outlier: 3.911A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.607A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.388A 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: 4.342A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 Processing helix chain 'B' and resid 1192 through 1232 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.745A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.520A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 209 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.603A pdb=" N ILE C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.622A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.523A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 4.111A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.944A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 475 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 501 through 514 Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 564 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.736A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.645A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.606A 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: 3.569A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 741 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 939 Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.702A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 4.497A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.517A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.723A 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: 3.635A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1093 removed outlier: 3.911A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C1084 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 4.607A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.387A 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: 4.342A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1232 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.553A pdb=" N GLU A 40 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.670A 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: 6.672A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.946A 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: 6.380A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.334A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1047 through 1049 removed outlier: 3.510A pdb=" N ILE A1056 " --> pdb=" O GLU A1048 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.553A pdb=" N GLU D 40 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.670A 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: 6.671A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.946A 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: 6.380A 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: 6.334A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1047 through 1049 removed outlier: 3.510A pdb=" N ILE D1056 " --> pdb=" O GLU D1048 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.552A pdb=" N GLU B 40 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.670A 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: 6.672A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.946A 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: 6.380A 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: 6.334A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 395 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1047 through 1049 removed outlier: 3.510A pdb=" N ILE B1056 " --> pdb=" O GLU B1048 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.553A pdb=" N GLU C 40 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 3.669A 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: 6.672A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.945A 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: 6.380A 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: 6.334A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 3.510A pdb=" N ILE C1056 " --> pdb=" O GLU C1048 " (cutoff:3.500A) 2077 hydrogen bonds defined for protein. 6191 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: 7.18 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5172 1.32 - 1.44: 8948 1.44 - 1.57: 19428 1.57 - 1.69: 0 1.69 - 1.81: 420 Bond restraints: 33968 Sorted by residual: bond pdb=" N SER D 47 " pdb=" CA SER D 47 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.44e+00 bond pdb=" N SER C 47 " pdb=" CA SER C 47 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.44e+00 bond pdb=" N ASN B1047 " pdb=" CA ASN B1047 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.19e-02 7.06e+03 6.16e+00 bond pdb=" N ASN A1047 " pdb=" CA ASN A1047 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.19e-02 7.06e+03 6.16e+00 ... (remaining 33963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 44828 1.91 - 3.82: 1257 3.82 - 5.73: 199 5.73 - 7.64: 60 7.64 - 9.55: 20 Bond angle restraints: 46364 Sorted by residual: angle pdb=" N LYS D 49 " pdb=" CA LYS D 49 " pdb=" C LYS D 49 " ideal model delta sigma weight residual 111.24 120.15 -8.91 1.29e+00 6.01e-01 4.77e+01 angle pdb=" N LYS C 49 " pdb=" CA LYS C 49 " pdb=" C LYS C 49 " ideal model delta sigma weight residual 111.24 120.12 -8.88 1.29e+00 6.01e-01 4.74e+01 angle pdb=" N LYS A 49 " pdb=" CA LYS A 49 " pdb=" C LYS A 49 " ideal model delta sigma weight residual 111.24 120.12 -8.88 1.29e+00 6.01e-01 4.74e+01 angle pdb=" N LYS B 49 " pdb=" CA LYS B 49 " pdb=" C LYS B 49 " ideal model delta sigma weight residual 111.24 120.09 -8.85 1.29e+00 6.01e-01 4.71e+01 angle pdb=" C ARG C 210 " pdb=" N GLY C 211 " pdb=" CA GLY C 211 " ideal model delta sigma weight residual 122.16 115.61 6.55 1.14e+00 7.69e-01 3.31e+01 ... (remaining 46359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 19613 24.66 - 49.32: 1375 49.32 - 73.98: 244 73.98 - 98.64: 8 98.64 - 123.30: 12 Dihedral angle restraints: 21252 sinusoidal: 8776 harmonic: 12476 Sorted by residual: dihedral pdb=" CBC Y01 B1403 " pdb=" CAR Y01 B1403 " pdb=" CAT Y01 B1403 " pdb=" CBH Y01 B1403 " ideal model delta sinusoidal sigma weight residual -57.13 66.17 -123.30 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CBC Y01 A1403 " pdb=" CAR Y01 A1403 " pdb=" CAT Y01 A1403 " pdb=" CBH Y01 A1403 " ideal model delta sinusoidal sigma weight residual -57.13 66.17 -123.30 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CBC Y01 D1403 " pdb=" CAR Y01 D1403 " pdb=" CAT Y01 D1403 " pdb=" CBH Y01 D1403 " ideal model delta sinusoidal sigma weight residual -57.13 66.17 -123.30 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 21249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5114 0.096 - 0.192: 266 0.192 - 0.289: 16 0.289 - 0.385: 0 0.385 - 0.481: 4 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CG LEU C 706 " pdb=" CB LEU C 706 " pdb=" CD1 LEU C 706 " pdb=" CD2 LEU C 706 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CG LEU D 706 " pdb=" CB LEU D 706 " pdb=" CD1 LEU D 706 " pdb=" CD2 LEU D 706 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CG LEU A 706 " pdb=" CB LEU A 706 " pdb=" CD1 LEU A 706 " pdb=" CD2 LEU A 706 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 5397 not shown) Planarity restraints: 5716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BMET D 988 " -0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C BMET D 988 " 0.084 2.00e-02 2.50e+03 pdb=" O BMET D 988 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR D 989 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BMET C 988 " -0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C BMET C 988 " 0.084 2.00e-02 2.50e+03 pdb=" O BMET C 988 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR C 989 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BMET A 988 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C BMET A 988 " -0.084 2.00e-02 2.50e+03 pdb=" O BMET A 988 " 0.031 2.00e-02 2.50e+03 pdb=" N TYR A 989 " 0.029 2.00e-02 2.50e+03 ... (remaining 5713 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 18531 3.04 - 3.50: 35779 3.50 - 3.97: 53779 3.97 - 4.43: 63712 4.43 - 4.90: 98894 Nonbonded interactions: 270695 Sorted by model distance: nonbonded pdb=" O LYS C 208 " pdb=" CG LYS C 208 " model vdw 2.572 3.440 nonbonded pdb=" O MET D 386 " pdb=" C LYS D 387 " model vdw 2.572 3.270 nonbonded pdb=" O LYS A 208 " pdb=" CG LYS A 208 " model vdw 2.573 3.440 nonbonded pdb=" O LYS D 208 " pdb=" CG LYS D 208 " model vdw 2.573 3.440 nonbonded pdb=" O LYS B 208 " pdb=" CG LYS B 208 " model vdw 2.573 3.440 ... (remaining 270690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 673 or resid 675 through 987 or resid 989 throu \ gh 1405)) selection = (chain 'B' and (resid 30 through 673 or resid 675 through 987 or resid 989 throu \ gh 1405)) selection = (chain 'C' and (resid 30 through 673 or resid 675 through 987 or resid 989 throu \ gh 1405)) selection = (chain 'D' and (resid 30 through 673 or resid 675 through 987 or resid 989 throu \ gh 1405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 41.840 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33968 Z= 0.216 Angle : 0.759 9.555 46364 Z= 0.431 Chirality : 0.049 0.481 5400 Planarity : 0.008 0.093 5716 Dihedral : 16.515 123.301 13188 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.50 % Allowed : 18.51 % Favored : 80.99 % 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: -0.45 (0.12), residues: 4248 helix: 0.23 (0.09), residues: 2692 sheet: -0.32 (0.34), residues: 272 loop : -1.23 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG C1196 TYR 0.040 0.002 TYR A 952 PHE 0.051 0.003 PHE B1173 TRP 0.033 0.003 TRP B 920 HIS 0.012 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00412 (33968) covalent geometry : angle 0.75896 (46364) hydrogen bonds : bond 0.11174 ( 2077) hydrogen bonds : angle 5.22511 ( 6191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.496 Fit side-chains REVERT: A 133 LEU cc_start: 0.9541 (mp) cc_final: 0.9303 (tp) REVERT: A 356 LEU cc_start: 0.8978 (mm) cc_final: 0.8384 (pt) REVERT: A 370 TYR cc_start: 0.8436 (m-80) cc_final: 0.8086 (m-80) REVERT: A 778 MET cc_start: 0.7894 (mtp) cc_final: 0.7542 (mtp) REVERT: D 133 LEU cc_start: 0.9560 (mp) cc_final: 0.9340 (tp) REVERT: D 356 LEU cc_start: 0.8977 (mm) cc_final: 0.8376 (pt) REVERT: D 370 TYR cc_start: 0.8445 (m-80) cc_final: 0.8088 (m-80) REVERT: D 778 MET cc_start: 0.7894 (mtp) cc_final: 0.7583 (mtp) REVERT: B 133 LEU cc_start: 0.9540 (mp) cc_final: 0.9304 (tp) REVERT: B 356 LEU cc_start: 0.8980 (mm) cc_final: 0.8378 (pt) REVERT: B 370 TYR cc_start: 0.8427 (m-80) cc_final: 0.8083 (m-80) REVERT: B 778 MET cc_start: 0.7896 (mtp) cc_final: 0.7584 (mtp) REVERT: C 133 LEU cc_start: 0.9560 (mp) cc_final: 0.9330 (tp) REVERT: C 356 LEU cc_start: 0.8974 (mm) cc_final: 0.8381 (pt) REVERT: C 370 TYR cc_start: 0.8450 (m-80) cc_final: 0.8091 (m-80) REVERT: C 778 MET cc_start: 0.7894 (mtp) cc_final: 0.7575 (mtp) outliers start: 12 outliers final: 12 residues processed: 229 average time/residue: 0.7993 time to fit residues: 216.3879 Evaluate side-chains 224 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1090 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 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 616 HIS A1092 ASN D 616 HIS D1092 ASN B 616 HIS B1092 ASN C 616 HIS C1092 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.078564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051806 restraints weight = 249792.540| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.18 r_work: 0.2779 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33968 Z= 0.172 Angle : 0.513 8.654 46364 Z= 0.267 Chirality : 0.038 0.161 5400 Planarity : 0.005 0.062 5716 Dihedral : 9.424 77.190 6316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.00 % Allowed : 18.57 % Favored : 80.43 % 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: 1.25 (0.13), residues: 4248 helix: 1.77 (0.10), residues: 2648 sheet: -0.21 (0.33), residues: 272 loop : -0.86 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.016 0.001 TYR C 958 PHE 0.011 0.001 PHE A1117 TRP 0.015 0.001 TRP D 621 HIS 0.003 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00390 (33968) covalent geometry : angle 0.51306 (46364) hydrogen bonds : bond 0.04611 ( 2077) hydrogen bonds : angle 3.92785 ( 6191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.445 Fit side-chains REVERT: A 356 LEU cc_start: 0.8963 (mm) cc_final: 0.8354 (pt) REVERT: A 370 TYR cc_start: 0.8597 (m-80) cc_final: 0.8152 (m-80) REVERT: A 778 MET cc_start: 0.7770 (mtp) cc_final: 0.7415 (mtm) REVERT: D 133 LEU cc_start: 0.9570 (mp) cc_final: 0.9299 (tp) REVERT: D 356 LEU cc_start: 0.8953 (mm) cc_final: 0.8340 (pt) REVERT: D 370 TYR cc_start: 0.8619 (m-80) cc_final: 0.8161 (m-80) REVERT: D 778 MET cc_start: 0.7774 (mtp) cc_final: 0.7419 (mtm) REVERT: B 356 LEU cc_start: 0.8958 (mm) cc_final: 0.8344 (pt) REVERT: B 370 TYR cc_start: 0.8599 (m-80) cc_final: 0.8149 (m-80) REVERT: B 778 MET cc_start: 0.7774 (mtp) cc_final: 0.7420 (mtm) REVERT: C 133 LEU cc_start: 0.9575 (mp) cc_final: 0.9298 (tp) REVERT: C 356 LEU cc_start: 0.8951 (mm) cc_final: 0.8339 (pt) REVERT: C 370 TYR cc_start: 0.8609 (m-80) cc_final: 0.8154 (m-80) REVERT: C 778 MET cc_start: 0.7785 (mtp) cc_final: 0.7432 (mtm) outliers start: 26 outliers final: 12 residues processed: 224 average time/residue: 0.7402 time to fit residues: 197.5087 Evaluate side-chains 222 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 110 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 301 optimal weight: 40.0000 chunk 309 optimal weight: 0.0020 chunk 282 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 ASN D1092 ASN B1092 ASN C1092 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052239 restraints weight = 240403.445| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.15 r_work: 0.2793 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33968 Z= 0.125 Angle : 0.462 6.330 46364 Z= 0.241 Chirality : 0.037 0.137 5400 Planarity : 0.004 0.054 5716 Dihedral : 8.094 57.959 6312 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.35 % Allowed : 18.91 % Favored : 79.74 % 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: 1.88 (0.13), residues: 4248 helix: 2.32 (0.10), residues: 2652 sheet: -0.12 (0.33), residues: 268 loop : -0.69 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.016 0.001 TYR A 958 PHE 0.009 0.001 PHE B1117 TRP 0.015 0.001 TRP A 31 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00278 (33968) covalent geometry : angle 0.46230 (46364) hydrogen bonds : bond 0.04223 ( 2077) hydrogen bonds : angle 3.78547 ( 6191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.002 Fit side-chains REVERT: A 370 TYR cc_start: 0.8579 (m-80) cc_final: 0.8122 (m-80) REVERT: A 778 MET cc_start: 0.7773 (mtp) cc_final: 0.7412 (mtp) REVERT: D 370 TYR cc_start: 0.8600 (m-80) cc_final: 0.8143 (m-80) REVERT: D 778 MET cc_start: 0.7797 (mtp) cc_final: 0.7417 (mtp) REVERT: B 370 TYR cc_start: 0.8585 (m-80) cc_final: 0.8136 (m-80) REVERT: B 778 MET cc_start: 0.7799 (mtp) cc_final: 0.7420 (mtp) REVERT: C 370 TYR cc_start: 0.8598 (m-80) cc_final: 0.8141 (m-80) REVERT: C 778 MET cc_start: 0.7796 (mtp) cc_final: 0.7429 (mtp) outliers start: 39 outliers final: 4 residues processed: 235 average time/residue: 0.7003 time to fit residues: 195.4683 Evaluate side-chains 211 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 99 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 320 optimal weight: 0.5980 chunk 233 optimal weight: 20.0000 chunk 342 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN D 716 GLN B 716 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN ** C 955 ASN ** 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 = 0.3663 r_free = 0.3663 target = 0.077363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050209 restraints weight = 259166.434| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.27 r_work: 0.2725 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33968 Z= 0.227 Angle : 0.526 6.779 46364 Z= 0.274 Chirality : 0.040 0.159 5400 Planarity : 0.004 0.050 5716 Dihedral : 7.596 58.258 6284 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.57 % Allowed : 18.79 % Favored : 79.64 % 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: 1.98 (0.13), residues: 4248 helix: 2.41 (0.10), residues: 2660 sheet: -0.48 (0.30), residues: 316 loop : -0.59 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.016 0.001 TYR A1028 PHE 0.014 0.001 PHE A1117 TRP 0.014 0.001 TRP C 740 HIS 0.005 0.001 HIS D 616 Details of bonding type rmsd covalent geometry : bond 0.00527 (33968) covalent geometry : angle 0.52648 (46364) hydrogen bonds : bond 0.04868 ( 2077) hydrogen bonds : angle 3.88745 ( 6191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.960 Fit side-chains REVERT: A 356 LEU cc_start: 0.8940 (mm) cc_final: 0.8315 (pt) REVERT: A 370 TYR cc_start: 0.8623 (m-80) cc_final: 0.8132 (m-80) REVERT: A 778 MET cc_start: 0.7926 (mtp) cc_final: 0.7562 (mtm) REVERT: D 356 LEU cc_start: 0.8941 (mm) cc_final: 0.8304 (pt) REVERT: D 370 TYR cc_start: 0.8610 (m-80) cc_final: 0.8121 (m-80) REVERT: D 778 MET cc_start: 0.7960 (mtp) cc_final: 0.7597 (mtm) REVERT: B 356 LEU cc_start: 0.8956 (mm) cc_final: 0.8355 (pt) REVERT: B 370 TYR cc_start: 0.8607 (m-80) cc_final: 0.8120 (m-80) REVERT: B 778 MET cc_start: 0.7961 (mtp) cc_final: 0.7597 (mtm) REVERT: C 356 LEU cc_start: 0.8931 (mm) cc_final: 0.8303 (pt) REVERT: C 370 TYR cc_start: 0.8605 (m-80) cc_final: 0.8117 (m-80) REVERT: C 778 MET cc_start: 0.7930 (mtp) cc_final: 0.7567 (mtm) outliers start: 46 outliers final: 8 residues processed: 231 average time/residue: 0.6526 time to fit residues: 180.2405 Evaluate side-chains 216 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 987 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 287 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051116 restraints weight = 240256.955| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.11 r_work: 0.2757 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33968 Z= 0.152 Angle : 0.483 7.399 46364 Z= 0.251 Chirality : 0.038 0.137 5400 Planarity : 0.004 0.049 5716 Dihedral : 7.390 59.249 6284 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.19 % Allowed : 19.89 % Favored : 78.92 % 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: 2.14 (0.13), residues: 4248 helix: 2.55 (0.10), residues: 2660 sheet: -0.48 (0.30), residues: 316 loop : -0.54 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.017 0.001 TYR A 958 PHE 0.011 0.001 PHE B1117 TRP 0.014 0.001 TRP D 740 HIS 0.004 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00345 (33968) covalent geometry : angle 0.48334 (46364) hydrogen bonds : bond 0.04450 ( 2077) hydrogen bonds : angle 3.77857 ( 6191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.051 Fit side-chains REVERT: A 37 TYR cc_start: 0.8714 (m-10) cc_final: 0.8468 (m-80) REVERT: A 370 TYR cc_start: 0.8590 (m-80) cc_final: 0.8105 (m-80) REVERT: A 778 MET cc_start: 0.7930 (mtp) cc_final: 0.7563 (mtm) REVERT: D 37 TYR cc_start: 0.8761 (m-10) cc_final: 0.8472 (m-80) REVERT: D 370 TYR cc_start: 0.8604 (m-80) cc_final: 0.8111 (m-80) REVERT: D 778 MET cc_start: 0.7980 (mtp) cc_final: 0.7612 (mtm) REVERT: B 37 TYR cc_start: 0.8752 (m-10) cc_final: 0.8459 (m-80) REVERT: B 370 TYR cc_start: 0.8586 (m-80) cc_final: 0.8102 (m-80) REVERT: B 778 MET cc_start: 0.7975 (mtp) cc_final: 0.7606 (mtm) REVERT: C 37 TYR cc_start: 0.8756 (m-10) cc_final: 0.8470 (m-80) REVERT: C 370 TYR cc_start: 0.8594 (m-80) cc_final: 0.8103 (m-80) REVERT: C 778 MET cc_start: 0.7936 (mtp) cc_final: 0.7569 (mtm) outliers start: 34 outliers final: 12 residues processed: 237 average time/residue: 0.7106 time to fit residues: 201.2341 Evaluate side-chains 223 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 987 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 401 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 358 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 421 optimal weight: 1.9990 chunk 349 optimal weight: 30.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050908 restraints weight = 255955.816| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.22 r_work: 0.2746 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33968 Z= 0.165 Angle : 0.489 6.617 46364 Z= 0.253 Chirality : 0.038 0.138 5400 Planarity : 0.004 0.047 5716 Dihedral : 7.264 59.832 6284 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.44 % Allowed : 19.76 % Favored : 78.80 % 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: 2.20 (0.13), residues: 4248 helix: 2.57 (0.10), residues: 2664 sheet: -0.44 (0.30), residues: 316 loop : -0.46 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 210 TYR 0.016 0.001 TYR A 958 PHE 0.012 0.001 PHE A1117 TRP 0.014 0.001 TRP D 740 HIS 0.004 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00379 (33968) covalent geometry : angle 0.48924 (46364) hydrogen bonds : bond 0.04481 ( 2077) hydrogen bonds : angle 3.76457 ( 6191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.394 Fit side-chains REVERT: A 37 TYR cc_start: 0.8752 (m-10) cc_final: 0.8522 (m-80) REVERT: A 179 MET cc_start: 0.8403 (tpt) cc_final: 0.8100 (tpt) REVERT: A 370 TYR cc_start: 0.8605 (m-80) cc_final: 0.8105 (m-80) REVERT: A 778 MET cc_start: 0.7944 (mtp) cc_final: 0.7569 (mtm) REVERT: D 37 TYR cc_start: 0.8760 (m-10) cc_final: 0.8494 (m-80) REVERT: D 356 LEU cc_start: 0.8871 (mm) cc_final: 0.8246 (pt) REVERT: D 370 TYR cc_start: 0.8626 (m-80) cc_final: 0.8119 (m-80) REVERT: D 778 MET cc_start: 0.7982 (mtp) cc_final: 0.7610 (mtm) REVERT: B 37 TYR cc_start: 0.8755 (m-10) cc_final: 0.8479 (m-80) REVERT: B 356 LEU cc_start: 0.8872 (mm) cc_final: 0.8243 (pt) REVERT: B 370 TYR cc_start: 0.8598 (m-80) cc_final: 0.8099 (m-80) REVERT: B 778 MET cc_start: 0.7978 (mtp) cc_final: 0.7606 (mtm) REVERT: C 37 TYR cc_start: 0.8747 (m-10) cc_final: 0.8483 (m-80) REVERT: C 179 MET cc_start: 0.8412 (tpt) cc_final: 0.8108 (tpt) REVERT: C 370 TYR cc_start: 0.8617 (m-80) cc_final: 0.8112 (m-80) REVERT: C 778 MET cc_start: 0.7954 (mtp) cc_final: 0.7581 (mtm) outliers start: 42 outliers final: 14 residues processed: 237 average time/residue: 0.7093 time to fit residues: 201.1205 Evaluate side-chains 226 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 987 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 346 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 354 optimal weight: 0.3980 chunk 278 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 396 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052653 restraints weight = 261026.366| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.29 r_work: 0.2796 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33968 Z= 0.100 Angle : 0.451 6.919 46364 Z= 0.234 Chirality : 0.037 0.131 5400 Planarity : 0.004 0.048 5716 Dihedral : 6.991 59.834 6284 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.56 % Allowed : 20.55 % Favored : 78.89 % 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: 2.33 (0.13), residues: 4248 helix: 2.62 (0.10), residues: 2700 sheet: -0.38 (0.30), residues: 316 loop : -0.39 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 210 TYR 0.018 0.001 TYR A 958 PHE 0.008 0.001 PHE B 679 TRP 0.015 0.001 TRP D 740 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00208 (33968) covalent geometry : angle 0.45087 (46364) hydrogen bonds : bond 0.03914 ( 2077) hydrogen bonds : angle 3.62701 ( 6191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 1.333 Fit side-chains REVERT: A 179 MET cc_start: 0.8445 (tpt) cc_final: 0.8192 (tpt) REVERT: A 356 LEU cc_start: 0.8873 (mm) cc_final: 0.8277 (pt) REVERT: A 370 TYR cc_start: 0.8612 (m-80) cc_final: 0.8131 (m-80) REVERT: A 778 MET cc_start: 0.7886 (mtp) cc_final: 0.7521 (mtm) REVERT: D 37 TYR cc_start: 0.8752 (m-10) cc_final: 0.8507 (m-10) REVERT: D 179 MET cc_start: 0.8433 (tpt) cc_final: 0.8187 (tpt) REVERT: D 370 TYR cc_start: 0.8590 (m-80) cc_final: 0.8109 (m-80) REVERT: D 778 MET cc_start: 0.7913 (mtp) cc_final: 0.7552 (mtm) REVERT: B 37 TYR cc_start: 0.8738 (m-10) cc_final: 0.8495 (m-80) REVERT: B 179 MET cc_start: 0.8492 (tpt) cc_final: 0.8127 (tpt) REVERT: B 370 TYR cc_start: 0.8608 (m-80) cc_final: 0.8129 (m-80) REVERT: B 778 MET cc_start: 0.7912 (mtp) cc_final: 0.7552 (mtm) REVERT: C 37 TYR cc_start: 0.8735 (m-10) cc_final: 0.8494 (m-10) REVERT: C 179 MET cc_start: 0.8457 (tpt) cc_final: 0.8205 (tpt) REVERT: C 356 LEU cc_start: 0.8845 (mm) cc_final: 0.8252 (pt) REVERT: C 370 TYR cc_start: 0.8588 (m-80) cc_final: 0.8107 (m-80) REVERT: C 778 MET cc_start: 0.7899 (mtp) cc_final: 0.7538 (mtm) outliers start: 14 outliers final: 3 residues processed: 225 average time/residue: 0.7454 time to fit residues: 198.7262 Evaluate side-chains 215 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 403 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 407 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 246 optimal weight: 7.9990 chunk 305 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 378 optimal weight: 7.9990 chunk 406 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052968 restraints weight = 233148.904| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.07 r_work: 0.2813 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33968 Z= 0.102 Angle : 0.452 6.858 46364 Z= 0.233 Chirality : 0.036 0.133 5400 Planarity : 0.004 0.046 5716 Dihedral : 6.850 59.852 6284 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.53 % Allowed : 20.67 % Favored : 78.80 % 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: 2.45 (0.13), residues: 4248 helix: 2.69 (0.10), residues: 2700 sheet: -0.14 (0.31), residues: 308 loop : -0.34 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 210 TYR 0.017 0.001 TYR A 958 PHE 0.008 0.001 PHE B1117 TRP 0.015 0.001 TRP D 740 HIS 0.002 0.000 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00219 (33968) covalent geometry : angle 0.45159 (46364) hydrogen bonds : bond 0.03839 ( 2077) hydrogen bonds : angle 3.57205 ( 6191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8414 (tpt) cc_final: 0.8108 (tpt) REVERT: A 370 TYR cc_start: 0.8583 (m-80) cc_final: 0.8131 (m-80) REVERT: A 778 MET cc_start: 0.7844 (mtp) cc_final: 0.7485 (mtm) REVERT: D 37 TYR cc_start: 0.8776 (m-10) cc_final: 0.8549 (m-10) REVERT: D 179 MET cc_start: 0.8414 (tpt) cc_final: 0.8120 (tpt) REVERT: D 370 TYR cc_start: 0.8567 (m-80) cc_final: 0.8105 (m-80) REVERT: D 778 MET cc_start: 0.7900 (mtp) cc_final: 0.7547 (mtm) REVERT: B 37 TYR cc_start: 0.8804 (m-10) cc_final: 0.8567 (m-80) REVERT: B 179 MET cc_start: 0.8491 (tpt) cc_final: 0.8155 (tpt) REVERT: B 370 TYR cc_start: 0.8572 (m-80) cc_final: 0.8120 (m-80) REVERT: B 778 MET cc_start: 0.7893 (mtp) cc_final: 0.7539 (mtm) REVERT: C 37 TYR cc_start: 0.8770 (m-10) cc_final: 0.8537 (m-10) REVERT: C 179 MET cc_start: 0.8422 (tpt) cc_final: 0.8123 (tpt) REVERT: C 370 TYR cc_start: 0.8571 (m-80) cc_final: 0.8107 (m-80) REVERT: C 778 MET cc_start: 0.7852 (mtp) cc_final: 0.7496 (mtm) outliers start: 13 outliers final: 5 residues processed: 223 average time/residue: 0.7567 time to fit residues: 199.7573 Evaluate side-chains 219 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 214 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 364 optimal weight: 5.9990 chunk 301 optimal weight: 40.0000 chunk 216 optimal weight: 9.9990 chunk 419 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 349 optimal weight: 30.0000 chunk 209 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052440 restraints weight = 270876.475| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.36 r_work: 0.2789 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33968 Z= 0.116 Angle : 0.459 6.783 46364 Z= 0.236 Chirality : 0.037 0.134 5400 Planarity : 0.004 0.045 5716 Dihedral : 6.800 59.819 6284 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.44 % Allowed : 20.55 % Favored : 79.02 % 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: 2.49 (0.13), residues: 4248 helix: 2.71 (0.10), residues: 2700 sheet: -0.11 (0.31), residues: 308 loop : -0.30 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 210 TYR 0.016 0.001 TYR A 958 PHE 0.009 0.001 PHE A1117 TRP 0.014 0.001 TRP D 740 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00257 (33968) covalent geometry : angle 0.45871 (46364) hydrogen bonds : bond 0.03932 ( 2077) hydrogen bonds : angle 3.58381 ( 6191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8454 (tpt) cc_final: 0.8156 (tpt) REVERT: A 370 TYR cc_start: 0.8605 (m-80) cc_final: 0.8148 (m-80) REVERT: A 778 MET cc_start: 0.7849 (mtp) cc_final: 0.7491 (mtm) REVERT: D 37 TYR cc_start: 0.8783 (m-10) cc_final: 0.8558 (m-10) REVERT: D 179 MET cc_start: 0.8464 (tpt) cc_final: 0.8172 (tpt) REVERT: D 370 TYR cc_start: 0.8581 (m-80) cc_final: 0.8118 (m-80) REVERT: D 778 MET cc_start: 0.7899 (mtp) cc_final: 0.7546 (mtm) REVERT: B 37 TYR cc_start: 0.8792 (m-10) cc_final: 0.8555 (m-80) REVERT: B 370 TYR cc_start: 0.8585 (m-80) cc_final: 0.8129 (m-80) REVERT: B 778 MET cc_start: 0.7895 (mtp) cc_final: 0.7542 (mtm) REVERT: C 37 TYR cc_start: 0.8784 (m-10) cc_final: 0.8554 (m-80) REVERT: C 179 MET cc_start: 0.8454 (tpt) cc_final: 0.8156 (tpt) REVERT: C 370 TYR cc_start: 0.8581 (m-80) cc_final: 0.8117 (m-80) REVERT: C 778 MET cc_start: 0.7872 (mtp) cc_final: 0.7515 (mtm) outliers start: 10 outliers final: 6 residues processed: 222 average time/residue: 0.7072 time to fit residues: 186.3233 Evaluate side-chains 218 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 366 optimal weight: 10.0000 chunk 349 optimal weight: 30.0000 chunk 377 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 272 optimal weight: 0.8980 chunk 230 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 352 optimal weight: 20.0000 chunk 229 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052615 restraints weight = 272204.696| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.37 r_work: 0.2795 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33968 Z= 0.109 Angle : 0.457 6.779 46364 Z= 0.236 Chirality : 0.037 0.133 5400 Planarity : 0.004 0.045 5716 Dihedral : 6.709 59.848 6284 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.35 % Allowed : 20.64 % Favored : 79.02 % 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: 2.52 (0.13), residues: 4248 helix: 2.74 (0.10), residues: 2696 sheet: -0.10 (0.31), residues: 308 loop : -0.31 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 210 TYR 0.016 0.001 TYR A 958 PHE 0.008 0.001 PHE A1117 TRP 0.014 0.001 TRP D 740 HIS 0.002 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00241 (33968) covalent geometry : angle 0.45690 (46364) hydrogen bonds : bond 0.03881 ( 2077) hydrogen bonds : angle 3.55984 ( 6191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8471 (tpt) cc_final: 0.8166 (tpt) REVERT: A 370 TYR cc_start: 0.8581 (m-80) cc_final: 0.8133 (m-80) REVERT: A 778 MET cc_start: 0.7848 (mtp) cc_final: 0.7492 (mtm) REVERT: D 37 TYR cc_start: 0.8788 (m-10) cc_final: 0.8560 (m-80) REVERT: D 179 MET cc_start: 0.8444 (tpt) cc_final: 0.8146 (tpt) REVERT: D 370 TYR cc_start: 0.8583 (m-80) cc_final: 0.8129 (m-80) REVERT: D 778 MET cc_start: 0.7874 (mtp) cc_final: 0.7526 (mtm) REVERT: B 37 TYR cc_start: 0.8791 (m-10) cc_final: 0.8579 (m-10) REVERT: B 179 MET cc_start: 0.8487 (tpt) cc_final: 0.8128 (tpt) REVERT: B 370 TYR cc_start: 0.8567 (m-80) cc_final: 0.8121 (m-80) REVERT: B 778 MET cc_start: 0.7866 (mtp) cc_final: 0.7518 (mtm) REVERT: C 179 MET cc_start: 0.8467 (tpt) cc_final: 0.8162 (tpt) REVERT: C 370 TYR cc_start: 0.8580 (m-80) cc_final: 0.8125 (m-80) REVERT: C 778 MET cc_start: 0.7851 (mtp) cc_final: 0.7497 (mtm) outliers start: 7 outliers final: 7 residues processed: 218 average time/residue: 0.7361 time to fit residues: 190.1951 Evaluate side-chains 219 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 369 optimal weight: 3.9990 chunk 356 optimal weight: 7.9990 chunk 389 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 377 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.078656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051997 restraints weight = 252225.231| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.22 r_work: 0.2776 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33968 Z= 0.138 Angle : 0.473 6.712 46364 Z= 0.243 Chirality : 0.037 0.136 5400 Planarity : 0.004 0.045 5716 Dihedral : 6.742 59.996 6284 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.35 % Allowed : 20.51 % Favored : 79.14 % 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: 2.54 (0.13), residues: 4248 helix: 2.75 (0.10), residues: 2676 sheet: -0.09 (0.31), residues: 308 loop : -0.22 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 210 TYR 0.015 0.001 TYR A 958 PHE 0.010 0.001 PHE A1117 TRP 0.014 0.001 TRP B 740 HIS 0.003 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00316 (33968) covalent geometry : angle 0.47317 (46364) hydrogen bonds : bond 0.04117 ( 2077) hydrogen bonds : angle 3.61966 ( 6191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13962.14 seconds wall clock time: 237 minutes 53.17 seconds (14273.17 seconds total)