Starting phenix.real_space_refine on Sat Feb 7 14:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7w_70209/02_2026/9o7w_70209.map" } resolution = 3.2 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 243 5.16 5 C 21499 2.51 5 N 5458 2.21 5 O 5660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s 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: 32860 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8037 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8029 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 735 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 380 Conformer: "B" Number of residues, atoms: 1061, 8029 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 735 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 380 bond proxies already assigned to first conformer: 8205 Chain: "B" Number of atoms: 7908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 7908 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1006} Chain breaks: 8 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 14, 'ASP:plan': 13, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 385 Chain: "C" Number of atoms: 8034 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8026 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, '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: 383 Conformer: "B" Number of residues, atoms: 1061, 8026 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, '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: 383 bond proxies already assigned to first conformer: 8202 Chain: "D" Number of atoms: 8041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8033 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 13, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 376 Conformer: "B" Number of residues, atoms: 1061, 8033 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 13, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 376 bond proxies already assigned to first conformer: 8209 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "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} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AMET A 988 " occ=0.56 ... (14 atoms not shown) pdb=" CE BMET A 988 " occ=0.44 residue: pdb=" N AMET C 988 " occ=0.53 ... (14 atoms not shown) pdb=" CE BMET C 988 " occ=0.47 residue: pdb=" N AMET D 988 " occ=0.55 ... (14 atoms not shown) pdb=" CE BMET D 988 " occ=0.45 Time building chain proxies: 12.56, per 1000 atoms: 0.38 Number of scatterers: 32860 At special positions: 0 Unit cell: (136.29, 135.464, 160.244, 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 243 16.00 O 5660 8.00 N 5458 7.00 C 21499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.04 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.04 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: 2.93 Conformation dependent library (CDL) restraints added in 2.4 seconds 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7984 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 14 sheets defined 67.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.692A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.576A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.632A pdb=" N ILE A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.646A 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 227 through 231 removed outlier: 3.720A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.578A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.172A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.510A pdb=" N ARG A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 4.111A 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: 3.856A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.699A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.617A 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: 3.621A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.786A pdb=" N GLY A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 4.176A pdb=" N LEU A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 847 through 872 Processing helix chain 'A' and resid 879 through 902 Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'A' and resid 918 through 940 removed outlier: 3.670A pdb=" N GLN A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 968 removed outlier: 3.741A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 4.588A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.626A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.788A 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: 3.767A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1094 removed outlier: 3.919A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.640A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.404A 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: 4.296A 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 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.038A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.733A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.672A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.951A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.643A pdb=" N ASP B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.533A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (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 566 Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.948A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.566A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.638A 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: 3.795A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 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 916 Processing helix chain 'B' and resid 918 through 940 removed outlier: 3.508A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 968 removed outlier: 3.722A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.540A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.729A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.804A 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: 3.774A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1094 removed outlier: 3.921A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.645A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.447A 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: 4.417A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B1141 " --> pdb=" O PHE B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.877A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 3.561A pdb=" N ARG B1196 " --> pdb=" O SER B1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.805A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.569A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 209 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.630A pdb=" N ILE C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.651A 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 227 through 231 removed outlier: 3.731A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.580A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 4.183A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.954A 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: 4.107A 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 removed outlier: 3.511A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) 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: 3.834A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.729A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.681A 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: 3.622A 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: 3.599A 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 767 removed outlier: 4.203A pdb=" N LEU C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 846 Processing helix chain 'C' and resid 847 through 872 Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 916 Processing helix chain 'C' and resid 918 through 939 Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.654A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 4.609A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.604A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.802A 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: 3.717A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1094 removed outlier: 3.922A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL C1084 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C1094 " --> pdb=" O VAL C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 4.625A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1126 No H-bonds generated for 'chain 'C' and resid 1124 through 1126' Processing helix chain 'C' and resid 1127 through 1145 removed outlier: 4.284A 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 helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.730A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.525A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.634A pdb=" N ILE D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.657A 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 227 through 231 removed outlier: 3.719A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.566A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.839A 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: 3.995A 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: 3.864A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.733A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.670A 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: 3.616A 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: 3.618A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.729A pdb=" N GLY D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 761 through 767 removed outlier: 4.213A pdb=" N LEU D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 846 Processing helix chain 'D' and resid 847 through 872 Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 916 Processing helix chain 'D' and resid 918 through 939 Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.736A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.599A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.625A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.776A 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: 3.756A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1094 removed outlier: 3.916A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 3.527A pdb=" N VAL D1098 " --> pdb=" O THR D1094 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.408A 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: 4.355A 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 sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.699A 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: 6.700A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.945A 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: 6.404A 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: 6.304A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 240 removed outlier: 7.036A pdb=" N PHE B 106 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 108 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU B 261 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP B 263 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 155 removed outlier: 8.145A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.684A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.696A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 261 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 123 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP C 263 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.307A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.682A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.683A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.397A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 removed outlier: 6.301A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) 2066 hydrogen bonds defined for protein. 6144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 3.91 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: 5657 1.32 - 1.45: 8495 1.45 - 1.58: 19108 1.58 - 1.70: 0 1.70 - 1.83: 410 Bond restraints: 33670 Sorted by residual: bond pdb=" C LEU B 414 " pdb=" O LEU B 414 " ideal model delta sigma weight residual 1.236 1.296 -0.059 1.15e-02 7.56e+03 2.66e+01 bond pdb=" C ILE B 380 " pdb=" O ILE B 380 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" CA SER C1201 " pdb=" CB SER C1201 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.55e-02 4.16e+03 1.35e+01 bond pdb=" C GLU A1216 " pdb=" O GLU A1216 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" CA SER D1201 " pdb=" CB SER D1201 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.55e-02 4.16e+03 1.17e+01 ... (remaining 33665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 44226 2.34 - 4.68: 1479 4.68 - 7.02: 168 7.02 - 9.36: 58 9.36 - 11.70: 11 Bond angle restraints: 45942 Sorted by residual: angle pdb=" C LYS B 389 " pdb=" CA LYS B 389 " pdb=" CB LYS B 389 " ideal model delta sigma weight residual 110.42 98.88 11.54 1.99e+00 2.53e-01 3.36e+01 angle pdb=" CB LYS C 212 " pdb=" CG LYS C 212 " pdb=" CD LYS C 212 " ideal model delta sigma weight residual 111.30 123.00 -11.70 2.30e+00 1.89e-01 2.59e+01 angle pdb=" N PRO D1125 " pdb=" CA PRO D1125 " pdb=" C PRO D1125 " ideal model delta sigma weight residual 110.70 116.82 -6.12 1.22e+00 6.72e-01 2.51e+01 angle pdb=" C SER C 207 " pdb=" N LYS C 208 " pdb=" CA LYS C 208 " ideal model delta sigma weight residual 122.08 114.21 7.87 1.59e+00 3.96e-01 2.45e+01 angle pdb=" CA LYS B 148 " pdb=" CB LYS B 148 " pdb=" CG LYS B 148 " ideal model delta sigma weight residual 114.10 123.89 -9.79 2.00e+00 2.50e-01 2.40e+01 ... (remaining 45937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 19642 24.44 - 48.88: 1233 48.88 - 73.33: 195 73.33 - 97.77: 7 97.77 - 122.21: 12 Dihedral angle restraints: 21089 sinusoidal: 8749 harmonic: 12340 Sorted by residual: dihedral pdb=" CA ILE B1162 " pdb=" C ILE B1162 " pdb=" N THR B1163 " pdb=" CA THR B1163 " ideal model delta harmonic sigma weight residual -180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA CYS B 214 " pdb=" C CYS B 214 " pdb=" N THR B 215 " pdb=" CA THR B 215 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LYS B 148 " pdb=" C LYS B 148 " pdb=" N LEU B 149 " pdb=" CA LEU B 149 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 21086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4443 0.070 - 0.141: 789 0.141 - 0.211: 102 0.211 - 0.281: 17 0.281 - 0.351: 4 Chirality restraints: 5355 Sorted by residual: chirality pdb=" CB ILE B1129 " pdb=" CA ILE B1129 " pdb=" CG1 ILE B1129 " pdb=" CG2 ILE B1129 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB THR B 215 " pdb=" CA THR B 215 " pdb=" OG1 THR B 215 " pdb=" CG2 THR B 215 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE D1129 " pdb=" CA ILE D1129 " pdb=" CG1 ILE D1129 " pdb=" CG2 ILE D1129 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 5352 not shown) Planarity restraints: 5655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 854 " -0.052 2.00e-02 2.50e+03 4.84e-02 4.10e+01 pdb=" CG PHE B 854 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 PHE B 854 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 854 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 854 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 854 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 854 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 866 " -0.028 2.00e-02 2.50e+03 3.04e-02 1.62e+01 pdb=" CG PHE B 866 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE B 866 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 866 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 866 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 866 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 866 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 393 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.53e+01 pdb=" C THR B 393 " -0.068 2.00e-02 2.50e+03 pdb=" O THR B 393 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 394 " 0.022 2.00e-02 2.50e+03 ... (remaining 5652 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 84 2.64 - 3.21: 28954 3.21 - 3.77: 52955 3.77 - 4.34: 69402 4.34 - 4.90: 114595 Nonbonded interactions: 265990 Sorted by model distance: nonbonded pdb=" O ASN C1047 " pdb=" OD1 ASN C1047 " model vdw 2.075 3.040 nonbonded pdb=" O ASN D1047 " pdb=" OD1 ASN D1047 " model vdw 2.100 3.040 nonbonded pdb=" OD1 ASP B 406 " pdb=" N LEU B 407 " model vdw 2.187 3.120 nonbonded pdb=" OE2 GLU A 895 " pdb=" NH2 ARG A 898 " model vdw 2.243 3.120 nonbonded pdb=" OE2 GLU A1180 " pdb=" NE ARG D 210 " model vdw 2.252 3.120 ... (remaining 265985 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 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 241 or resid 249 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 0 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 357 or (resid 358 through 360 and (name N or name CA o \ r name C or name O or name CB )) or resid 361 through 385 or (resid 386 through \ 387 and (name N or name CA or name C or name O or name CB )) or resid 388 or (re \ sid 389 and (name N or name CA or name C or name O or name CB )) or resid 390 th \ rough 394 or (resid 395 through 397 and (name N or name CA or name C or name O o \ r name CB )) or resid 398 or resid 404 through 406 or (resid 407 through 408 and \ (name N or name CA or name C or name O or name CB )) or resid 409 through 412 o \ r (resid 413 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 14 through 480 or (resid 481 and (name N or name CA or name C or name O or name \ CB )) or resid 482 through 649 or (resid 650 and (name N or name CA or name C or \ name O or name CB )) or resid 651 through 986 or (resid 987 and (name N or name \ CA or name C or name O or name CB )) or resid 989 through 1161 or (resid 1162 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1163 through 14 \ 06)) selection = (chain 'B' and (resid 30 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 357 or (resid 358 through 360 a \ nd (name N or name CA or name C or name O or name CB )) or resid 361 through 480 \ or (resid 481 and (name N or name CA or name C or name O or name CB )) or resid \ 482 through 987 or resid 989 through 1406)) selection = (chain 'C' and (resid 30 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 241 or resid 249 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 0 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 385 or (resid 386 through 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 or (resid 389 and (name N or name \ CA or name C or name O or name CB )) or resid 390 through 394 or (resid 395 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ resid 404 through 406 or (resid 407 through 408 and (name N or name CA or name \ C or name O or name CB )) or resid 409 through 412 or (resid 413 and (name N or \ name CA or name C or name O or name CB )) or resid 414 through 494 or (resid 495 \ and (name N or name CA or name C or name O or name CB )) or resid 496 through 6 \ 49 or (resid 650 and (name N or name CA or name C or name O or name CB )) or res \ id 651 through 986 or (resid 987 and (name N or name CA or name C or name O or n \ ame CB )) or resid 989 through 1161 or (resid 1162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1163 through 1406)) selection = (chain 'D' and (resid 30 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 241 or resid 249 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 0 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 357 or (resid 358 through 360 and (name N or name CA o \ r name C or name O or name CB )) or resid 361 through 385 or (resid 386 through \ 387 and (name N or name CA or name C or name O or name CB )) or resid 388 or (re \ sid 389 and (name N or name CA or name C or name O or name CB )) or resid 390 th \ rough 394 or (resid 395 through 397 and (name N or name CA or name C or name O o \ r name CB )) or resid 398 or resid 404 through 406 or (resid 407 through 408 and \ (name N or name CA or name C or name O or name CB )) or resid 409 through 412 o \ r (resid 413 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 14 through 480 or (resid 481 and (name N or name CA or name C or name O or name \ CB )) or resid 482 through 649 or (resid 650 and (name N or name CA or name C or \ name O or name CB )) or resid 651 through 986 or (resid 987 and (name N or name \ CA or name C or name O or name CB )) or resid 989 through 1161 or (resid 1162 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1163 through 11 \ 94 or (resid 1195 and (name N or name CA or name C or name O or name CB )) or re \ sid 1196 through 1406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.240 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33674 Z= 0.340 Angle : 0.957 11.700 45950 Z= 0.575 Chirality : 0.056 0.351 5355 Planarity : 0.008 0.109 5655 Dihedral : 15.650 122.209 13093 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 0.60 % Allowed : 15.66 % Favored : 83.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.68 % 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: -1.10 (0.11), residues: 4181 helix: -0.31 (0.09), residues: 2658 sheet: -0.63 (0.35), residues: 244 loop : -1.40 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 357 TYR 0.041 0.002 TYR B1181 PHE 0.110 0.003 PHE B 854 TRP 0.050 0.002 TRP B 184 HIS 0.013 0.002 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00600 (33670) covalent geometry : angle 0.95655 (45942) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.05745 ( 8) hydrogen bonds : bond 0.12987 ( 2066) hydrogen bonds : angle 5.87843 ( 6144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8963 (mmm) cc_final: 0.8630 (mmm) REVERT: A 370 TYR cc_start: 0.8259 (m-80) cc_final: 0.7957 (m-10) REVERT: B 184 TRP cc_start: 0.7419 (m-10) cc_final: 0.7214 (m-10) REVERT: B 212 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5922 (ttpt) REVERT: B 239 TYR cc_start: 0.6853 (t80) cc_final: 0.6586 (t80) REVERT: B 255 MET cc_start: 0.7428 (mmp) cc_final: 0.7226 (mmp) REVERT: B 388 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7008 (mptt) REVERT: B 746 MET cc_start: 0.8316 (ttm) cc_final: 0.7977 (ttt) REVERT: C 121 MET cc_start: 0.8587 (mmm) cc_final: 0.8200 (mmm) REVERT: C 370 TYR cc_start: 0.8673 (m-80) cc_final: 0.8405 (m-80) REVERT: C 625 MET cc_start: 0.9168 (mtp) cc_final: 0.8741 (mtt) REVERT: C 778 MET cc_start: 0.7309 (mtp) cc_final: 0.7071 (mtm) REVERT: C 1207 MET cc_start: 0.8859 (ttm) cc_final: 0.8618 (mtm) REVERT: D 37 TYR cc_start: 0.9132 (m-10) cc_final: 0.8928 (m-80) REVERT: D 121 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8430 (mmm) outliers start: 19 outliers final: 7 residues processed: 274 average time/residue: 0.2235 time to fit residues: 100.0617 Evaluate side-chains 239 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 229 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 1062 LYS Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1204 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.0770 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS B 955 ASN B1092 ASN B1093 ASN B1215 ASN C1092 ASN C1215 ASN D 240 GLN D 402 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.083356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056635 restraints weight = 226189.545| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.39 r_work: 0.2768 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 33674 Z= 0.113 Angle : 0.512 8.336 45950 Z= 0.266 Chirality : 0.037 0.186 5355 Planarity : 0.005 0.069 5655 Dihedral : 8.816 84.956 6252 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.04 % Allowed : 15.37 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 0.77 (0.13), residues: 4181 helix: 1.37 (0.10), residues: 2656 sheet: -0.72 (0.32), residues: 280 loop : -0.99 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 210 TYR 0.019 0.001 TYR C 345 PHE 0.049 0.001 PHE B 854 TRP 0.026 0.001 TRP B 142 HIS 0.011 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00236 (33670) covalent geometry : angle 0.51166 (45942) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.53584 ( 8) hydrogen bonds : bond 0.04368 ( 2066) hydrogen bonds : angle 4.14743 ( 6144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.184 Fit side-chains REVERT: A 121 MET cc_start: 0.9025 (mmm) cc_final: 0.8570 (mmm) REVERT: A 370 TYR cc_start: 0.8205 (m-80) cc_final: 0.7919 (m-10) REVERT: B 142 TRP cc_start: 0.6309 (m-10) cc_final: 0.6103 (m-10) REVERT: B 252 LEU cc_start: 0.8221 (mt) cc_final: 0.7912 (pp) REVERT: B 255 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7229 (mmp) REVERT: B 897 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8691 (ttp) REVERT: C 121 MET cc_start: 0.8698 (mmm) cc_final: 0.8344 (mmm) REVERT: C 625 MET cc_start: 0.9169 (mtp) cc_final: 0.8685 (mtt) REVERT: C 778 MET cc_start: 0.7466 (mtp) cc_final: 0.7213 (mtm) REVERT: D 37 TYR cc_start: 0.9126 (m-10) cc_final: 0.8922 (m-80) REVERT: D 121 MET cc_start: 0.9056 (mmm) cc_final: 0.8782 (mmm) REVERT: D 255 MET cc_start: 0.8174 (ttm) cc_final: 0.7958 (ttp) REVERT: D 457 MET cc_start: 0.9385 (tpp) cc_final: 0.9120 (tpt) REVERT: D 625 MET cc_start: 0.9220 (mtt) cc_final: 0.8962 (mtt) outliers start: 33 outliers final: 7 residues processed: 258 average time/residue: 0.2004 time to fit residues: 88.7271 Evaluate side-chains 232 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 978 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 214 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS A 955 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN D 402 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.079122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051435 restraints weight = 197851.736| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.22 r_work: 0.2608 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33674 Z= 0.262 Angle : 0.613 10.500 45950 Z= 0.314 Chirality : 0.042 0.280 5355 Planarity : 0.005 0.063 5655 Dihedral : 7.576 58.891 6233 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.88 % Allowed : 15.44 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 1.40 (0.13), residues: 4181 helix: 1.95 (0.10), residues: 2615 sheet: -0.45 (0.32), residues: 279 loop : -0.88 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 210 TYR 0.037 0.002 TYR C 370 PHE 0.037 0.002 PHE B 854 TRP 0.029 0.002 TRP B 184 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00606 (33670) covalent geometry : angle 0.61311 (45942) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.55609 ( 8) hydrogen bonds : bond 0.05270 ( 2066) hydrogen bonds : angle 4.15800 ( 6144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.9070 (mmm) cc_final: 0.8468 (mmm) REVERT: A 370 TYR cc_start: 0.8379 (m-80) cc_final: 0.8052 (m-10) REVERT: A 671 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8671 (tt0) REVERT: A 875 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8835 (mm-30) REVERT: B 255 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6999 (mmp) REVERT: B 778 MET cc_start: 0.7652 (ptm) cc_final: 0.7090 (ptm) REVERT: B 897 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (mtp) REVERT: C 121 MET cc_start: 0.8782 (mmm) cc_final: 0.8482 (mmm) REVERT: C 625 MET cc_start: 0.9236 (mtp) cc_final: 0.9031 (mtp) REVERT: C 778 MET cc_start: 0.7755 (mtp) cc_final: 0.7521 (mtm) REVERT: C 987 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8539 (tmm) REVERT: D 37 TYR cc_start: 0.9041 (m-10) cc_final: 0.8810 (m-80) REVERT: D 121 MET cc_start: 0.9011 (mmm) cc_final: 0.8669 (mmm) REVERT: D 875 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8795 (mm-30) outliers start: 28 outliers final: 8 residues processed: 245 average time/residue: 0.1814 time to fit residues: 77.7657 Evaluate side-chains 233 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 233 optimal weight: 0.0170 chunk 44 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 223 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 385 optimal weight: 0.8980 chunk 356 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.080448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053568 restraints weight = 166088.928| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.90 r_work: 0.2682 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33674 Z= 0.128 Angle : 0.484 8.992 45950 Z= 0.252 Chirality : 0.038 0.247 5355 Planarity : 0.004 0.054 5655 Dihedral : 7.205 58.672 6233 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.73 % Allowed : 15.78 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 4181 helix: 2.36 (0.10), residues: 2641 sheet: -0.43 (0.32), residues: 277 loop : -0.80 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.018 0.001 TYR A 958 PHE 0.023 0.001 PHE B 854 TRP 0.034 0.001 TRP B 184 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00283 (33670) covalent geometry : angle 0.48355 (45942) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.44993 ( 8) hydrogen bonds : bond 0.04355 ( 2066) hydrogen bonds : angle 3.91473 ( 6144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9055 (mmm) cc_final: 0.8444 (mmm) REVERT: A 370 TYR cc_start: 0.8207 (m-80) cc_final: 0.7888 (m-10) REVERT: A 875 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8680 (mm-30) REVERT: B 179 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8867 (mmt) REVERT: B 255 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6940 (mmp) REVERT: B 778 MET cc_start: 0.7422 (ptm) cc_final: 0.7059 (ptm) REVERT: B 897 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8892 (mtp) REVERT: C 121 MET cc_start: 0.8732 (mmm) cc_final: 0.8442 (mmm) REVERT: C 625 MET cc_start: 0.9202 (mtp) cc_final: 0.8805 (mtt) REVERT: C 778 MET cc_start: 0.7670 (mtp) cc_final: 0.7425 (mtm) REVERT: D 37 TYR cc_start: 0.9009 (m-10) cc_final: 0.8794 (m-80) REVERT: D 121 MET cc_start: 0.8955 (mmm) cc_final: 0.8611 (mmm) REVERT: D 875 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8698 (mm-30) outliers start: 23 outliers final: 8 residues processed: 245 average time/residue: 0.1821 time to fit residues: 77.9574 Evaluate side-chains 234 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1167 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 176 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 386 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN D 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052941 restraints weight = 175888.133| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.49 r_work: 0.2681 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33674 Z= 0.144 Angle : 0.485 7.049 45950 Z= 0.252 Chirality : 0.038 0.269 5355 Planarity : 0.004 0.048 5655 Dihedral : 7.086 59.125 6233 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.66 % Allowed : 16.29 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.09 (0.13), residues: 4181 helix: 2.53 (0.10), residues: 2639 sheet: -0.34 (0.32), residues: 277 loop : -0.73 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 210 TYR 0.016 0.001 TYR C 958 PHE 0.021 0.001 PHE B 866 TRP 0.031 0.001 TRP B 184 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00327 (33670) covalent geometry : angle 0.48489 (45942) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.45170 ( 8) hydrogen bonds : bond 0.04282 ( 2066) hydrogen bonds : angle 3.86397 ( 6144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9044 (mmm) cc_final: 0.8423 (mmm) REVERT: A 255 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: A 370 TYR cc_start: 0.8393 (m-80) cc_final: 0.7730 (m-80) REVERT: A 875 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8690 (mm-30) REVERT: B 255 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6676 (tpt) REVERT: B 778 MET cc_start: 0.7479 (ptm) cc_final: 0.7252 (ptm) REVERT: B 897 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8906 (mtp) REVERT: C 121 MET cc_start: 0.8738 (mmm) cc_final: 0.8472 (mmm) REVERT: C 778 MET cc_start: 0.7691 (mtp) cc_final: 0.7447 (mtm) REVERT: D 37 TYR cc_start: 0.8919 (m-10) cc_final: 0.8709 (m-80) REVERT: D 121 MET cc_start: 0.8972 (mmm) cc_final: 0.8661 (mmm) REVERT: D 756 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8516 (tt) REVERT: D 875 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8701 (mm-30) outliers start: 21 outliers final: 6 residues processed: 237 average time/residue: 0.1838 time to fit residues: 75.6117 Evaluate side-chains 233 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 313 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 358 optimal weight: 9.9990 chunk 385 optimal weight: 2.9990 chunk 122 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS D 402 HIS D 610 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.080534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.053449 restraints weight = 215935.950| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.42 r_work: 0.2666 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33674 Z= 0.112 Angle : 0.462 7.372 45950 Z= 0.241 Chirality : 0.037 0.179 5355 Planarity : 0.004 0.047 5655 Dihedral : 6.899 59.891 6232 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.79 % Allowed : 15.88 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.23 (0.13), residues: 4181 helix: 2.61 (0.10), residues: 2671 sheet: -0.14 (0.33), residues: 271 loop : -0.74 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 210 TYR 0.017 0.001 TYR A 958 PHE 0.015 0.001 PHE B 854 TRP 0.029 0.001 TRP B 184 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00244 (33670) covalent geometry : angle 0.46241 (45942) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.39062 ( 8) hydrogen bonds : bond 0.04033 ( 2066) hydrogen bonds : angle 3.78963 ( 6144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9048 (mmm) cc_final: 0.8428 (mmm) REVERT: A 255 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (ttp) REVERT: A 370 TYR cc_start: 0.8258 (m-80) cc_final: 0.7657 (m-80) REVERT: B 255 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6800 (tpt) REVERT: B 897 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8951 (mtp) REVERT: C 121 MET cc_start: 0.8773 (mmm) cc_final: 0.8514 (mmm) REVERT: C 255 MET cc_start: 0.8411 (ptm) cc_final: 0.8206 (ptm) REVERT: C 778 MET cc_start: 0.7572 (mtp) cc_final: 0.7327 (mtm) REVERT: D 37 TYR cc_start: 0.9000 (m-10) cc_final: 0.8786 (m-80) REVERT: D 121 MET cc_start: 0.8990 (mmm) cc_final: 0.8679 (mmm) REVERT: D 457 MET cc_start: 0.9331 (tpt) cc_final: 0.9125 (tpt) REVERT: D 756 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8497 (tt) REVERT: D 875 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8753 (mm-30) outliers start: 25 outliers final: 6 residues processed: 241 average time/residue: 0.1796 time to fit residues: 75.9614 Evaluate side-chains 231 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 397 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 385 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 418 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 HIS B 716 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 402 HIS D 716 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.049758 restraints weight = 174268.649| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.38 r_work: 0.2626 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 33674 Z= 0.261 Angle : 0.565 7.852 45950 Z= 0.292 Chirality : 0.041 0.173 5355 Planarity : 0.004 0.069 5655 Dihedral : 7.123 59.967 6232 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.85 % Allowed : 15.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.05 (0.13), residues: 4181 helix: 2.48 (0.10), residues: 2630 sheet: -0.18 (0.33), residues: 276 loop : -0.71 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG D1183 TYR 0.017 0.001 TYR D1028 PHE 0.027 0.001 PHE B 866 TRP 0.032 0.002 TRP B 184 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00607 (33670) covalent geometry : angle 0.56480 (45942) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.54480 ( 8) hydrogen bonds : bond 0.04957 ( 2066) hydrogen bonds : angle 4.03776 ( 6144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.172 Fit side-chains REVERT: A 121 MET cc_start: 0.9049 (mmm) cc_final: 0.8432 (mmm) REVERT: A 255 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8476 (ttp) REVERT: A 370 TYR cc_start: 0.8320 (m-80) cc_final: 0.7717 (m-80) REVERT: A 626 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9006 (tttp) REVERT: A 671 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8777 (tt0) REVERT: A 875 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8618 (mm-30) REVERT: B 255 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6909 (tpt) REVERT: B 897 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8840 (mtp) REVERT: C 121 MET cc_start: 0.8794 (mmm) cc_final: 0.8533 (mmm) REVERT: C 386 MET cc_start: 0.5575 (mmt) cc_final: 0.5355 (mmt) REVERT: D 37 TYR cc_start: 0.8902 (m-10) cc_final: 0.8668 (m-80) REVERT: D 121 MET cc_start: 0.8946 (mmm) cc_final: 0.8620 (mmm) REVERT: D 756 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8511 (tp) REVERT: D 875 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8620 (mm-30) outliers start: 27 outliers final: 11 residues processed: 240 average time/residue: 0.1877 time to fit residues: 78.5840 Evaluate side-chains 236 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 261 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 408 optimal weight: 0.8980 chunk 225 optimal weight: 20.0000 chunk 419 optimal weight: 0.8980 chunk 276 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 377 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052956 restraints weight = 187393.550| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.89 r_work: 0.2672 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33674 Z= 0.105 Angle : 0.467 8.477 45950 Z= 0.243 Chirality : 0.037 0.165 5355 Planarity : 0.004 0.047 5655 Dihedral : 6.853 59.176 6232 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.47 % Allowed : 16.22 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.29 (0.13), residues: 4181 helix: 2.65 (0.10), residues: 2672 sheet: -0.13 (0.33), residues: 276 loop : -0.71 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.018 0.001 TYR C 958 PHE 0.012 0.001 PHE B 866 TRP 0.021 0.001 TRP A 31 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00222 (33670) covalent geometry : angle 0.46706 (45942) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.36005 ( 8) hydrogen bonds : bond 0.04056 ( 2066) hydrogen bonds : angle 3.79946 ( 6144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9017 (mmm) cc_final: 0.8373 (mmm) REVERT: A 370 TYR cc_start: 0.8273 (m-80) cc_final: 0.7610 (m-80) REVERT: A 386 MET cc_start: 0.6461 (mmt) cc_final: 0.6154 (mmm) REVERT: A 875 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8687 (mm-30) REVERT: B 255 MET cc_start: 0.7554 (mmp) cc_final: 0.6821 (tpt) REVERT: B 897 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8852 (mtp) REVERT: C 121 MET cc_start: 0.8747 (mmm) cc_final: 0.8514 (mmm) REVERT: D 37 TYR cc_start: 0.8922 (m-10) cc_final: 0.8697 (m-80) REVERT: D 121 MET cc_start: 0.8932 (mmm) cc_final: 0.8595 (mmm) REVERT: D 370 TYR cc_start: 0.8012 (m-10) cc_final: 0.7650 (m-10) REVERT: D 875 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8724 (mm-30) outliers start: 15 outliers final: 7 residues processed: 232 average time/residue: 0.1867 time to fit residues: 74.4239 Evaluate side-chains 229 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 312 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.079182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.051290 restraints weight = 186902.748| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.94 r_work: 0.2621 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33674 Z= 0.198 Angle : 0.524 8.713 45950 Z= 0.271 Chirality : 0.039 0.182 5355 Planarity : 0.004 0.081 5655 Dihedral : 6.936 59.048 6232 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.54 % Allowed : 16.19 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.24 (0.13), residues: 4181 helix: 2.63 (0.10), residues: 2635 sheet: -0.14 (0.33), residues: 276 loop : -0.68 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.016 0.001 TYR D1028 PHE 0.021 0.001 PHE B 866 TRP 0.022 0.001 TRP A 31 HIS 0.006 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00458 (33670) covalent geometry : angle 0.52387 (45942) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.49711 ( 8) hydrogen bonds : bond 0.04559 ( 2066) hydrogen bonds : angle 3.91716 ( 6144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.9003 (mmm) cc_final: 0.8365 (mmm) REVERT: A 370 TYR cc_start: 0.8238 (m-80) cc_final: 0.7621 (m-80) REVERT: A 386 MET cc_start: 0.6657 (mmt) cc_final: 0.6431 (mmm) REVERT: A 626 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9006 (tttp) REVERT: A 671 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8757 (tt0) REVERT: B 255 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6968 (tpt) REVERT: B 897 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8859 (mtp) REVERT: C 121 MET cc_start: 0.8759 (mmm) cc_final: 0.8507 (mmm) REVERT: D 37 TYR cc_start: 0.8942 (m-10) cc_final: 0.8697 (m-80) REVERT: D 121 MET cc_start: 0.8927 (mmm) cc_final: 0.8556 (mmm) REVERT: D 370 TYR cc_start: 0.7987 (m-10) cc_final: 0.7625 (m-10) REVERT: D 875 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8745 (mm-30) outliers start: 17 outliers final: 8 residues processed: 234 average time/residue: 0.1807 time to fit residues: 73.4150 Evaluate side-chains 233 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 372 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 315 optimal weight: 40.0000 chunk 49 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 335 optimal weight: 0.0030 chunk 284 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.079592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051789 restraints weight = 189398.064| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.93 r_work: 0.2633 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 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 = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33674 Z= 0.159 Angle : 0.497 9.009 45950 Z= 0.258 Chirality : 0.038 0.173 5355 Planarity : 0.004 0.083 5655 Dihedral : 6.840 58.022 6232 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.41 % Allowed : 16.26 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.25 (0.13), residues: 4181 helix: 2.63 (0.10), residues: 2642 sheet: -0.12 (0.33), residues: 276 loop : -0.65 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.016 0.001 TYR D 958 PHE 0.017 0.001 PHE B 866 TRP 0.022 0.001 TRP A 31 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00365 (33670) covalent geometry : angle 0.49739 (45942) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.44869 ( 8) hydrogen bonds : bond 0.04350 ( 2066) hydrogen bonds : angle 3.87295 ( 6144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.9004 (mmm) cc_final: 0.8376 (mmm) REVERT: A 370 TYR cc_start: 0.8292 (m-80) cc_final: 0.7644 (m-80) REVERT: A 626 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8973 (tttp) REVERT: A 671 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8686 (tt0) REVERT: B 255 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6995 (tpt) REVERT: B 897 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8892 (mtp) REVERT: C 121 MET cc_start: 0.8745 (mmm) cc_final: 0.8498 (mmm) REVERT: C 625 MET cc_start: 0.9068 (mtt) cc_final: 0.8814 (mtt) REVERT: D 37 TYR cc_start: 0.8884 (m-10) cc_final: 0.8631 (m-80) REVERT: D 121 MET cc_start: 0.8922 (mmm) cc_final: 0.8552 (mmm) REVERT: D 370 TYR cc_start: 0.8037 (m-10) cc_final: 0.7645 (m-10) REVERT: D 875 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8731 (mm-30) outliers start: 13 outliers final: 8 residues processed: 228 average time/residue: 0.1781 time to fit residues: 70.5088 Evaluate side-chains 231 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 875 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 146 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 388 optimal weight: 0.1980 chunk 237 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 368 optimal weight: 0.8980 chunk 4 optimal weight: 50.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053477 restraints weight = 181131.456| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.92 r_work: 0.2678 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33674 Z= 0.104 Angle : 0.460 8.835 45950 Z= 0.239 Chirality : 0.037 0.164 5355 Planarity : 0.004 0.076 5655 Dihedral : 6.646 59.936 6232 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.38 % Allowed : 16.38 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % 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: 2.37 (0.13), residues: 4181 helix: 2.70 (0.10), residues: 2677 sheet: -0.08 (0.33), residues: 276 loop : -0.64 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.017 0.001 TYR C 958 PHE 0.012 0.001 PHE B 866 TRP 0.023 0.001 TRP A 31 HIS 0.004 0.000 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00225 (33670) covalent geometry : angle 0.45968 (45942) SS BOND : bond 0.00038 ( 4) SS BOND : angle 0.41043 ( 8) hydrogen bonds : bond 0.03871 ( 2066) hydrogen bonds : angle 3.73991 ( 6144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8480.93 seconds wall clock time: 146 minutes 1.28 seconds (8761.28 seconds total)