Starting phenix.real_space_refine on Sun Jul 5 00:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0m_37982/07_2026/8x0m_37982.map" } resolution = 3.5 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= 0.008 sd= 0.067 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 189 5.16 5 C 15278 2.51 5 N 4200 2.21 5 O 4605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24274 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "F" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "G" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "I" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "J" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "K" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 5.09, per 1000 atoms: 0.21 Number of scatterers: 24274 At special positions: 0 Unit cell: (161.7, 162.8, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 189 16.00 O 4605 8.00 N 4200 7.00 C 15278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 929 " distance=2.03 Simple disulfide: pdb=" SG CYS C 877 " - pdb=" SG CYS C 909 " distance=2.03 Simple disulfide: pdb=" SG CYS C 878 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS C 893 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1086 " distance=2.04 Simple disulfide: pdb=" SG CYS C1116 " - pdb=" SG CYS C1191 " distance=2.03 Simple disulfide: pdb=" SG CYS C1121 " - pdb=" SG CYS C1195 " distance=2.03 Simple disulfide: pdb=" SG CYS C1143 " - pdb=" SG CYS C1185 " distance=2.03 Simple disulfide: pdb=" SG CYS F 352 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 355 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 424 " - pdb=" SG CYS F 438 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 598 " distance=2.04 Simple disulfide: pdb=" SG CYS F 534 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 536 " - pdb=" SG CYS F 553 " distance=2.03 Simple disulfide: pdb=" SG CYS G 864 " - pdb=" SG CYS G 929 " distance=2.03 Simple disulfide: pdb=" SG CYS G 877 " - pdb=" SG CYS G 909 " distance=2.03 Simple disulfide: pdb=" SG CYS G 878 " - pdb=" SG CYS G 911 " distance=2.03 Simple disulfide: pdb=" SG CYS G 883 " - pdb=" SG CYS G 893 " distance=2.03 Simple disulfide: pdb=" SG CYS G1074 " - pdb=" SG CYS G1086 " distance=2.03 Simple disulfide: pdb=" SG CYS G1116 " - pdb=" SG CYS G1191 " distance=2.03 Simple disulfide: pdb=" SG CYS G1121 " - pdb=" SG CYS G1195 " distance=2.03 Simple disulfide: pdb=" SG CYS G1143 " - pdb=" SG CYS G1185 " distance=2.03 Simple disulfide: pdb=" SG CYS J 352 " - pdb=" SG CYS J 458 " distance=2.03 Simple disulfide: pdb=" SG CYS J 355 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 424 " - pdb=" SG CYS J 438 " distance=2.03 Simple disulfide: pdb=" SG CYS J 486 " - pdb=" SG CYS J 598 " distance=2.03 Simple disulfide: pdb=" SG CYS J 534 " - pdb=" SG CYS J 558 " distance=2.03 Simple disulfide: pdb=" SG CYS J 536 " - pdb=" SG CYS J 553 " distance=2.03 Simple disulfide: pdb=" SG CYS K 864 " - pdb=" SG CYS K 929 " distance=2.03 Simple disulfide: pdb=" SG CYS K 877 " - pdb=" SG CYS K 909 " distance=2.03 Simple disulfide: pdb=" SG CYS K 878 " - pdb=" SG CYS K 911 " distance=2.03 Simple disulfide: pdb=" SG CYS K 883 " - pdb=" SG CYS K 893 " distance=2.03 Simple disulfide: pdb=" SG CYS K1074 " - pdb=" SG CYS K1086 " distance=2.04 Simple disulfide: pdb=" SG CYS K1116 " - pdb=" SG CYS K1191 " distance=2.03 Simple disulfide: pdb=" SG CYS K1121 " - pdb=" SG CYS K1195 " distance=2.03 Simple disulfide: pdb=" SG CYS K1143 " - pdb=" SG CYS K1185 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 90 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 83 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG C1701 " - " ASN C 956 " " NAG G1701 " - " ASN G 956 " " NAG K1701 " - " ASN K 956 " " NAG L 1 " - " ASN B 533 " " NAG M 1 " - " ASN B 595 " " NAG N 1 " - " ASN F 533 " " NAG O 1 " - " ASN F 595 " " NAG P 1 " - " ASN J 533 " " NAG Q 1 " - " ASN J 595 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 985.3 milliseconds 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 70 sheets defined 15.5% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.851A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.810A pdb=" N ARG A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.550A pdb=" N THR B 345 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 695 through 735 removed outlier: 3.614A pdb=" N THR B 699 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Proline residue: B 731 - end of helix removed outlier: 3.734A pdb=" N LEU B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 735 " --> pdb=" O PRO B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'C' and resid 1053 through 1061 removed outlier: 3.554A pdb=" N TYR C1057 " --> pdb=" O SER C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1069 Processing helix chain 'C' and resid 1070 through 1074 removed outlier: 3.948A pdb=" N GLY C1073 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C1074 " --> pdb=" O PRO C1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1070 through 1074' Processing helix chain 'C' and resid 1098 through 1102 Processing helix chain 'C' and resid 1219 through 1253 removed outlier: 3.640A pdb=" N ARG C1253 " --> pdb=" O ILE C1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.958A pdb=" N ASP E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.523A pdb=" N MET E 177 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.542A pdb=" N PHE F 339 " --> pdb=" O SER F 336 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL F 341 " --> pdb=" O HIS F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 695 through 735 Proline residue: F 731 - end of helix removed outlier: 3.619A pdb=" N LEU F 734 " --> pdb=" O THR F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 748 Processing helix chain 'G' and resid 1053 through 1062 removed outlier: 3.685A pdb=" N TYR G1057 " --> pdb=" O SER G1053 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1069 removed outlier: 3.605A pdb=" N THR G1068 " --> pdb=" O ALA G1065 " (cutoff:3.500A) Processing helix chain 'G' and resid 1070 through 1074 removed outlier: 4.024A pdb=" N GLY G1073 " --> pdb=" O ALA G1070 " (cutoff:3.500A) Processing helix chain 'G' and resid 1098 through 1102 removed outlier: 3.774A pdb=" N ALA G1101 " --> pdb=" O PRO G1098 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G1102 " --> pdb=" O ASP G1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1098 through 1102' Processing helix chain 'G' and resid 1219 through 1253 removed outlier: 3.750A pdb=" N ARG G1253 " --> pdb=" O ILE G1249 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.636A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 158 removed outlier: 3.979A pdb=" N LEU I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.759A pdb=" N ARG I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.581A pdb=" N ASN J 340 " --> pdb=" O GLN J 337 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL J 341 " --> pdb=" O HIS J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 554 through 556 No H-bonds generated for 'chain 'J' and resid 554 through 556' Processing helix chain 'J' and resid 683 through 695 Processing helix chain 'J' and resid 695 through 730 removed outlier: 3.607A pdb=" N THR J 699 " --> pdb=" O TYR J 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 731 through 735 removed outlier: 3.689A pdb=" N THR J 735 " --> pdb=" O TYR J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 748 Processing helix chain 'K' and resid 1053 through 1061 removed outlier: 3.642A pdb=" N TYR K1057 " --> pdb=" O SER K1053 " (cutoff:3.500A) Processing helix chain 'K' and resid 1065 through 1069 Processing helix chain 'K' and resid 1070 through 1074 removed outlier: 4.101A pdb=" N GLY K1073 " --> pdb=" O ALA K1070 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS K1074 " --> pdb=" O PRO K1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1070 through 1074' Processing helix chain 'K' and resid 1098 through 1102 removed outlier: 3.877A pdb=" N ALA K1101 " --> pdb=" O PRO K1098 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE K1102 " --> pdb=" O ASP K1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1098 through 1102' Processing helix chain 'K' and resid 1219 through 1253 removed outlier: 3.770A pdb=" N ARG K1253 " --> pdb=" O ILE K1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.872A pdb=" N GLY A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS A 125 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 193 removed outlier: 4.652A pdb=" N PHE A 207 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.836A pdb=" N ILE A 223 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AA5, first strand: chain 'B' and resid 367 through 371 removed outlier: 7.055A pdb=" N GLN B 382 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 370 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 380 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 437 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL B 426 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 389 removed outlier: 12.208A pdb=" N GLN B 386 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N THR B 398 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 388 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 417 through 419 removed outlier: 4.658A pdb=" N GLU B 442 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 481 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AB3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AB4, first strand: chain 'B' and resid 639 through 643 Processing sheet with id=AB5, first strand: chain 'C' and resid 818 through 823 Processing sheet with id=AB6, first strand: chain 'C' and resid 830 through 834 removed outlier: 5.430A pdb=" N MET C 846 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 951 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 848 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 949 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 850 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 856 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR C 941 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN C 858 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 939 " --> pdb=" O ASN C 858 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 860 " --> pdb=" O TYR C 937 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR C 937 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 862 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER C 935 " --> pdb=" O ILE C 862 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 955 through 962 removed outlier: 6.785A pdb=" N SER C 935 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 862 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR C 937 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 860 " --> pdb=" O TYR C 937 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 939 " --> pdb=" O ASN C 858 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN C 858 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR C 941 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 856 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 850 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 949 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 848 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 951 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET C 846 " --> pdb=" O MET C 951 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AB9, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AC1, first strand: chain 'C' and resid 1018 through 1019 Processing sheet with id=AC2, first strand: chain 'C' and resid 1035 through 1036 Processing sheet with id=AC3, first strand: chain 'C' and resid 1112 through 1121 removed outlier: 5.582A pdb=" N ASP C1113 " --> pdb=" O LYS C1136 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C1136 " --> pdb=" O ASP C1113 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1130 " --> pdb=" O ALA C1119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1158 through 1161 Processing sheet with id=AC5, first strand: chain 'E' and resid 149 through 150 removed outlier: 6.128A pdb=" N HIS E 125 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR E 132 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 191 through 193 removed outlier: 4.722A pdb=" N PHE E 207 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 222 through 224 removed outlier: 7.184A pdb=" N ILE E 223 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 350 through 352 Processing sheet with id=AC9, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.089A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 27.719A pdb=" N LYS F 380 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 22.981A pdb=" N ASP F 404 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 17.221A pdb=" N GLN F 382 " --> pdb=" O TYR F 402 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N TYR F 402 " --> pdb=" O GLN F 382 " (cutoff:3.500A) removed outlier: 11.839A pdb=" N SER F 384 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE F 400 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N GLN F 386 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N THR F 398 " --> pdb=" O GLN F 386 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 388 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.089A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N HIS F 432 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N ALA F 385 " --> pdb=" O MET F 430 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N MET F 430 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ILE F 387 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N GLY F 428 " --> pdb=" O ILE F 387 " (cutoff:3.500A) removed outlier: 16.728A pdb=" N ILE F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 19.112A pdb=" N VAL F 426 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 417 through 419 removed outlier: 4.473A pdb=" N GLU F 442 " --> pdb=" O TYR F 462 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 482 through 489 Processing sheet with id=AD4, first strand: chain 'F' and resid 569 through 570 Processing sheet with id=AD5, first strand: chain 'F' and resid 508 through 510 removed outlier: 4.625A pdb=" N VAL F 560 " --> pdb=" O ASP F 510 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD7, first strand: chain 'F' and resid 607 through 609 Processing sheet with id=AD8, first strand: chain 'F' and resid 639 through 643 Processing sheet with id=AD9, first strand: chain 'G' and resid 817 through 823 Processing sheet with id=AE1, first strand: chain 'G' and resid 830 through 834 removed outlier: 5.134A pdb=" N MET G 846 " --> pdb=" O MET G 951 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET G 951 " --> pdb=" O MET G 846 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL G 848 " --> pdb=" O ARG G 949 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG G 949 " --> pdb=" O VAL G 848 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 850 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 830 through 834 Processing sheet with id=AE3, first strand: chain 'G' and resid 858 through 863 removed outlier: 6.266A pdb=" N LEU G 859 " --> pdb=" O LYS G 938 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS G 938 " --> pdb=" O LEU G 859 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR G 861 " --> pdb=" O ALA G 936 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE5, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE6, first strand: chain 'G' and resid 1018 through 1019 Processing sheet with id=AE7, first strand: chain 'G' and resid 1035 through 1036 Processing sheet with id=AE8, first strand: chain 'G' and resid 1112 through 1121 removed outlier: 7.180A pdb=" N LEU G1114 " --> pdb=" O LYS G1136 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LYS G1136 " --> pdb=" O LEU G1114 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS G1116 " --> pdb=" O THR G1134 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR G1134 " --> pdb=" O CYS G1116 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL G1118 " --> pdb=" O THR G1132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR G1132 " --> pdb=" O VAL G1118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AF1, first strand: chain 'I' and resid 149 through 150 Processing sheet with id=AF2, first strand: chain 'I' and resid 257 through 259 removed outlier: 4.756A pdb=" N PHE I 207 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ALA I 199 " --> pdb=" O PRO I 210 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 257 through 259 removed outlier: 7.152A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 350 through 352 Processing sheet with id=AF5, first strand: chain 'J' and resid 367 through 371 removed outlier: 7.058A pdb=" N GLN J 382 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL J 370 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS J 380 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS J 437 " --> pdb=" O VAL J 426 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL J 426 " --> pdb=" O LYS J 437 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 386 through 389 removed outlier: 3.710A pdb=" N GLY J 388 " --> pdb=" O LYS J 399 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS J 399 " --> pdb=" O GLY J 388 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 417 through 419 removed outlier: 4.408A pdb=" N GLU J 442 " --> pdb=" O TYR J 462 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 482 through 489 Processing sheet with id=AF9, first strand: chain 'J' and resid 569 through 570 Processing sheet with id=AG1, first strand: chain 'J' and resid 514 through 517 Processing sheet with id=AG2, first strand: chain 'J' and resid 542 through 544 Processing sheet with id=AG3, first strand: chain 'J' and resid 607 through 609 Processing sheet with id=AG4, first strand: chain 'J' and resid 639 through 643 Processing sheet with id=AG5, first strand: chain 'K' and resid 817 through 823 Processing sheet with id=AG6, first strand: chain 'K' and resid 830 through 834 removed outlier: 5.430A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 955 through 962 removed outlier: 6.777A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AG9, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AH1, first strand: chain 'K' and resid 902 through 903 Processing sheet with id=AH2, first strand: chain 'K' and resid 1018 through 1019 Processing sheet with id=AH3, first strand: chain 'K' and resid 1035 through 1036 Processing sheet with id=AH4, first strand: chain 'K' and resid 1112 through 1121 removed outlier: 6.877A pdb=" N LEU K1114 " --> pdb=" O LYS K1136 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS K1136 " --> pdb=" O LEU K1114 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N CYS K1116 " --> pdb=" O THR K1134 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR K1134 " --> pdb=" O CYS K1116 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL K1118 " --> pdb=" O THR K1132 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR K1132 " --> pdb=" O VAL K1118 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 1158 through 1161 Processing sheet with id=AH6, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AH7, first strand: chain 'H' and resid 87 through 89 990 hydrogen bonds defined for protein. 2466 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: 5.71 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7917 1.34 - 1.47: 6157 1.47 - 1.60: 10571 1.60 - 1.72: 1 1.72 - 1.85: 255 Bond restraints: 24901 Sorted by residual: bond pdb=" CB PRO A 216 " pdb=" CG PRO A 216 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" CB ASN J 545 " pdb=" CG ASN J 545 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.85e+00 bond pdb=" CE LYS G1227 " pdb=" NZ LYS G1227 " ideal model delta sigma weight residual 1.489 1.427 0.062 3.00e-02 1.11e+03 4.24e+00 ... (remaining 24896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 33652 3.15 - 6.29: 216 6.29 - 9.44: 21 9.44 - 12.59: 3 12.59 - 15.74: 3 Bond angle restraints: 33895 Sorted by residual: angle pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" CD PRO A 216 " ideal model delta sigma weight residual 112.00 96.26 15.74 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA CYS J 598 " pdb=" CB CYS J 598 " pdb=" SG CYS J 598 " ideal model delta sigma weight residual 114.40 127.40 -13.00 2.30e+00 1.89e-01 3.20e+01 angle pdb=" C GLU G1061 " pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " ideal model delta sigma weight residual 111.35 120.99 -9.64 1.72e+00 3.38e-01 3.14e+01 angle pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " pdb=" CG GLU G1061 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" N GLU G1061 " pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " ideal model delta sigma weight residual 111.65 104.51 7.14 1.40e+00 5.10e-01 2.60e+01 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12948 17.98 - 35.96: 1670 35.96 - 53.95: 447 53.95 - 71.93: 69 71.93 - 89.91: 31 Dihedral angle restraints: 15165 sinusoidal: 6128 harmonic: 9037 Sorted by residual: dihedral pdb=" CB CYS H 83 " pdb=" SG CYS H 83 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 175.89 -82.89 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " pdb=" SG CYS F 598 " pdb=" CB CYS F 598 " ideal model delta sinusoidal sigma weight residual -86.00 -166.90 80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS F 355 " pdb=" SG CYS F 355 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual 93.00 172.43 -79.43 1 1.00e+01 1.00e-02 7.84e+01 ... (remaining 15162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3762 0.125 - 0.250: 40 0.250 - 0.376: 1 0.376 - 0.501: 0 0.501 - 0.626: 1 Chirality restraints: 3804 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN F 595 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 595 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" C PRO A 216 " pdb=" CB PRO A 216 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 3801 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 215 " 0.088 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO A 216 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 595 " -0.003 2.00e-02 2.50e+03 3.53e-02 1.56e+01 pdb=" CG ASN B 595 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 595 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 595 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 545 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C ASN J 545 " -0.052 2.00e-02 2.50e+03 pdb=" O ASN J 545 " 0.020 2.00e-02 2.50e+03 pdb=" N SER J 546 " 0.017 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 722 2.70 - 3.25: 22776 3.25 - 3.80: 36401 3.80 - 4.35: 43184 4.35 - 4.90: 75667 Nonbonded interactions: 178750 Sorted by model distance: nonbonded pdb=" OH TYR B 402 " pdb=" OD1 ASP B 450 " model vdw 2.146 3.040 nonbonded pdb=" O PRO E 189 " pdb=" OH TYR E 193 " model vdw 2.161 3.040 nonbonded pdb=" O PRO A 189 " pdb=" OH TYR A 193 " model vdw 2.169 3.040 nonbonded pdb=" O THR E 211 " pdb=" OG1 THR E 244 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 112 " pdb=" OE2 GLU D 114 " model vdw 2.189 3.040 ... (remaining 178745 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.810 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 24964 Z= 0.161 Angle : 0.724 17.530 34036 Z= 0.377 Chirality : 0.046 0.626 3804 Planarity : 0.005 0.120 4362 Dihedral : 16.788 89.911 9233 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.68 % Allowed : 32.73 % Favored : 66.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % 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: -0.18 (0.15), residues: 3106 helix: 2.85 (0.28), residues: 327 sheet: 0.44 (0.17), residues: 972 loop : -1.04 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 949 TYR 0.031 0.002 TYR K 861 PHE 0.034 0.002 PHE B 339 TRP 0.023 0.001 TRP I 251 HIS 0.005 0.001 HIS F 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (24901) covalent geometry : angle 0.70328 / 0.37 (33895) SS BOND : bond 0.00311 / 0.18 ( 48) SS BOND : angle 1.40664 / 0.87 ( 96) hydrogen bonds : bond 0.11436 / 7.50 ( 943) hydrogen bonds : angle 5.29821 / 3.71 ( 2466) link_BETA1-4 : bond 0.00727 / 0.45 ( 6) link_BETA1-4 : angle 1.72960 / 0.97 ( 18) link_NAG-ASN : bond 0.00952 / 0.73 ( 9) link_NAG-ASN : angle 5.49814 / 4.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 694 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.5866 (p0) cc_final: 0.5277 (p0) REVERT: C 1018 ILE cc_start: 0.7917 (pt) cc_final: 0.7681 (pt) REVERT: C 1188 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7923 (ttm110) REVERT: F 394 ASN cc_start: 0.7742 (t0) cc_final: 0.7210 (t0) REVERT: F 658 MET cc_start: 0.7345 (tmm) cc_final: 0.7010 (tmm) REVERT: G 1019 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7232 (mm-40) REVERT: J 586 LYS cc_start: 0.6799 (mptt) cc_final: 0.6222 (mmtp) REVERT: K 1029 TYR cc_start: 0.8305 (t80) cc_final: 0.7607 (t80) REVERT: K 1227 LYS cc_start: 0.7743 (pttt) cc_final: 0.7428 (pttt) outliers start: 18 outliers final: 12 residues processed: 700 average time/residue: 0.1643 time to fit residues: 177.2161 Evaluate side-chains 704 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 692 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 251 TRP Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1190 THR Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain K residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 9.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 557 GLN E 125 HIS G 845 GLN G 847 GLN G 954 ASN G1067 ASN G1148 HIS G1201 HIS J 461 GLN J 686 GLN J 689 GLN K1079 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115643 restraints weight = 40995.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118858 restraints weight = 17670.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120904 restraints weight = 9530.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122269 restraints weight = 6097.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123120 restraints weight = 4452.356| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24964 Z= 0.107 Angle : 0.587 17.417 34036 Z= 0.294 Chirality : 0.044 0.506 3804 Planarity : 0.004 0.053 4362 Dihedral : 4.811 51.262 3706 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.43 % Allowed : 28.66 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.09 (0.15), residues: 3106 helix: 2.97 (0.28), residues: 324 sheet: 0.50 (0.17), residues: 972 loop : -0.99 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 836 TYR 0.021 0.001 TYR B 532 PHE 0.011 0.001 PHE C 910 TRP 0.013 0.001 TRP D 102 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (24901) covalent geometry : angle 0.56928 / 0.29 (33895) SS BOND : bond 0.00550 / 0.22 ( 48) SS BOND : angle 0.98478 / 0.62 ( 96) hydrogen bonds : bond 0.03476 / 2.38 ( 943) hydrogen bonds : angle 4.60782 / 3.23 ( 2466) link_BETA1-4 : bond 0.00613 / 0.40 ( 6) link_BETA1-4 : angle 1.16011 / 0.70 ( 18) link_NAG-ASN : bond 0.01007 / 0.77 ( 9) link_NAG-ASN : angle 4.82441 / 4.44 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 704 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6714 (mmmt) REVERT: B 396 ASP cc_start: 0.7221 (t0) cc_final: 0.6946 (t0) REVERT: B 462 TYR cc_start: 0.7883 (t80) cc_final: 0.7533 (t80) REVERT: B 566 LYS cc_start: 0.7134 (mmmm) cc_final: 0.6886 (mmmm) REVERT: B 586 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7870 (mtmt) REVERT: C 917 GLN cc_start: 0.8482 (tt0) cc_final: 0.8150 (tt0) REVERT: E 113 MET cc_start: 0.4913 (mmp) cc_final: 0.4549 (mmp) REVERT: F 659 GLU cc_start: 0.7290 (tt0) cc_final: 0.6897 (tt0) REVERT: G 914 GLU cc_start: 0.7599 (mp0) cc_final: 0.7148 (mp0) REVERT: G 1021 ARG cc_start: 0.8844 (mmt180) cc_final: 0.8561 (mmt-90) REVERT: G 1148 HIS cc_start: 0.8204 (m-70) cc_final: 0.7897 (m170) REVERT: I 113 MET cc_start: 0.7127 (mmm) cc_final: 0.6858 (mmm) REVERT: J 475 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (p) REVERT: J 529 LYS cc_start: 0.8168 (tppt) cc_final: 0.7692 (tppt) REVERT: J 545 ASN cc_start: 0.8623 (t0) cc_final: 0.8382 (t0) REVERT: J 586 LYS cc_start: 0.6770 (mptt) cc_final: 0.6313 (mmtp) REVERT: K 1019 GLN cc_start: 0.7516 (mt0) cc_final: 0.7064 (mm-40) REVERT: K 1029 TYR cc_start: 0.8372 (t80) cc_final: 0.7495 (t80) REVERT: K 1226 GLN cc_start: 0.8002 (tp40) cc_final: 0.7775 (tt0) REVERT: K 1227 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7460 (pttt) outliers start: 91 outliers final: 52 residues processed: 747 average time/residue: 0.1703 time to fit residues: 198.4428 Evaluate side-chains 745 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 691 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 665 ASN Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1137 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 689 GLN Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1079 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain D residue 115 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 283 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 chunk 248 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 623 HIS E 125 HIS F 461 GLN ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 845 GLN G 847 GLN G 917 GLN G 954 ASN G1201 HIS J 559 HIS J 664 ASN J 686 GLN K1045 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113450 restraints weight = 40923.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116663 restraints weight = 17386.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118655 restraints weight = 9351.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120013 restraints weight = 6005.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120768 restraints weight = 4390.587| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24964 Z= 0.131 Angle : 0.590 17.463 34036 Z= 0.294 Chirality : 0.044 0.525 3804 Planarity : 0.004 0.056 4362 Dihedral : 4.464 52.974 3691 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.85 % Allowed : 28.21 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.12 (0.15), residues: 3106 helix: 2.92 (0.28), residues: 324 sheet: 0.49 (0.16), residues: 978 loop : -1.01 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 949 TYR 0.023 0.001 TYR G 891 PHE 0.021 0.001 PHE C1235 TRP 0.009 0.001 TRP B 642 HIS 0.014 0.001 HIS J 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24901) covalent geometry : angle 0.57016 / 0.29 (33895) SS BOND : bond 0.00428 / 0.21 ( 48) SS BOND : angle 1.37719 / 0.87 ( 96) hydrogen bonds : bond 0.03616 / 2.48 ( 943) hydrogen bonds : angle 4.48260 / 3.14 ( 2466) link_BETA1-4 : bond 0.00357 / 0.24 ( 6) link_BETA1-4 : angle 1.12532 / 0.65 ( 18) link_NAG-ASN : bond 0.00903 / 0.70 ( 9) link_NAG-ASN : angle 4.81244 / 4.41 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 710 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6765 (mmmt) REVERT: B 462 TYR cc_start: 0.7944 (t80) cc_final: 0.7602 (t80) REVERT: B 711 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 845 GLN cc_start: 0.7686 (mt0) cc_final: 0.7366 (mt0) REVERT: C 917 GLN cc_start: 0.8533 (tt0) cc_final: 0.8218 (tt0) REVERT: C 1024 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7069 (mm-30) REVERT: C 1095 MET cc_start: 0.7016 (ppp) cc_final: 0.6523 (ppp) REVERT: C 1188 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: E 113 MET cc_start: 0.4971 (mmp) cc_final: 0.4577 (mmp) REVERT: F 394 ASN cc_start: 0.7712 (t0) cc_final: 0.7210 (t0) REVERT: F 556 GLU cc_start: 0.7933 (pm20) cc_final: 0.7719 (pm20) REVERT: F 659 GLU cc_start: 0.7171 (tt0) cc_final: 0.6946 (tt0) REVERT: F 686 GLN cc_start: 0.7758 (mt0) cc_final: 0.7547 (mt0) REVERT: F 694 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7806 (mp) REVERT: G 945 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7746 (mtpp) REVERT: G 1019 GLN cc_start: 0.7661 (mm-40) cc_final: 0.6962 (mm-40) REVERT: G 1021 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8506 (mmt-90) REVERT: G 1061 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6726 (tm-30) REVERT: G 1139 LYS cc_start: 0.8454 (pttt) cc_final: 0.8055 (ptmm) REVERT: G 1148 HIS cc_start: 0.8217 (m-70) cc_final: 0.7688 (m-70) REVERT: J 341 VAL cc_start: 0.7936 (m) cc_final: 0.7732 (p) REVERT: J 467 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7121 (mm-40) REVERT: J 496 THR cc_start: 0.7743 (p) cc_final: 0.7451 (p) REVERT: J 529 LYS cc_start: 0.8212 (tppt) cc_final: 0.7549 (tppt) REVERT: J 545 ASN cc_start: 0.8604 (t0) cc_final: 0.8322 (t0) REVERT: J 586 LYS cc_start: 0.7100 (mptt) cc_final: 0.6647 (mmtp) REVERT: J 713 SER cc_start: 0.8103 (t) cc_final: 0.7826 (t) REVERT: K 1019 GLN cc_start: 0.7799 (mt0) cc_final: 0.7409 (mm110) REVERT: K 1223 SER cc_start: 0.7870 (t) cc_final: 0.7636 (t) REVERT: K 1226 GLN cc_start: 0.8068 (tp40) cc_final: 0.7850 (tt0) REVERT: K 1227 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7395 (pttt) outliers start: 102 outliers final: 61 residues processed: 760 average time/residue: 0.1699 time to fit residues: 199.7831 Evaluate side-chains 768 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 704 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1137 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 218 optimal weight: 8.9990 chunk 81 optimal weight: 0.0040 chunk 82 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G 954 ASN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN J 689 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113345 restraints weight = 40632.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116565 restraints weight = 17243.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118613 restraints weight = 9207.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119670 restraints weight = 5884.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120671 restraints weight = 4463.959| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24964 Z= 0.133 Angle : 0.588 17.118 34036 Z= 0.292 Chirality : 0.045 0.538 3804 Planarity : 0.004 0.056 4362 Dihedral : 4.367 53.466 3691 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.88 % Allowed : 28.85 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.11 (0.15), residues: 3106 helix: 2.93 (0.28), residues: 324 sheet: 0.53 (0.17), residues: 978 loop : -1.03 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 949 TYR 0.024 0.001 TYR G 891 PHE 0.023 0.001 PHE F 570 TRP 0.009 0.001 TRP B 642 HIS 0.024 0.001 HIS B 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (24901) covalent geometry : angle 0.56981 / 0.29 (33895) SS BOND : bond 0.00289 / 0.15 ( 48) SS BOND : angle 1.13592 / 0.75 ( 96) hydrogen bonds : bond 0.03583 / 2.47 ( 943) hydrogen bonds : angle 4.42316 / 3.09 ( 2466) link_BETA1-4 : bond 0.00408 / 0.27 ( 6) link_BETA1-4 : angle 1.13935 / 0.66 ( 18) link_NAG-ASN : bond 0.00889 / 0.69 ( 9) link_NAG-ASN : angle 4.79605 / 4.37 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 725 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6965 (mmmt) REVERT: A 251 TRP cc_start: 0.6851 (m-10) cc_final: 0.6607 (m-90) REVERT: B 394 ASN cc_start: 0.7915 (p0) cc_final: 0.7654 (p0) REVERT: B 396 ASP cc_start: 0.7523 (t0) cc_final: 0.7087 (t0) REVERT: B 462 TYR cc_start: 0.7974 (t80) cc_final: 0.7574 (t80) REVERT: C 1024 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7026 (mm-30) REVERT: C 1059 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 1095 MET cc_start: 0.6980 (ppp) cc_final: 0.6526 (ppp) REVERT: C 1117 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8200 (p) REVERT: C 1227 LYS cc_start: 0.8219 (mttt) cc_final: 0.7712 (mttt) REVERT: E 113 MET cc_start: 0.4971 (mmp) cc_final: 0.4580 (mmp) REVERT: F 340 ASN cc_start: 0.6903 (m110) cc_final: 0.6248 (p0) REVERT: F 394 ASN cc_start: 0.7679 (t0) cc_final: 0.7175 (t0) REVERT: F 511 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8182 (mmm160) REVERT: F 659 GLU cc_start: 0.7165 (tt0) cc_final: 0.6957 (tt0) REVERT: F 685 HIS cc_start: 0.7648 (p90) cc_final: 0.7070 (p90) REVERT: F 694 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7785 (mp) REVERT: G 914 GLU cc_start: 0.7619 (mp0) cc_final: 0.6959 (mp0) REVERT: G 945 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7654 (mtpp) REVERT: G 1019 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7148 (mm-40) REVERT: G 1021 ARG cc_start: 0.8819 (mmt180) cc_final: 0.8463 (mmt-90) REVERT: G 1061 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6664 (tm-30) REVERT: G 1139 LYS cc_start: 0.8448 (pttt) cc_final: 0.8059 (ptmm) REVERT: G 1144 SER cc_start: 0.8503 (t) cc_final: 0.8128 (m) REVERT: G 1148 HIS cc_start: 0.8218 (m-70) cc_final: 0.7932 (m-70) REVERT: J 341 VAL cc_start: 0.7913 (m) cc_final: 0.7698 (p) REVERT: J 467 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7178 (mm-40) REVERT: J 496 THR cc_start: 0.7814 (p) cc_final: 0.7507 (p) REVERT: J 498 GLU cc_start: 0.6901 (pm20) cc_final: 0.6560 (pm20) REVERT: J 529 LYS cc_start: 0.8195 (tppt) cc_final: 0.7475 (tppt) REVERT: J 533 ASN cc_start: 0.8465 (t0) cc_final: 0.7697 (t0) REVERT: J 586 LYS cc_start: 0.7002 (mptt) cc_final: 0.6525 (mmtp) REVERT: J 634 GLU cc_start: 0.7317 (tp30) cc_final: 0.7018 (tp30) REVERT: J 713 SER cc_start: 0.8128 (t) cc_final: 0.7909 (t) REVERT: K 1019 GLN cc_start: 0.7927 (mt0) cc_final: 0.7666 (mt0) REVERT: K 1029 TYR cc_start: 0.8375 (t80) cc_final: 0.8135 (t80) REVERT: K 1130 VAL cc_start: 0.8105 (p) cc_final: 0.7770 (t) REVERT: K 1181 VAL cc_start: 0.8360 (t) cc_final: 0.8134 (m) REVERT: K 1223 SER cc_start: 0.7945 (t) cc_final: 0.7736 (t) REVERT: K 1226 GLN cc_start: 0.8093 (tp40) cc_final: 0.7881 (tt0) outliers start: 103 outliers final: 72 residues processed: 769 average time/residue: 0.1635 time to fit residues: 194.9634 Evaluate side-chains 785 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 710 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 689 GLN Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1168 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1213 VAL Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 254 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 301 optimal weight: 40.0000 chunk 296 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 262 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS ** F 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G 954 ASN G1001 ASN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108241 restraints weight = 40463.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111411 restraints weight = 17498.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113447 restraints weight = 9615.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114697 restraints weight = 6273.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115631 restraints weight = 4702.193| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24964 Z= 0.136 Angle : 0.599 17.149 34036 Z= 0.298 Chirality : 0.044 0.516 3804 Planarity : 0.004 0.057 4362 Dihedral : 4.365 54.934 3691 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.79 % Allowed : 28.28 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.10 (0.15), residues: 3106 helix: 2.94 (0.27), residues: 324 sheet: 0.55 (0.17), residues: 978 loop : -1.03 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 949 TYR 0.030 0.002 TYR B 397 PHE 0.021 0.001 PHE K1235 TRP 0.009 0.001 TRP B 642 HIS 0.009 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24901) covalent geometry : angle 0.57989 / 0.29 (33895) SS BOND : bond 0.00256 / 0.14 ( 48) SS BOND : angle 1.01323 / 0.65 ( 96) hydrogen bonds : bond 0.03633 / 2.52 ( 943) hydrogen bonds : angle 4.39044 / 3.06 ( 2466) link_BETA1-4 : bond 0.00360 / 0.24 ( 6) link_BETA1-4 : angle 1.11418 / 0.67 ( 18) link_NAG-ASN : bond 0.00959 / 0.74 ( 9) link_NAG-ASN : angle 5.02590 / 4.55 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 741 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7520 (mmmt) cc_final: 0.7096 (mmmt) REVERT: A 211 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 251 TRP cc_start: 0.6881 (m-10) cc_final: 0.6609 (m-90) REVERT: B 387 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7264 (mt) REVERT: B 394 ASN cc_start: 0.7915 (p0) cc_final: 0.7668 (p0) REVERT: B 395 HIS cc_start: 0.7397 (t-90) cc_final: 0.7023 (t-90) REVERT: B 462 TYR cc_start: 0.7983 (t80) cc_final: 0.7559 (t80) REVERT: B 517 GLN cc_start: 0.7746 (mm110) cc_final: 0.7541 (mm-40) REVERT: B 586 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7633 (mtpp) REVERT: B 711 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 954 ASN cc_start: 0.7516 (p0) cc_final: 0.7182 (p0) REVERT: C 983 SER cc_start: 0.8804 (t) cc_final: 0.8270 (p) REVERT: C 1021 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.8480 (tpt170) REVERT: C 1024 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 1059 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 1095 MET cc_start: 0.7025 (ppp) cc_final: 0.6473 (ppp) REVERT: C 1117 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (p) REVERT: C 1214 PHE cc_start: 0.8166 (t80) cc_final: 0.7791 (t80) REVERT: C 1227 LYS cc_start: 0.8243 (mttt) cc_final: 0.7745 (mttt) REVERT: E 113 MET cc_start: 0.5099 (mmp) cc_final: 0.4710 (mmp) REVERT: F 394 ASN cc_start: 0.7633 (t0) cc_final: 0.7111 (t0) REVERT: F 511 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8208 (mmm160) REVERT: F 556 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: F 679 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8133 (mtmm) REVERT: F 694 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7766 (mp) REVERT: G 914 GLU cc_start: 0.7611 (mp0) cc_final: 0.7001 (mp0) REVERT: G 945 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7630 (mtpp) REVERT: G 1019 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7264 (mm-40) REVERT: G 1059 LEU cc_start: 0.8490 (tp) cc_final: 0.8238 (mt) REVERT: G 1061 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6701 (tm-30) REVERT: G 1144 SER cc_start: 0.8489 (t) cc_final: 0.8141 (m) REVERT: G 1148 HIS cc_start: 0.8204 (m-70) cc_final: 0.7734 (m-70) REVERT: I 142 LYS cc_start: 0.7730 (tmmt) cc_final: 0.7446 (tmtt) REVERT: J 341 VAL cc_start: 0.7928 (m) cc_final: 0.7703 (p) REVERT: J 467 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7169 (mm-40) REVERT: J 529 LYS cc_start: 0.8209 (tppt) cc_final: 0.7275 (tppt) REVERT: J 533 ASN cc_start: 0.8513 (t0) cc_final: 0.7792 (t0) REVERT: J 545 ASN cc_start: 0.8644 (t0) cc_final: 0.8379 (t0) REVERT: J 567 LYS cc_start: 0.7436 (mmtp) cc_final: 0.7175 (mmtt) REVERT: J 586 LYS cc_start: 0.7083 (mptt) cc_final: 0.6552 (mmtp) REVERT: J 634 GLU cc_start: 0.7317 (tp30) cc_final: 0.7085 (tp30) REVERT: K 1001 ASN cc_start: 0.7853 (m-40) cc_final: 0.7375 (m-40) REVERT: K 1019 GLN cc_start: 0.8001 (mt0) cc_final: 0.7765 (mt0) REVERT: K 1130 VAL cc_start: 0.8071 (p) cc_final: 0.7765 (t) REVERT: K 1150 ASN cc_start: 0.8361 (t0) cc_final: 0.8130 (t0) REVERT: K 1181 VAL cc_start: 0.8365 (t) cc_final: 0.8147 (m) REVERT: K 1223 SER cc_start: 0.7986 (t) cc_final: 0.7785 (t) REVERT: K 1226 GLN cc_start: 0.8122 (tp40) cc_final: 0.7921 (tt0) outliers start: 127 outliers final: 81 residues processed: 804 average time/residue: 0.1613 time to fit residues: 201.0199 Evaluate side-chains 814 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 725 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1043 MET Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 689 GLN Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1213 VAL Chi-restraints excluded: chain K residue 1227 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 0.0020 chunk 178 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 623 HIS C1019 GLN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 GLN F 559 HIS G 847 GLN G 954 ASN G1075 GLN G1155 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1079 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106100 restraints weight = 40299.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109242 restraints weight = 17433.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111261 restraints weight = 9632.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112570 restraints weight = 6280.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113433 restraints weight = 4682.623| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24964 Z= 0.176 Angle : 0.633 18.331 34036 Z= 0.316 Chirality : 0.046 0.542 3804 Planarity : 0.004 0.058 4362 Dihedral : 4.494 57.280 3691 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.79 % Allowed : 28.43 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.11 (0.15), residues: 3106 helix: 2.87 (0.28), residues: 324 sheet: 0.50 (0.17), residues: 969 loop : -0.98 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 229 TYR 0.025 0.002 TYR G 891 PHE 0.021 0.002 PHE K1235 TRP 0.011 0.001 TRP D 102 HIS 0.009 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (24901) covalent geometry : angle 0.61174 / 0.31 (33895) SS BOND : bond 0.00570 / 0.38 ( 48) SS BOND : angle 1.55221 / 0.83 ( 96) hydrogen bonds : bond 0.03988 / 2.77 ( 943) hydrogen bonds : angle 4.46214 / 3.10 ( 2466) link_BETA1-4 : bond 0.00456 / 0.32 ( 6) link_BETA1-4 : angle 1.20268 / 0.71 ( 18) link_NAG-ASN : bond 0.00903 / 0.69 ( 9) link_NAG-ASN : angle 5.08834 / 4.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 750 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7115 (mmmt) REVERT: A 211 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 251 TRP cc_start: 0.6927 (m-10) cc_final: 0.6628 (m-90) REVERT: B 387 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 394 ASN cc_start: 0.7916 (p0) cc_final: 0.7689 (p0) REVERT: B 395 HIS cc_start: 0.7445 (t-90) cc_final: 0.7048 (t-90) REVERT: B 396 ASP cc_start: 0.7715 (t0) cc_final: 0.7034 (t0) REVERT: B 462 TYR cc_start: 0.8018 (t80) cc_final: 0.7568 (t80) REVERT: B 484 ILE cc_start: 0.8213 (mm) cc_final: 0.7944 (mt) REVERT: B 517 GLN cc_start: 0.7786 (mm110) cc_final: 0.7561 (mm-40) REVERT: B 586 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7589 (mtpp) REVERT: B 711 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 920 GLU cc_start: 0.7686 (pm20) cc_final: 0.7319 (pm20) REVERT: C 954 ASN cc_start: 0.7538 (p0) cc_final: 0.7210 (p0) REVERT: C 983 SER cc_start: 0.8802 (t) cc_final: 0.8251 (p) REVERT: C 1018 ILE cc_start: 0.8005 (pt) cc_final: 0.7779 (pt) REVERT: C 1021 ARG cc_start: 0.8882 (tpp-160) cc_final: 0.8176 (mmt180) REVERT: C 1024 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6885 (mm-30) REVERT: C 1059 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8115 (mp) REVERT: C 1095 MET cc_start: 0.6983 (ppp) cc_final: 0.6380 (ppp) REVERT: C 1117 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 1214 PHE cc_start: 0.8182 (t80) cc_final: 0.7938 (t80) REVERT: C 1227 LYS cc_start: 0.8278 (mttt) cc_final: 0.7814 (mttt) REVERT: E 113 MET cc_start: 0.5128 (mmp) cc_final: 0.4766 (mmp) REVERT: F 394 ASN cc_start: 0.7614 (t0) cc_final: 0.7118 (t0) REVERT: F 511 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8236 (mmm160) REVERT: F 516 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8041 (tp40) REVERT: F 584 LYS cc_start: 0.5226 (OUTLIER) cc_final: 0.4942 (ttmm) REVERT: F 586 LYS cc_start: 0.7394 (pttt) cc_final: 0.7083 (pptt) REVERT: F 679 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8128 (mtmm) REVERT: F 694 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7835 (mp) REVERT: G 839 TYR cc_start: 0.7676 (m-80) cc_final: 0.7450 (m-80) REVERT: G 914 GLU cc_start: 0.7592 (mp0) cc_final: 0.6975 (mp0) REVERT: G 945 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7684 (mtpp) REVERT: G 1019 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7294 (mm-40) REVERT: G 1059 LEU cc_start: 0.8507 (tp) cc_final: 0.8272 (mt) REVERT: G 1061 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6769 (tm-30) REVERT: G 1144 SER cc_start: 0.8524 (t) cc_final: 0.8189 (m) REVERT: I 142 LYS cc_start: 0.7998 (tmmt) cc_final: 0.7687 (tmtt) REVERT: I 177 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.2837 (mpp) REVERT: I 221 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7515 (mtt180) REVERT: J 341 VAL cc_start: 0.7966 (m) cc_final: 0.7747 (p) REVERT: J 387 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7339 (mt) REVERT: J 467 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7189 (mm-40) REVERT: J 522 LYS cc_start: 0.8191 (tttp) cc_final: 0.7587 (tttp) REVERT: J 529 LYS cc_start: 0.8253 (tppt) cc_final: 0.7251 (tppt) REVERT: J 533 ASN cc_start: 0.8510 (t0) cc_final: 0.7807 (t0) REVERT: J 544 THR cc_start: 0.7855 (p) cc_final: 0.7270 (p) REVERT: J 545 ASN cc_start: 0.8640 (t0) cc_final: 0.8413 (t0) REVERT: J 567 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7290 (mmtt) REVERT: J 586 LYS cc_start: 0.7022 (mptt) cc_final: 0.6464 (mmtp) REVERT: K 876 LYS cc_start: 0.7809 (tttp) cc_final: 0.7453 (tttm) REVERT: K 960 ASP cc_start: 0.7735 (p0) cc_final: 0.7408 (p0) REVERT: K 1019 GLN cc_start: 0.8111 (mt0) cc_final: 0.7852 (mt0) REVERT: K 1022 THR cc_start: 0.8508 (t) cc_final: 0.8016 (p) REVERT: K 1115 THR cc_start: 0.8637 (t) cc_final: 0.8317 (p) REVERT: K 1130 VAL cc_start: 0.8094 (p) cc_final: 0.7787 (t) REVERT: K 1181 VAL cc_start: 0.8365 (t) cc_final: 0.8155 (m) outliers start: 127 outliers final: 93 residues processed: 806 average time/residue: 0.1676 time to fit residues: 209.1288 Evaluate side-chains 836 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 731 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 516 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1168 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1213 VAL Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 120 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 233 optimal weight: 0.0060 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 GLN G 847 GLN G 954 ASN G1075 GLN G1155 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105748 restraints weight = 40809.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109010 restraints weight = 17931.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111170 restraints weight = 10063.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112454 restraints weight = 6647.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113387 restraints weight = 5053.453| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24964 Z= 0.119 Angle : 0.619 17.790 34036 Z= 0.306 Chirality : 0.044 0.533 3804 Planarity : 0.004 0.058 4362 Dihedral : 4.421 59.629 3691 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.60 % Allowed : 28.47 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.11 (0.15), residues: 3106 helix: 2.92 (0.27), residues: 324 sheet: 0.55 (0.17), residues: 975 loop : -1.03 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 836 TYR 0.026 0.001 TYR J 402 PHE 0.024 0.001 PHE C1235 TRP 0.009 0.001 TRP B 642 HIS 0.013 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (24901) covalent geometry : angle 0.59944 / 0.30 (33895) SS BOND : bond 0.00374 / 0.22 ( 48) SS BOND : angle 1.24731 / 0.75 ( 96) hydrogen bonds : bond 0.03583 / 2.48 ( 943) hydrogen bonds : angle 4.42320 / 3.08 ( 2466) link_BETA1-4 : bond 0.00392 / 0.26 ( 6) link_BETA1-4 : angle 1.17179 / 0.69 ( 18) link_NAG-ASN : bond 0.00926 / 0.72 ( 9) link_NAG-ASN : angle 4.98481 / 4.56 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 745 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7590 (mmmt) cc_final: 0.7111 (mmmt) REVERT: A 251 TRP cc_start: 0.6933 (m-10) cc_final: 0.6643 (m-90) REVERT: B 387 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7397 (mt) REVERT: B 394 ASN cc_start: 0.7928 (p0) cc_final: 0.7702 (p0) REVERT: B 395 HIS cc_start: 0.7448 (t-90) cc_final: 0.7022 (t-90) REVERT: B 396 ASP cc_start: 0.7650 (t0) cc_final: 0.6951 (t0) REVERT: B 462 TYR cc_start: 0.8003 (t80) cc_final: 0.7556 (t80) REVERT: B 467 GLN cc_start: 0.7517 (mm110) cc_final: 0.7313 (mm110) REVERT: B 484 ILE cc_start: 0.8198 (mm) cc_final: 0.7919 (mt) REVERT: B 517 GLN cc_start: 0.7797 (mm110) cc_final: 0.7496 (mm-40) REVERT: B 586 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7568 (mtpp) REVERT: B 622 ASP cc_start: 0.7175 (m-30) cc_final: 0.6840 (m-30) REVERT: B 711 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8010 (mp) REVERT: C 920 GLU cc_start: 0.7639 (pm20) cc_final: 0.7288 (pm20) REVERT: C 954 ASN cc_start: 0.7543 (p0) cc_final: 0.7212 (p0) REVERT: C 983 SER cc_start: 0.8805 (t) cc_final: 0.8256 (p) REVERT: C 1018 ILE cc_start: 0.8005 (pt) cc_final: 0.7767 (pt) REVERT: C 1021 ARG cc_start: 0.8876 (tpp-160) cc_final: 0.8132 (mmt180) REVERT: C 1024 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6849 (mm-30) REVERT: C 1059 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 1095 MET cc_start: 0.6992 (ppp) cc_final: 0.6373 (ppp) REVERT: C 1117 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (p) REVERT: C 1214 PHE cc_start: 0.8186 (t80) cc_final: 0.7977 (t80) REVERT: C 1227 LYS cc_start: 0.8271 (mttt) cc_final: 0.7794 (mttt) REVERT: E 113 MET cc_start: 0.5224 (mmp) cc_final: 0.4831 (mmp) REVERT: E 139 LYS cc_start: 0.7889 (tptt) cc_final: 0.7655 (mptt) REVERT: F 394 ASN cc_start: 0.7774 (t0) cc_final: 0.7284 (t0) REVERT: F 511 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8102 (mmm160) REVERT: F 584 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4864 (ttmm) REVERT: F 586 LYS cc_start: 0.7377 (pttt) cc_final: 0.7059 (pptt) REVERT: F 658 MET cc_start: 0.7301 (tmm) cc_final: 0.7033 (tmm) REVERT: F 679 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: F 694 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7759 (mp) REVERT: G 836 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7188 (ttp80) REVERT: G 839 TYR cc_start: 0.7628 (m-80) cc_final: 0.6031 (m-80) REVERT: G 914 GLU cc_start: 0.7604 (mp0) cc_final: 0.6930 (mp0) REVERT: G 930 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: G 945 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7647 (mtpp) REVERT: G 989 ASP cc_start: 0.7172 (m-30) cc_final: 0.6967 (m-30) REVERT: G 1019 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7400 (mm-40) REVERT: G 1038 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8362 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8477 (tp) cc_final: 0.8263 (mt) REVERT: G 1061 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6801 (tm-30) REVERT: G 1144 SER cc_start: 0.8477 (t) cc_final: 0.8114 (m) REVERT: G 1148 HIS cc_start: 0.8217 (m-70) cc_final: 0.7790 (m-70) REVERT: G 1150 ASN cc_start: 0.8311 (p0) cc_final: 0.7818 (p0) REVERT: I 142 LYS cc_start: 0.7990 (tmmt) cc_final: 0.7710 (tmtt) REVERT: I 149 VAL cc_start: 0.8380 (m) cc_final: 0.8042 (t) REVERT: I 177 MET cc_start: 0.3419 (OUTLIER) cc_final: 0.2870 (mpp) REVERT: I 221 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7508 (mtt180) REVERT: J 341 VAL cc_start: 0.7952 (m) cc_final: 0.7727 (p) REVERT: J 387 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7291 (mt) REVERT: J 467 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7199 (mm-40) REVERT: J 486 CYS cc_start: 0.5391 (p) cc_final: 0.4979 (p) REVERT: J 522 LYS cc_start: 0.8174 (tttp) cc_final: 0.7559 (tttp) REVERT: J 529 LYS cc_start: 0.8251 (tppt) cc_final: 0.7323 (tppt) REVERT: J 544 THR cc_start: 0.7832 (p) cc_final: 0.7256 (p) REVERT: J 545 ASN cc_start: 0.8635 (t0) cc_final: 0.8396 (t0) REVERT: J 567 LYS cc_start: 0.7476 (mmtp) cc_final: 0.7239 (mmtt) REVERT: J 586 LYS cc_start: 0.6967 (mptt) cc_final: 0.6407 (mmtp) REVERT: K 876 LYS cc_start: 0.7757 (tttp) cc_final: 0.7408 (tttm) REVERT: K 960 ASP cc_start: 0.7727 (p0) cc_final: 0.7400 (p0) REVERT: K 1019 GLN cc_start: 0.8047 (mt0) cc_final: 0.7799 (mt0) REVERT: K 1022 THR cc_start: 0.8539 (t) cc_final: 0.8055 (p) REVERT: K 1115 THR cc_start: 0.8623 (t) cc_final: 0.8312 (p) REVERT: K 1130 VAL cc_start: 0.8061 (p) cc_final: 0.7775 (t) REVERT: K 1181 VAL cc_start: 0.8361 (t) cc_final: 0.8143 (m) outliers start: 122 outliers final: 96 residues processed: 797 average time/residue: 0.1633 time to fit residues: 201.2074 Evaluate side-chains 840 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 734 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1217 MET Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN B 340 ASN B 395 HIS B 545 ASN B 623 HIS C1050 GLN ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 GLN F 517 GLN G 847 GLN G 954 ASN G1155 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109082 restraints weight = 40652.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112376 restraints weight = 17290.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114421 restraints weight = 9374.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115851 restraints weight = 6046.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116715 restraints weight = 4437.980| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24964 Z= 0.117 Angle : 0.618 17.615 34036 Z= 0.305 Chirality : 0.044 0.525 3804 Planarity : 0.004 0.057 4362 Dihedral : 4.345 55.785 3691 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.79 % Allowed : 28.77 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.07 (0.15), residues: 3106 helix: 2.94 (0.28), residues: 324 sheet: 0.57 (0.17), residues: 975 loop : -1.00 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 206 TYR 0.030 0.001 TYR K1029 PHE 0.030 0.001 PHE C1235 TRP 0.011 0.001 TRP I 251 HIS 0.009 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (24901) covalent geometry : angle 0.60040 / 0.30 (33895) SS BOND : bond 0.00386 / 0.23 ( 48) SS BOND : angle 1.15753 / 0.70 ( 96) hydrogen bonds : bond 0.03468 / 2.40 ( 943) hydrogen bonds : angle 4.37881 / 3.05 ( 2466) link_BETA1-4 : bond 0.00395 / 0.27 ( 6) link_BETA1-4 : angle 1.19140 / 0.71 ( 18) link_NAG-ASN : bond 0.00907 / 0.70 ( 9) link_NAG-ASN : angle 4.89572 / 4.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 754 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7590 (mmmt) cc_final: 0.7102 (mmmt) REVERT: A 251 TRP cc_start: 0.6906 (m-10) cc_final: 0.6671 (m-90) REVERT: B 387 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7341 (mt) REVERT: B 394 ASN cc_start: 0.7981 (p0) cc_final: 0.7666 (p0) REVERT: B 395 HIS cc_start: 0.7320 (t70) cc_final: 0.6879 (t70) REVERT: B 462 TYR cc_start: 0.7997 (t80) cc_final: 0.7533 (t80) REVERT: B 484 ILE cc_start: 0.8154 (mm) cc_final: 0.7877 (mt) REVERT: B 517 GLN cc_start: 0.7790 (mm110) cc_final: 0.7483 (mm-40) REVERT: B 586 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7572 (mtpp) REVERT: B 711 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 920 GLU cc_start: 0.7577 (pm20) cc_final: 0.7219 (pm20) REVERT: C 950 VAL cc_start: 0.7864 (t) cc_final: 0.7257 (m) REVERT: C 954 ASN cc_start: 0.7512 (p0) cc_final: 0.7178 (p0) REVERT: C 983 SER cc_start: 0.8790 (t) cc_final: 0.8269 (p) REVERT: C 1018 ILE cc_start: 0.7989 (pt) cc_final: 0.7771 (pt) REVERT: C 1021 ARG cc_start: 0.8907 (tpp-160) cc_final: 0.8222 (mmt180) REVERT: C 1024 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6876 (mm-30) REVERT: C 1059 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8116 (mp) REVERT: C 1095 MET cc_start: 0.6898 (ppp) cc_final: 0.6276 (ppp) REVERT: C 1117 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8136 (p) REVERT: C 1227 LYS cc_start: 0.8288 (mttt) cc_final: 0.7829 (mttt) REVERT: E 113 MET cc_start: 0.5194 (mmp) cc_final: 0.4839 (mmp) REVERT: F 394 ASN cc_start: 0.7798 (t0) cc_final: 0.7343 (t0) REVERT: F 511 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.8091 (mmm160) REVERT: F 584 LYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4868 (ttmm) REVERT: F 679 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8118 (mtmm) REVERT: G 836 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7203 (ttp80) REVERT: G 839 TYR cc_start: 0.7633 (m-80) cc_final: 0.6042 (m-80) REVERT: G 914 GLU cc_start: 0.7572 (mp0) cc_final: 0.6965 (mp0) REVERT: G 930 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7845 (ttp-110) REVERT: G 945 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7642 (mtpp) REVERT: G 1019 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7316 (mm-40) REVERT: G 1038 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8362 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8463 (tp) cc_final: 0.8252 (mt) REVERT: G 1061 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6851 (tm-30) REVERT: G 1144 SER cc_start: 0.8417 (t) cc_final: 0.8042 (m) REVERT: G 1148 HIS cc_start: 0.8242 (m-70) cc_final: 0.7836 (m-70) REVERT: G 1150 ASN cc_start: 0.8310 (p0) cc_final: 0.7818 (p0) REVERT: G 1213 VAL cc_start: 0.8629 (p) cc_final: 0.8425 (t) REVERT: I 142 LYS cc_start: 0.8091 (tmmt) cc_final: 0.7752 (tmtt) REVERT: I 149 VAL cc_start: 0.8411 (m) cc_final: 0.8179 (t) REVERT: I 177 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.3138 (mpp) REVERT: I 221 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7414 (mtt180) REVERT: J 341 VAL cc_start: 0.7888 (m) cc_final: 0.7656 (p) REVERT: J 387 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7284 (mt) REVERT: J 529 LYS cc_start: 0.8270 (tppt) cc_final: 0.7405 (tppt) REVERT: J 544 THR cc_start: 0.7799 (p) cc_final: 0.7272 (p) REVERT: J 545 ASN cc_start: 0.8622 (t0) cc_final: 0.8413 (t0) REVERT: J 567 LYS cc_start: 0.7433 (mmtp) cc_final: 0.7227 (mmtt) REVERT: J 586 LYS cc_start: 0.6949 (mptt) cc_final: 0.6389 (mmtp) REVERT: K 876 LYS cc_start: 0.7796 (tttp) cc_final: 0.7451 (tttm) REVERT: K 917 GLN cc_start: 0.8697 (tt0) cc_final: 0.8449 (tp40) REVERT: K 938 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8133 (mtmm) REVERT: K 1019 GLN cc_start: 0.7971 (mt0) cc_final: 0.7723 (mt0) REVERT: K 1022 THR cc_start: 0.8581 (t) cc_final: 0.8089 (p) REVERT: K 1115 THR cc_start: 0.8630 (t) cc_final: 0.8315 (p) REVERT: K 1130 VAL cc_start: 0.8071 (p) cc_final: 0.7771 (t) REVERT: K 1156 GLU cc_start: 0.7251 (pm20) cc_final: 0.7025 (pm20) REVERT: K 1181 VAL cc_start: 0.8357 (t) cc_final: 0.8141 (m) outliers start: 127 outliers final: 98 residues processed: 809 average time/residue: 0.1598 time to fit residues: 199.8401 Evaluate side-chains 831 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 724 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 833 HIS Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1217 MET Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 146 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 395 HIS B 557 GLN E 125 HIS ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 954 ASN ** G 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1079 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106059 restraints weight = 40536.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109176 restraints weight = 17475.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111203 restraints weight = 9619.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112546 restraints weight = 6255.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113337 restraints weight = 4630.262| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24964 Z= 0.112 Angle : 0.624 17.453 34036 Z= 0.308 Chirality : 0.044 0.524 3804 Planarity : 0.004 0.056 4362 Dihedral : 4.310 54.971 3691 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.22 % Allowed : 29.37 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.04 (0.15), residues: 3106 helix: 2.94 (0.27), residues: 324 sheet: 0.58 (0.17), residues: 975 loop : -0.98 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.025 0.001 TYR G 891 PHE 0.029 0.001 PHE K1235 TRP 0.010 0.001 TRP D 102 HIS 0.011 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (24901) covalent geometry : angle 0.60659 / 0.30 (33895) SS BOND : bond 0.00338 / 0.20 ( 48) SS BOND : angle 1.22590 / 0.79 ( 96) hydrogen bonds : bond 0.03357 / 2.32 ( 943) hydrogen bonds : angle 4.39616 / 3.05 ( 2466) link_BETA1-4 : bond 0.00481 / 0.32 ( 6) link_BETA1-4 : angle 1.18825 / 0.71 ( 18) link_NAG-ASN : bond 0.00907 / 0.70 ( 9) link_NAG-ASN : angle 4.81390 / 4.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 734 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7113 (mmmt) REVERT: A 251 TRP cc_start: 0.6956 (m-10) cc_final: 0.6736 (m-90) REVERT: A 258 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7411 (ttp-170) REVERT: B 387 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7269 (mt) REVERT: B 394 ASN cc_start: 0.8010 (p0) cc_final: 0.7695 (p0) REVERT: B 395 HIS cc_start: 0.7406 (t-90) cc_final: 0.7060 (t-90) REVERT: B 396 ASP cc_start: 0.7646 (t0) cc_final: 0.6934 (t0) REVERT: B 462 TYR cc_start: 0.8004 (t80) cc_final: 0.7514 (t80) REVERT: B 484 ILE cc_start: 0.8158 (mm) cc_final: 0.7887 (mt) REVERT: B 517 GLN cc_start: 0.7794 (mm110) cc_final: 0.7480 (mm-40) REVERT: B 586 LYS cc_start: 0.8176 (mmmm) cc_final: 0.7569 (mtpp) REVERT: B 711 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8058 (mp) REVERT: C 920 GLU cc_start: 0.7561 (pm20) cc_final: 0.7197 (pm20) REVERT: C 950 VAL cc_start: 0.7807 (t) cc_final: 0.7161 (m) REVERT: C 983 SER cc_start: 0.8763 (t) cc_final: 0.8224 (p) REVERT: C 998 GLU cc_start: 0.6272 (mp0) cc_final: 0.5934 (mp0) REVERT: C 1018 ILE cc_start: 0.7986 (pt) cc_final: 0.7782 (pt) REVERT: C 1021 ARG cc_start: 0.8909 (tpp-160) cc_final: 0.8216 (mmt180) REVERT: C 1024 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 1059 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8115 (mp) REVERT: C 1095 MET cc_start: 0.6969 (ppp) cc_final: 0.6333 (ppp) REVERT: C 1117 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8130 (p) REVERT: C 1227 LYS cc_start: 0.8262 (mttt) cc_final: 0.7843 (mttt) REVERT: E 113 MET cc_start: 0.5209 (mmp) cc_final: 0.4814 (mmp) REVERT: F 394 ASN cc_start: 0.7819 (t0) cc_final: 0.7342 (t0) REVERT: F 511 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8073 (mmm160) REVERT: F 584 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4892 (ttmm) REVERT: F 586 LYS cc_start: 0.7316 (pttt) cc_final: 0.6974 (pptt) REVERT: F 679 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: G 836 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7197 (ttp80) REVERT: G 839 TYR cc_start: 0.7681 (m-80) cc_final: 0.6114 (m-80) REVERT: G 914 GLU cc_start: 0.7560 (mp0) cc_final: 0.6916 (mp0) REVERT: G 930 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7855 (ttp-110) REVERT: G 945 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7619 (mtpp) REVERT: G 1000 PHE cc_start: 0.7998 (m-80) cc_final: 0.7727 (m-80) REVERT: G 1019 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7284 (mm-40) REVERT: G 1059 LEU cc_start: 0.8453 (tp) cc_final: 0.8229 (mt) REVERT: G 1061 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6903 (tm-30) REVERT: G 1144 SER cc_start: 0.8333 (t) cc_final: 0.7960 (m) REVERT: G 1148 HIS cc_start: 0.8236 (m-70) cc_final: 0.7831 (m-70) REVERT: G 1150 ASN cc_start: 0.8332 (p0) cc_final: 0.7808 (p0) REVERT: I 126 GLU cc_start: 0.6393 (tp30) cc_final: 0.5824 (tp30) REVERT: I 149 VAL cc_start: 0.8399 (m) cc_final: 0.8187 (t) REVERT: I 177 MET cc_start: 0.3617 (OUTLIER) cc_final: 0.3205 (mpp) REVERT: I 221 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7446 (mtt180) REVERT: J 348 TYR cc_start: 0.8607 (p90) cc_final: 0.8124 (p90) REVERT: J 351 TYR cc_start: 0.7952 (t80) cc_final: 0.7653 (t80) REVERT: J 387 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7244 (mt) REVERT: J 529 LYS cc_start: 0.8309 (tppt) cc_final: 0.7470 (tppt) REVERT: J 544 THR cc_start: 0.7782 (p) cc_final: 0.7352 (p) REVERT: J 567 LYS cc_start: 0.7409 (mmtp) cc_final: 0.7138 (mmtt) REVERT: J 586 LYS cc_start: 0.6947 (mptt) cc_final: 0.6396 (mmtp) REVERT: K 917 GLN cc_start: 0.8693 (tt0) cc_final: 0.8460 (tp40) REVERT: K 938 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8121 (mtmm) REVERT: K 1019 GLN cc_start: 0.7925 (mt0) cc_final: 0.7670 (mt0) REVERT: K 1022 THR cc_start: 0.8574 (t) cc_final: 0.8064 (p) REVERT: K 1115 THR cc_start: 0.8624 (t) cc_final: 0.8311 (p) REVERT: K 1130 VAL cc_start: 0.8059 (p) cc_final: 0.7756 (t) REVERT: K 1156 GLU cc_start: 0.7241 (pm20) cc_final: 0.7019 (pm20) REVERT: K 1181 VAL cc_start: 0.8355 (t) cc_final: 0.8138 (m) outliers start: 112 outliers final: 90 residues processed: 779 average time/residue: 0.1638 time to fit residues: 196.6975 Evaluate side-chains 822 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 723 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 196 optimal weight: 0.0770 chunk 215 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 395 HIS B 545 ASN B 557 GLN ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS F 517 GLN G 954 ASN ** G 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1079 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109593 restraints weight = 40609.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112890 restraints weight = 17262.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114967 restraints weight = 9305.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116305 restraints weight = 6009.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117274 restraints weight = 4416.390| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24964 Z= 0.111 Angle : 0.632 17.377 34036 Z= 0.312 Chirality : 0.044 0.520 3804 Planarity : 0.004 0.056 4362 Dihedral : 4.264 53.969 3691 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.15 % Allowed : 29.64 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.02 (0.15), residues: 3106 helix: 2.94 (0.27), residues: 324 sheet: 0.61 (0.17), residues: 990 loop : -0.97 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 206 TYR 0.024 0.001 TYR J 402 PHE 0.027 0.001 PHE C1235 TRP 0.014 0.001 TRP I 251 HIS 0.012 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (24901) covalent geometry : angle 0.61439 / 0.31 (33895) SS BOND : bond 0.00356 / 0.21 ( 48) SS BOND : angle 1.16091 / 0.73 ( 96) hydrogen bonds : bond 0.03274 / 2.26 ( 943) hydrogen bonds : angle 4.35542 / 3.03 ( 2466) link_BETA1-4 : bond 0.00397 / 0.26 ( 6) link_BETA1-4 : angle 1.17883 / 0.69 ( 18) link_NAG-ASN : bond 0.00901 / 0.70 ( 9) link_NAG-ASN : angle 4.85293 / 4.46 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 726 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7119 (mmmt) REVERT: A 251 TRP cc_start: 0.6986 (m-10) cc_final: 0.6768 (m-90) REVERT: B 387 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7239 (mt) REVERT: B 394 ASN cc_start: 0.8014 (p0) cc_final: 0.7706 (p0) REVERT: B 395 HIS cc_start: 0.7285 (t70) cc_final: 0.6886 (t70) REVERT: B 462 TYR cc_start: 0.8011 (t80) cc_final: 0.7530 (t80) REVERT: B 484 ILE cc_start: 0.8175 (mm) cc_final: 0.7893 (mt) REVERT: B 517 GLN cc_start: 0.7808 (mm110) cc_final: 0.7481 (mm-40) REVERT: B 586 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7578 (mtpp) REVERT: B 711 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 920 GLU cc_start: 0.7563 (pm20) cc_final: 0.7182 (pm20) REVERT: C 950 VAL cc_start: 0.7708 (t) cc_final: 0.7057 (m) REVERT: C 983 SER cc_start: 0.8745 (t) cc_final: 0.8194 (p) REVERT: C 998 GLU cc_start: 0.6254 (mp0) cc_final: 0.5926 (mp0) REVERT: C 1021 ARG cc_start: 0.8949 (tpp-160) cc_final: 0.8257 (mmt180) REVERT: C 1024 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6915 (mm-30) REVERT: C 1059 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 1095 MET cc_start: 0.6973 (ppp) cc_final: 0.6321 (ppp) REVERT: C 1117 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (p) REVERT: C 1227 LYS cc_start: 0.8247 (mttt) cc_final: 0.7812 (mttt) REVERT: E 113 MET cc_start: 0.5149 (mmp) cc_final: 0.4763 (mmp) REVERT: F 363 SER cc_start: 0.8578 (t) cc_final: 0.8312 (p) REVERT: F 394 ASN cc_start: 0.7812 (t0) cc_final: 0.7379 (t0) REVERT: F 511 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.8035 (mmm160) REVERT: F 584 LYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4884 (ttmm) REVERT: F 586 LYS cc_start: 0.7330 (pttt) cc_final: 0.6980 (pptt) REVERT: F 679 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8101 (mtmm) REVERT: G 914 GLU cc_start: 0.7582 (mp0) cc_final: 0.6936 (mp0) REVERT: G 930 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7844 (ttp-110) REVERT: G 945 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7599 (mtpp) REVERT: G 1000 PHE cc_start: 0.7956 (m-80) cc_final: 0.7661 (m-80) REVERT: G 1019 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7347 (mm-40) REVERT: G 1059 LEU cc_start: 0.8434 (tp) cc_final: 0.8184 (mt) REVERT: G 1061 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6898 (tm-30) REVERT: G 1144 SER cc_start: 0.8310 (t) cc_final: 0.7953 (m) REVERT: G 1148 HIS cc_start: 0.8231 (m-70) cc_final: 0.7841 (m-70) REVERT: G 1150 ASN cc_start: 0.8336 (p0) cc_final: 0.7800 (p0) REVERT: I 126 GLU cc_start: 0.6289 (tp30) cc_final: 0.5756 (tp30) REVERT: I 177 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3437 (mpp) REVERT: I 221 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7416 (mtt180) REVERT: J 351 TYR cc_start: 0.7919 (t80) cc_final: 0.7693 (t80) REVERT: J 486 CYS cc_start: 0.5460 (p) cc_final: 0.5086 (p) REVERT: J 529 LYS cc_start: 0.8262 (tppt) cc_final: 0.7539 (tppt) REVERT: J 544 THR cc_start: 0.7836 (p) cc_final: 0.7594 (p) REVERT: J 567 LYS cc_start: 0.7408 (mmtp) cc_final: 0.7132 (mmtt) REVERT: J 586 LYS cc_start: 0.6948 (mptt) cc_final: 0.6430 (mmtp) REVERT: K 917 GLN cc_start: 0.8686 (tt0) cc_final: 0.8452 (tp40) REVERT: K 938 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8130 (mtmm) REVERT: K 1019 GLN cc_start: 0.7916 (mt0) cc_final: 0.7681 (mt0) REVERT: K 1022 THR cc_start: 0.8564 (t) cc_final: 0.8052 (p) REVERT: K 1115 THR cc_start: 0.8623 (t) cc_final: 0.8308 (p) REVERT: K 1130 VAL cc_start: 0.8076 (p) cc_final: 0.7768 (t) REVERT: K 1156 GLU cc_start: 0.7242 (pm20) cc_final: 0.7000 (pm20) REVERT: K 1181 VAL cc_start: 0.8357 (t) cc_final: 0.8140 (m) outliers start: 110 outliers final: 91 residues processed: 772 average time/residue: 0.1636 time to fit residues: 194.7493 Evaluate side-chains 826 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 727 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1223 SER Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1168 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 139 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 395 HIS B 557 GLN ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS G 954 ASN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1079 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110272 restraints weight = 40411.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113462 restraints weight = 16871.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115506 restraints weight = 8944.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116778 restraints weight = 5669.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117653 restraints weight = 4130.847| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 24964 Z= 0.149 Angle : 0.775 59.186 34036 Z= 0.410 Chirality : 0.044 0.520 3804 Planarity : 0.004 0.056 4362 Dihedral : 4.264 53.958 3691 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.07 % Allowed : 29.94 % Favored : 65.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % 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: -0.01 (0.15), residues: 3106 helix: 2.94 (0.27), residues: 324 sheet: 0.61 (0.17), residues: 990 loop : -0.97 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 206 TYR 0.022 0.001 TYR J 402 PHE 0.025 0.001 PHE K1235 TRP 0.031 0.001 TRP E 195 HIS 0.010 0.001 HIS F 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (24901) covalent geometry : angle 0.76154 / 0.41 (33895) SS BOND : bond 0.00339 / 0.19 ( 48) SS BOND : angle 1.15250 / 0.72 ( 96) hydrogen bonds : bond 0.03358 / 2.31 ( 943) hydrogen bonds : angle 4.36000 / 3.04 ( 2466) link_BETA1-4 : bond 0.00395 / 0.26 ( 6) link_BETA1-4 : angle 1.18039 / 0.69 ( 18) link_NAG-ASN : bond 0.00900 / 0.70 ( 9) link_NAG-ASN : angle 4.84762 / 4.45 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.94 seconds wall clock time: 89 minutes 12.09 seconds (5352.09 seconds total)