Starting phenix.real_space_refine on Fri May 23 16:14:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_37982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_37982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_37982.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_37982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0m_37982/05_2025/8x0m_37982.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.64, per 1000 atoms: 0.60 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: 6.31 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4.26 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: 11.64 Time building geometry restraints manager: 7.48 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: 0.03 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.460 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 9.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP I 251 HIS 0.005 0.001 HIS F 623 PHE 0.034 0.002 PHE B 339 TYR 0.031 0.002 TYR K 861 ARG 0.012 0.001 ARG G 949 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 9) link_NAG-ASN : angle 5.49814 ( 27) link_BETA1-4 : bond 0.00727 ( 6) link_BETA1-4 : angle 1.72960 ( 18) hydrogen bonds : bond 0.11436 ( 943) hydrogen bonds : angle 5.29821 ( 2466) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.40664 ( 96) covalent geometry : bond 0.00358 (24901) covalent geometry : angle 0.70328 (33895) *********************** 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 : 2.446 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: 0.3672 time to fit residues: 391.0548 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 : 2.616 ------------------------------------------------------------------------------- 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 258 optimal weight: 10.0000 chunk 231 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 954 ASN G1148 HIS ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110145 restraints weight = 40319.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113355 restraints weight = 17048.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115407 restraints weight = 9144.443| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24964 Z= 0.216 Angle : 0.666 16.860 34036 Z= 0.339 Chirality : 0.048 0.542 3804 Planarity : 0.005 0.066 4362 Dihedral : 5.184 51.869 3706 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.68 % Allowed : 27.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3106 helix: 2.76 (0.28), residues: 324 sheet: 0.40 (0.17), residues: 960 loop : -1.14 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 251 HIS 0.007 0.001 HIS F 395 PHE 0.021 0.002 PHE C 910 TYR 0.022 0.002 TYR C 896 ARG 0.008 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01100 ( 9) link_NAG-ASN : angle 5.35548 ( 27) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 1.16901 ( 18) hydrogen bonds : bond 0.04619 ( 943) hydrogen bonds : angle 4.67016 ( 2466) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.23498 ( 96) covalent geometry : bond 0.00495 (24901) covalent geometry : angle 0.64629 (33895) *********************** 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 886 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 762 time to evaluate : 2.786 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: symmetry clash REVERT: A 139 LYS cc_start: 0.7415 (mmmt) cc_final: 0.6925 (mmmt) REVERT: A 211 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7804 (p) REVERT: B 395 HIS cc_start: 0.7566 (t-90) cc_final: 0.7241 (t-90) REVERT: B 396 ASP cc_start: 0.7712 (t0) cc_final: 0.7229 (t0) REVERT: B 462 TYR cc_start: 0.7990 (t80) cc_final: 0.7637 (t80) REVERT: B 484 ILE cc_start: 0.8225 (mm) cc_final: 0.7952 (mt) REVERT: B 498 GLU cc_start: 0.7047 (pm20) cc_final: 0.6846 (pm20) REVERT: B 566 LYS cc_start: 0.7442 (mmmm) cc_final: 0.7233 (mmmm) REVERT: B 677 GLU cc_start: 0.7683 (pm20) cc_final: 0.7279 (pm20) REVERT: C 818 HIS cc_start: 0.6013 (t-90) cc_final: 0.5720 (t-90) REVERT: C 930 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8238 (ttp-110) REVERT: C 1024 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 1095 MET cc_start: 0.7108 (ppp) cc_final: 0.6631 (ppp) REVERT: E 113 MET cc_start: 0.5052 (mmp) cc_final: 0.4676 (mmp) REVERT: E 165 LYS cc_start: 0.8629 (tptp) cc_final: 0.8422 (tptp) REVERT: E 252 ASN cc_start: 0.7915 (t0) cc_final: 0.7666 (t0) REVERT: F 394 ASN cc_start: 0.7699 (t0) cc_final: 0.7174 (t0) REVERT: F 399 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7573 (mtpp) REVERT: F 589 ILE cc_start: 0.8583 (tt) cc_final: 0.8371 (tt) REVERT: F 638 TYR cc_start: 0.8508 (p90) cc_final: 0.8158 (p90) REVERT: F 659 GLU cc_start: 0.7436 (tt0) cc_final: 0.7105 (tt0) REVERT: F 686 GLN cc_start: 0.7892 (mt0) cc_final: 0.7668 (mt0) REVERT: F 694 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7871 (mp) REVERT: G 914 GLU cc_start: 0.7643 (mp0) cc_final: 0.7124 (mp0) REVERT: G 945 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7804 (mtpp) REVERT: G 954 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7527 (t0) REVERT: G 1019 GLN cc_start: 0.7800 (mm-40) cc_final: 0.6882 (mm-40) REVERT: G 1082 ARG cc_start: 0.8341 (ptt-90) cc_final: 0.8141 (ptt-90) REVERT: G 1144 SER cc_start: 0.8625 (t) cc_final: 0.8309 (m) REVERT: I 113 MET cc_start: 0.7253 (mmm) cc_final: 0.6960 (mmm) REVERT: I 142 LYS cc_start: 0.7702 (tmmt) cc_final: 0.7361 (tmtt) REVERT: I 193 TYR cc_start: 0.8106 (m-80) cc_final: 0.7650 (m-80) REVERT: J 363 SER cc_start: 0.8504 (t) cc_final: 0.8152 (p) REVERT: J 467 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7132 (mm-40) REVERT: J 473 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8057 (mmtp) REVERT: J 496 THR cc_start: 0.7906 (p) cc_final: 0.7601 (p) REVERT: J 529 LYS cc_start: 0.8228 (tppt) cc_final: 0.7514 (tppt) REVERT: J 547 ASP cc_start: 0.7764 (p0) cc_final: 0.7479 (p0) REVERT: J 567 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7262 (mmtt) REVERT: J 600 VAL cc_start: 0.8563 (p) cc_final: 0.8240 (t) REVERT: J 713 SER cc_start: 0.8183 (t) cc_final: 0.7944 (t) REVERT: K 876 LYS cc_start: 0.7788 (tttp) cc_final: 0.7468 (tttm) REVERT: K 960 ASP cc_start: 0.7698 (p0) cc_final: 0.7401 (p0) REVERT: K 970 THR cc_start: 0.8509 (t) cc_final: 0.8257 (m) REVERT: K 997 ASP cc_start: 0.7638 (p0) cc_final: 0.7316 (p0) REVERT: K 1001 ASN cc_start: 0.7986 (m-40) cc_final: 0.7653 (m-40) REVERT: K 1019 GLN cc_start: 0.8133 (mt0) cc_final: 0.7765 (mt0) REVERT: K 1115 THR cc_start: 0.8631 (t) cc_final: 0.8326 (p) REVERT: K 1223 SER cc_start: 0.8050 (t) cc_final: 0.7840 (t) outliers start: 124 outliers final: 67 residues processed: 821 average time/residue: 0.3534 time to fit residues: 445.5220 Evaluate side-chains 812 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 742 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 211 THR 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 709 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 869 VAL 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 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 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 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 846 MET Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 954 ASN 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 1142 ASP Chi-restraints excluded: chain G residue 1158 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1217 MET Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 242 SER 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 623 HIS Chi-restraints excluded: chain J residue 655 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 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1093 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 292 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 557 GLN ** B 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN ** F 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G1001 ASN G1075 GLN G1155 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN I 197 HIS J 461 GLN J 559 HIS J 686 GLN J 689 GLN K1031 ASN K1079 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108085 restraints weight = 40408.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111392 restraints weight = 17299.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113508 restraints weight = 9412.997| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24964 Z= 0.179 Angle : 0.622 17.965 34036 Z= 0.315 Chirality : 0.046 0.545 3804 Planarity : 0.005 0.063 4362 Dihedral : 4.835 53.862 3695 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.41 % Allowed : 28.39 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3106 helix: 2.78 (0.28), residues: 324 sheet: 0.39 (0.17), residues: 969 loop : -1.15 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 642 HIS 0.015 0.001 HIS B 685 PHE 0.023 0.002 PHE C1235 TYR 0.028 0.002 TYR B 397 ARG 0.006 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00895 ( 9) link_NAG-ASN : angle 5.06902 ( 27) link_BETA1-4 : bond 0.00344 ( 6) link_BETA1-4 : angle 1.20330 ( 18) hydrogen bonds : bond 0.04250 ( 943) hydrogen bonds : angle 4.60059 ( 2466) SS BOND : bond 0.00347 ( 48) SS BOND : angle 1.25775 ( 96) covalent geometry : bond 0.00410 (24901) covalent geometry : angle 0.60197 (33895) *********************** 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 873 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 756 time to evaluate : 2.861 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: 0.7594 (mmmt) cc_final: 0.7144 (mmmt) REVERT: A 201 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: A 211 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 395 HIS cc_start: 0.7546 (t-90) cc_final: 0.7104 (t-90) REVERT: B 396 ASP cc_start: 0.7736 (t0) cc_final: 0.7184 (t0) REVERT: B 462 TYR cc_start: 0.8006 (t80) cc_final: 0.7590 (t80) REVERT: B 484 ILE cc_start: 0.8192 (mm) cc_final: 0.7897 (mt) REVERT: B 498 GLU cc_start: 0.7047 (pm20) cc_final: 0.6845 (pm20) REVERT: B 517 GLN cc_start: 0.7852 (mm110) cc_final: 0.7632 (mm-40) REVERT: B 677 GLU cc_start: 0.7678 (pm20) cc_final: 0.7272 (pm20) REVERT: B 711 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8027 (mp) REVERT: C 818 HIS cc_start: 0.6171 (t-90) cc_final: 0.5890 (t-90) REVERT: C 819 SER cc_start: 0.8266 (m) cc_final: 0.7941 (p) REVERT: C 930 ARG cc_start: 0.8469 (ttp-110) cc_final: 0.8238 (ttp-110) REVERT: C 997 ASP cc_start: 0.7867 (p0) cc_final: 0.6915 (p0) REVERT: C 1018 ILE cc_start: 0.8031 (pt) cc_final: 0.7799 (pt) REVERT: C 1021 ARG cc_start: 0.8897 (tpp-160) cc_final: 0.8600 (tpt170) REVERT: C 1024 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 1095 MET cc_start: 0.7068 (ppp) cc_final: 0.6550 (ppp) REVERT: C 1117 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8257 (p) REVERT: C 1214 PHE cc_start: 0.8184 (t80) cc_final: 0.7881 (t80) REVERT: E 113 MET cc_start: 0.5124 (mmp) cc_final: 0.4733 (mmp) REVERT: F 394 ASN cc_start: 0.7692 (t0) cc_final: 0.7179 (t0) REVERT: F 399 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7616 (mtpp) REVERT: F 511 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8265 (mmm160) REVERT: F 638 TYR cc_start: 0.8550 (p90) cc_final: 0.8233 (p90) REVERT: F 659 GLU cc_start: 0.7395 (tt0) cc_final: 0.7165 (tt0) REVERT: F 686 GLN cc_start: 0.7879 (mt0) cc_final: 0.7674 (mt0) REVERT: F 694 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7913 (mp) REVERT: G 945 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7706 (mtpp) REVERT: G 954 ASN cc_start: 0.7936 (t0) cc_final: 0.7374 (t0) REVERT: G 1019 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7192 (mm-40) REVERT: G 1059 LEU cc_start: 0.8501 (tp) cc_final: 0.8253 (mt) REVERT: G 1061 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6806 (tm-30) REVERT: G 1144 SER cc_start: 0.8701 (t) cc_final: 0.8291 (m) REVERT: I 113 MET cc_start: 0.7334 (mmm) cc_final: 0.6998 (mmm) REVERT: I 142 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7578 (tmtt) REVERT: I 193 TYR cc_start: 0.8074 (m-80) cc_final: 0.7698 (m-80) REVERT: J 373 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7397 (mm-30) REVERT: J 467 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7254 (mm-40) REVERT: J 496 THR cc_start: 0.7896 (p) cc_final: 0.7611 (p) REVERT: J 498 GLU cc_start: 0.6932 (pm20) cc_final: 0.6590 (pm20) REVERT: J 529 LYS cc_start: 0.8200 (tppt) cc_final: 0.7476 (tppt) REVERT: J 547 ASP cc_start: 0.7794 (p0) cc_final: 0.7462 (p0) REVERT: J 567 LYS cc_start: 0.7557 (mmtp) cc_final: 0.7349 (mmtt) REVERT: J 713 SER cc_start: 0.8206 (t) cc_final: 0.7990 (t) REVERT: K 876 LYS cc_start: 0.7808 (tttp) cc_final: 0.7461 (tttm) REVERT: K 960 ASP cc_start: 0.7694 (p0) cc_final: 0.7432 (p0) REVERT: K 970 THR cc_start: 0.8473 (t) cc_final: 0.8160 (p) REVERT: K 1001 ASN cc_start: 0.7980 (m-40) cc_final: 0.7621 (m-40) REVERT: K 1019 GLN cc_start: 0.8138 (mt0) cc_final: 0.7854 (mt0) REVERT: K 1115 THR cc_start: 0.8627 (t) cc_final: 0.8284 (p) REVERT: K 1130 VAL cc_start: 0.8074 (p) cc_final: 0.7769 (t) REVERT: K 1223 SER cc_start: 0.8063 (t) cc_final: 0.7859 (t) outliers start: 117 outliers final: 75 residues processed: 811 average time/residue: 0.3680 time to fit residues: 457.5589 Evaluate side-chains 813 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 733 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 ASP 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 C residue 833 HIS Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE 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 1181 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE 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 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET 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 982 SER Chi-restraints excluded: chain G residue 1024 GLU 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 G residue 1199 LYS Chi-restraints excluded: chain G residue 1218 SER 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 190 GLU Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 450 ASP 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 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 143 optimal weight: 0.0870 chunk 274 optimal weight: 0.6980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 337 GLN B 340 ASN ** B 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 GLN F 565 HIS F 661 HIS G 847 GLN G1067 ASN G1075 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 686 GLN J 689 GLN K1079 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108694 restraints weight = 40687.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112004 restraints weight = 17302.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114050 restraints weight = 9378.511| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1847 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= 0.125 Angle : 0.601 17.256 34036 Z= 0.299 Chirality : 0.045 0.543 3804 Planarity : 0.004 0.060 4362 Dihedral : 4.622 57.283 3695 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.71 % Allowed : 28.58 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3106 helix: 2.82 (0.28), residues: 324 sheet: 0.46 (0.16), residues: 978 loop : -1.12 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 642 HIS 0.014 0.001 HIS B 685 PHE 0.016 0.001 PHE C1235 TYR 0.028 0.001 TYR B 397 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 9) link_NAG-ASN : angle 4.90166 ( 27) link_BETA1-4 : bond 0.00406 ( 6) link_BETA1-4 : angle 1.15039 ( 18) hydrogen bonds : bond 0.03783 ( 943) hydrogen bonds : angle 4.51399 ( 2466) SS BOND : bond 0.00310 ( 48) SS BOND : angle 1.04236 ( 96) covalent geometry : bond 0.00286 (24901) covalent geometry : angle 0.58263 (33895) *********************** 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 870 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 745 time to evaluate : 2.718 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: 0.7613 (mmmt) cc_final: 0.7143 (mmmt) REVERT: A 211 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 395 HIS cc_start: 0.7536 (t-90) cc_final: 0.7108 (t-90) REVERT: B 396 ASP cc_start: 0.7709 (t0) cc_final: 0.7088 (t0) REVERT: B 462 TYR cc_start: 0.7975 (t80) cc_final: 0.7555 (t80) REVERT: B 484 ILE cc_start: 0.8164 (mm) cc_final: 0.7883 (mt) REVERT: B 517 GLN cc_start: 0.7925 (mm110) cc_final: 0.7687 (mm-40) REVERT: B 679 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7884 (mtpp) REVERT: B 711 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8015 (mp) REVERT: C 818 HIS cc_start: 0.6267 (t-90) cc_final: 0.6019 (t-90) REVERT: C 819 SER cc_start: 0.8271 (m) cc_final: 0.7924 (p) REVERT: C 930 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8227 (ttp-110) REVERT: C 954 ASN cc_start: 0.7642 (p0) cc_final: 0.7314 (p0) REVERT: C 983 SER cc_start: 0.8798 (t) cc_final: 0.8233 (p) REVERT: C 997 ASP cc_start: 0.8075 (p0) cc_final: 0.7869 (p0) REVERT: C 1014 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8212 (mmt180) REVERT: C 1018 ILE cc_start: 0.8031 (pt) cc_final: 0.7759 (pt) REVERT: C 1021 ARG cc_start: 0.8890 (tpp-160) cc_final: 0.8545 (tpt170) REVERT: C 1024 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 1059 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 1095 MET cc_start: 0.7073 (ppp) cc_final: 0.6511 (ppp) REVERT: C 1117 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 1166 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8079 (mmtp) REVERT: C 1214 PHE cc_start: 0.8175 (t80) cc_final: 0.7933 (t80) REVERT: E 113 MET cc_start: 0.5301 (mmp) cc_final: 0.4908 (mmp) REVERT: F 394 ASN cc_start: 0.7714 (t0) cc_final: 0.7206 (t0) REVERT: F 459 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (ttm170) REVERT: F 511 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8254 (mmm160) REVERT: F 516 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: F 586 LYS cc_start: 0.7323 (pttt) cc_final: 0.7028 (pptt) REVERT: F 593 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8284 (tt) REVERT: F 638 TYR cc_start: 0.8535 (p90) cc_final: 0.8222 (p90) REVERT: F 659 GLU cc_start: 0.7199 (tt0) cc_final: 0.6978 (tt0) REVERT: F 686 GLN cc_start: 0.7827 (mt0) cc_final: 0.7613 (mt0) REVERT: F 694 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7773 (mp) REVERT: F 699 THR cc_start: 0.7933 (t) cc_final: 0.7719 (p) REVERT: G 914 GLU cc_start: 0.7612 (mp0) cc_final: 0.6968 (mp0) REVERT: G 945 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7659 (mtpp) REVERT: G 954 ASN cc_start: 0.7810 (t0) cc_final: 0.7360 (t0) REVERT: G 1019 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7361 (mm-40) REVERT: G 1038 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8361 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8470 (tp) cc_final: 0.8218 (mt) REVERT: G 1061 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6834 (tm-30) REVERT: G 1082 ARG cc_start: 0.8355 (ptt90) cc_final: 0.8045 (ptt-90) REVERT: G 1144 SER cc_start: 0.8600 (t) cc_final: 0.8231 (m) REVERT: G 1150 ASN cc_start: 0.8301 (p0) cc_final: 0.7843 (p0) REVERT: G 1214 PHE cc_start: 0.8254 (t80) cc_final: 0.8026 (t80) REVERT: I 142 LYS cc_start: 0.7888 (tmmt) cc_final: 0.7618 (tmtt) REVERT: I 193 TYR cc_start: 0.8173 (m-80) cc_final: 0.7797 (m-80) REVERT: I 265 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7210 (tm-30) REVERT: J 373 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7408 (mm-30) REVERT: J 467 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7211 (mm-40) REVERT: J 496 THR cc_start: 0.7838 (p) cc_final: 0.7560 (p) REVERT: J 498 GLU cc_start: 0.6882 (pm20) cc_final: 0.6530 (pm20) REVERT: J 529 LYS cc_start: 0.8237 (tppt) cc_final: 0.7451 (tppt) REVERT: J 544 THR cc_start: 0.7773 (p) cc_final: 0.7532 (t) REVERT: J 547 ASP cc_start: 0.7818 (p0) cc_final: 0.7556 (p0) REVERT: J 586 LYS cc_start: 0.7001 (mptt) cc_final: 0.6448 (mmtp) REVERT: J 713 SER cc_start: 0.8265 (t) cc_final: 0.8052 (t) REVERT: K 876 LYS cc_start: 0.7776 (tttp) cc_final: 0.7409 (tttm) REVERT: K 970 THR cc_start: 0.8470 (t) cc_final: 0.8143 (p) REVERT: K 1019 GLN cc_start: 0.8030 (mt0) cc_final: 0.7789 (mt0) REVERT: K 1115 THR cc_start: 0.8599 (t) cc_final: 0.8294 (p) REVERT: K 1130 VAL cc_start: 0.8058 (p) cc_final: 0.7767 (t) outliers start: 125 outliers final: 78 residues processed: 804 average time/residue: 0.3676 time to fit residues: 452.9147 Evaluate side-chains 832 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 745 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 A residue 211 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE 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 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1059 LEU 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 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 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE 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 444 LEU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 516 GLN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 593 LEU 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 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU 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 854 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 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1199 LYS 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 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 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 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 1095 MET Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS G 847 GLN G1075 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 545 ASN J 559 HIS J 686 GLN J 689 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108247 restraints weight = 40630.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111561 restraints weight = 17260.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113643 restraints weight = 9330.643| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24964 Z= 0.134 Angle : 0.607 17.385 34036 Z= 0.303 Chirality : 0.045 0.547 3804 Planarity : 0.004 0.059 4362 Dihedral : 4.610 58.103 3695 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.83 % Allowed : 28.88 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3106 helix: 2.84 (0.28), residues: 324 sheet: 0.45 (0.16), residues: 978 loop : -1.03 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 642 HIS 0.012 0.001 HIS B 685 PHE 0.024 0.001 PHE C1235 TYR 0.025 0.001 TYR B 397 ARG 0.005 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 9) link_NAG-ASN : angle 4.90574 ( 27) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 1.16952 ( 18) hydrogen bonds : bond 0.03792 ( 943) hydrogen bonds : angle 4.54365 ( 2466) SS BOND : bond 0.00313 ( 48) SS BOND : angle 1.17978 ( 96) covalent geometry : bond 0.00308 (24901) covalent geometry : angle 0.58852 (33895) *********************** 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 886 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 758 time to evaluate : 2.424 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: A 139 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7134 (mmmt) REVERT: B 343 LYS cc_start: 0.8674 (mptt) cc_final: 0.8453 (mptt) REVERT: B 395 HIS cc_start: 0.7554 (t-90) cc_final: 0.7099 (t-90) REVERT: B 396 ASP cc_start: 0.7768 (t0) cc_final: 0.7122 (t0) REVERT: B 462 TYR cc_start: 0.7979 (t80) cc_final: 0.7570 (t80) REVERT: B 484 ILE cc_start: 0.8225 (mm) cc_final: 0.7956 (mt) REVERT: B 517 GLN cc_start: 0.7938 (mm110) cc_final: 0.7676 (mm-40) REVERT: B 586 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8012 (mtpt) REVERT: B 679 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7903 (mtpp) REVERT: B 711 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8044 (mp) REVERT: C 818 HIS cc_start: 0.6432 (t-90) cc_final: 0.6198 (t-90) REVERT: C 819 SER cc_start: 0.8270 (m) cc_final: 0.7929 (p) REVERT: C 930 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8234 (ttp-110) REVERT: C 954 ASN cc_start: 0.7606 (p0) cc_final: 0.7264 (p0) REVERT: C 983 SER cc_start: 0.8846 (t) cc_final: 0.8292 (p) REVERT: C 997 ASP cc_start: 0.8080 (p0) cc_final: 0.7780 (p0) REVERT: C 1014 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8283 (mmt180) REVERT: C 1021 ARG cc_start: 0.8900 (tpp-160) cc_final: 0.8532 (tpt170) REVERT: C 1024 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6889 (mm-30) REVERT: C 1059 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7952 (mp) REVERT: C 1095 MET cc_start: 0.7050 (ppp) cc_final: 0.6448 (ppp) REVERT: C 1117 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8218 (p) REVERT: C 1166 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8119 (mmtp) REVERT: C 1227 LYS cc_start: 0.8257 (mttt) cc_final: 0.7796 (mttt) REVERT: E 113 MET cc_start: 0.5233 (mmp) cc_final: 0.4846 (mmp) REVERT: F 394 ASN cc_start: 0.7734 (t0) cc_final: 0.7213 (t0) REVERT: F 430 MET cc_start: 0.7344 (ttp) cc_final: 0.7013 (ttp) REVERT: F 459 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8449 (ttm170) REVERT: F 511 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8249 (mmm160) REVERT: F 548 MET cc_start: 0.7001 (mpp) cc_final: 0.6553 (mpp) REVERT: F 570 PHE cc_start: 0.8177 (t80) cc_final: 0.7971 (t80) REVERT: F 586 LYS cc_start: 0.7304 (pttt) cc_final: 0.7036 (pptt) REVERT: F 638 TYR cc_start: 0.8517 (p90) cc_final: 0.8142 (p90) REVERT: F 659 GLU cc_start: 0.7199 (tt0) cc_final: 0.6974 (tt0) REVERT: F 686 GLN cc_start: 0.7835 (mt0) cc_final: 0.7613 (mt0) REVERT: G 910 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: G 912 ASP cc_start: 0.7788 (m-30) cc_final: 0.7364 (t0) REVERT: G 914 GLU cc_start: 0.7623 (mp0) cc_final: 0.6935 (mp0) REVERT: G 945 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7689 (mtpp) REVERT: G 1019 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7246 (mm-40) REVERT: G 1059 LEU cc_start: 0.8472 (tp) cc_final: 0.8230 (mt) REVERT: G 1061 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6838 (tm-30) REVERT: G 1091 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8816 (pt) REVERT: G 1144 SER cc_start: 0.8544 (t) cc_final: 0.8189 (m) REVERT: G 1150 ASN cc_start: 0.8306 (p0) cc_final: 0.7810 (p0) REVERT: G 1213 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8401 (t) REVERT: I 142 LYS cc_start: 0.7959 (tmmt) cc_final: 0.7695 (tmtt) REVERT: I 177 MET cc_start: 0.3568 (OUTLIER) cc_final: 0.3324 (mpp) REVERT: I 193 TYR cc_start: 0.8252 (m-80) cc_final: 0.7854 (m-80) REVERT: I 221 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7332 (mtt180) REVERT: I 265 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7203 (tm-30) REVERT: J 373 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7407 (mm-30) REVERT: J 467 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7229 (mm-40) REVERT: J 529 LYS cc_start: 0.8258 (tppt) cc_final: 0.7247 (tppt) REVERT: J 533 ASN cc_start: 0.8265 (t0) cc_final: 0.7319 (t0) REVERT: J 544 THR cc_start: 0.7735 (p) cc_final: 0.6942 (t) REVERT: J 547 ASP cc_start: 0.7853 (p0) cc_final: 0.7535 (p0) REVERT: J 586 LYS cc_start: 0.7010 (mptt) cc_final: 0.6445 (mmtp) REVERT: K 876 LYS cc_start: 0.7794 (tttp) cc_final: 0.7427 (tttm) REVERT: K 970 THR cc_start: 0.8470 (t) cc_final: 0.8144 (p) REVERT: K 1001 ASN cc_start: 0.7925 (m-40) cc_final: 0.7437 (m-40) REVERT: K 1019 GLN cc_start: 0.8066 (mt0) cc_final: 0.7857 (mt0) REVERT: K 1079 ASN cc_start: 0.8478 (t0) cc_final: 0.8255 (t0) REVERT: K 1084 MET cc_start: 0.7738 (mtm) cc_final: 0.7530 (mtp) REVERT: K 1115 THR cc_start: 0.8598 (t) cc_final: 0.8286 (p) REVERT: K 1130 VAL cc_start: 0.8050 (p) cc_final: 0.7770 (t) outliers start: 128 outliers final: 88 residues processed: 814 average time/residue: 0.3665 time to fit residues: 454.3142 Evaluate side-chains 841 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 743 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET 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 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE 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 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS 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 1014 ARG 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 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS 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 444 LEU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 558 CYS 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 694 LEU 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 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 1091 ILE Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1199 LYS Chi-restraints excluded: chain G residue 1213 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 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 365 VAL 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 687 ILE Chi-restraints excluded: chain J residue 689 GLN 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 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1107 GLU 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 1240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 262 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS F 517 GLN F 559 HIS G 847 GLN G 954 ASN G1075 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107479 restraints weight = 40024.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110662 restraints weight = 16782.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112692 restraints weight = 8939.186| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24964 Z= 0.162 Angle : 0.630 17.119 34036 Z= 0.314 Chirality : 0.045 0.524 3804 Planarity : 0.004 0.059 4362 Dihedral : 4.680 59.243 3695 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.58 % Allowed : 27.75 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3106 helix: 2.82 (0.28), residues: 324 sheet: 0.42 (0.17), residues: 972 loop : -1.05 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.011 0.001 HIS B 685 PHE 0.020 0.002 PHE C1235 TYR 0.024 0.002 TYR B 397 ARG 0.005 0.000 ARG G1082 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 9) link_NAG-ASN : angle 5.13391 ( 27) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 1.19688 ( 18) hydrogen bonds : bond 0.04027 ( 943) hydrogen bonds : angle 4.53002 ( 2466) SS BOND : bond 0.00462 ( 48) SS BOND : angle 1.27973 ( 96) covalent geometry : bond 0.00371 (24901) covalent geometry : angle 0.60956 (33895) *********************** 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 920 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 772 time to evaluate : 2.877 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: A 139 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7128 (mmmt) REVERT: B 395 HIS cc_start: 0.7549 (t-90) cc_final: 0.7019 (t-90) REVERT: B 396 ASP cc_start: 0.7822 (t0) cc_final: 0.7203 (t0) REVERT: B 462 TYR cc_start: 0.8003 (t80) cc_final: 0.7521 (t80) REVERT: B 484 ILE cc_start: 0.8284 (mm) cc_final: 0.8020 (mt) REVERT: B 517 GLN cc_start: 0.7962 (mm110) cc_final: 0.7675 (mm-40) REVERT: B 532 TYR cc_start: 0.8359 (p90) cc_final: 0.8095 (p90) REVERT: B 711 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (mp) REVERT: C 818 HIS cc_start: 0.6579 (t-90) cc_final: 0.6304 (t-90) REVERT: C 819 SER cc_start: 0.8182 (m) cc_final: 0.7785 (p) REVERT: C 857 LEU cc_start: 0.8449 (mt) cc_final: 0.8243 (mt) REVERT: C 930 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8207 (ttp-110) REVERT: C 954 ASN cc_start: 0.7623 (p0) cc_final: 0.7275 (p0) REVERT: C 983 SER cc_start: 0.8821 (t) cc_final: 0.8285 (p) REVERT: C 997 ASP cc_start: 0.8073 (p0) cc_final: 0.7032 (p0) REVERT: C 998 GLU cc_start: 0.6372 (mp0) cc_final: 0.5856 (mp0) REVERT: C 1014 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8186 (mmt180) REVERT: C 1018 ILE cc_start: 0.8048 (pt) cc_final: 0.7828 (pt) REVERT: C 1021 ARG cc_start: 0.8945 (tpp-160) cc_final: 0.8333 (tpt170) REVERT: C 1024 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6846 (mm-30) REVERT: C 1059 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 1095 MET cc_start: 0.7063 (ppp) cc_final: 0.6393 (ppp) REVERT: C 1117 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8218 (p) REVERT: C 1166 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8161 (mmtp) REVERT: C 1227 LYS cc_start: 0.8261 (mttt) cc_final: 0.7819 (mttt) REVERT: E 113 MET cc_start: 0.5282 (mmp) cc_final: 0.4929 (mmp) REVERT: E 195 TRP cc_start: 0.8274 (t60) cc_final: 0.7983 (t60) REVERT: E 209 ILE cc_start: 0.8436 (tp) cc_final: 0.8198 (tp) REVERT: F 370 VAL cc_start: 0.8641 (t) cc_final: 0.8419 (m) REVERT: F 394 ASN cc_start: 0.7742 (t0) cc_final: 0.7260 (t0) REVERT: F 399 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8176 (mtpp) REVERT: F 430 MET cc_start: 0.7399 (ttp) cc_final: 0.7103 (ttp) REVERT: F 459 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8469 (ttm170) REVERT: F 548 MET cc_start: 0.7099 (mpp) cc_final: 0.6642 (mpp) REVERT: F 566 LYS cc_start: 0.7259 (mmmt) cc_final: 0.7039 (mmmt) REVERT: F 570 PHE cc_start: 0.8265 (t80) cc_final: 0.8051 (t80) REVERT: F 586 LYS cc_start: 0.7360 (pttt) cc_final: 0.7082 (pptt) REVERT: F 638 TYR cc_start: 0.8556 (p90) cc_final: 0.8238 (p90) REVERT: F 686 GLN cc_start: 0.7862 (mt0) cc_final: 0.7649 (mt0) REVERT: F 694 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7780 (mp) REVERT: F 699 THR cc_start: 0.7929 (t) cc_final: 0.7695 (p) REVERT: G 844 LEU cc_start: 0.7327 (mm) cc_final: 0.7118 (mt) REVERT: G 912 ASP cc_start: 0.7794 (m-30) cc_final: 0.7394 (t0) REVERT: G 914 GLU cc_start: 0.7616 (mp0) cc_final: 0.6941 (mp0) REVERT: G 945 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7689 (mtpp) REVERT: G 954 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7485 (t0) REVERT: G 982 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8513 (p) REVERT: G 1019 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7300 (mm-40) REVERT: G 1059 LEU cc_start: 0.8481 (tp) cc_final: 0.8257 (mt) REVERT: G 1061 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6895 (tm-30) REVERT: G 1144 SER cc_start: 0.8540 (t) cc_final: 0.8229 (m) REVERT: G 1150 ASN cc_start: 0.8279 (p0) cc_final: 0.7765 (p0) REVERT: G 1213 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8404 (t) REVERT: I 126 GLU cc_start: 0.6483 (tp30) cc_final: 0.5905 (tp30) REVERT: I 142 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7821 (tmtt) REVERT: I 149 VAL cc_start: 0.8272 (m) cc_final: 0.8019 (t) REVERT: I 177 MET cc_start: 0.3981 (OUTLIER) cc_final: 0.3655 (mpp) REVERT: I 193 TYR cc_start: 0.8408 (m-80) cc_final: 0.7933 (m-80) REVERT: I 221 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: J 373 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7360 (mm-30) REVERT: J 387 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7341 (mt) REVERT: J 402 TYR cc_start: 0.8267 (p90) cc_final: 0.7990 (p90) REVERT: J 467 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7243 (mm-40) REVERT: J 522 LYS cc_start: 0.8236 (tttp) cc_final: 0.7602 (tttp) REVERT: J 529 LYS cc_start: 0.8296 (tppt) cc_final: 0.7368 (tppt) REVERT: J 533 ASN cc_start: 0.8332 (t0) cc_final: 0.7411 (t0) REVERT: J 544 THR cc_start: 0.7748 (p) cc_final: 0.7068 (t) REVERT: J 547 ASP cc_start: 0.7757 (p0) cc_final: 0.7520 (p0) REVERT: J 586 LYS cc_start: 0.6998 (mptt) cc_final: 0.6430 (mmtp) REVERT: K 822 MET cc_start: 0.8017 (ptp) cc_final: 0.7700 (ptm) REVERT: K 876 LYS cc_start: 0.7875 (tttp) cc_final: 0.7490 (tttm) REVERT: K 938 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8180 (mtmm) REVERT: K 970 THR cc_start: 0.8470 (t) cc_final: 0.8141 (p) REVERT: K 986 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 1014 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8095 (mmt90) REVERT: K 1019 GLN cc_start: 0.8127 (mt0) cc_final: 0.7829 (mt0) REVERT: K 1079 ASN cc_start: 0.8529 (t0) cc_final: 0.8315 (t0) REVERT: K 1084 MET cc_start: 0.7736 (mtm) cc_final: 0.7529 (mtp) REVERT: K 1115 THR cc_start: 0.8622 (t) cc_final: 0.8296 (p) REVERT: K 1130 VAL cc_start: 0.8059 (p) cc_final: 0.7765 (t) outliers start: 148 outliers final: 101 residues processed: 838 average time/residue: 0.3737 time to fit residues: 478.9708 Evaluate side-chains 874 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 759 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 345 THR 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 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 589 ILE 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 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS 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 1014 ARG 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 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS 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 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS 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 694 LEU 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 854 GLU Chi-restraints excluded: chain G residue 870 VAL 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 954 ASN Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 982 SER 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 1158 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1213 VAL 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 170 CYS Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 387 ILE 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 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL 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 986 THR Chi-restraints excluded: chain K residue 1014 ARG 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 1186 SER Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 207 optimal weight: 0.0670 chunk 304 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 overall best weight: 2.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 551 ASN C1209 HIS E 125 HIS F 517 GLN ** F 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G 954 ASN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106008 restraints weight = 40241.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109201 restraints weight = 16772.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111230 restraints weight = 8923.560| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24964 Z= 0.161 Angle : 0.629 18.117 34036 Z= 0.316 Chirality : 0.045 0.535 3804 Planarity : 0.004 0.058 4362 Dihedral : 4.682 56.840 3695 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.02 % Allowed : 28.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3106 helix: 2.83 (0.28), residues: 324 sheet: 0.39 (0.17), residues: 978 loop : -1.06 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.019 0.001 HIS F 559 PHE 0.026 0.002 PHE C1235 TYR 0.033 0.002 TYR B 397 ARG 0.005 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 9) link_NAG-ASN : angle 5.10572 ( 27) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.22308 ( 18) hydrogen bonds : bond 0.04044 ( 943) hydrogen bonds : angle 4.56263 ( 2466) SS BOND : bond 0.00380 ( 48) SS BOND : angle 1.29449 ( 96) covalent geometry : bond 0.00370 (24901) covalent geometry : angle 0.60958 (33895) *********************** 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 903 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 770 time to evaluate : 2.539 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: A 139 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7127 (mmmt) REVERT: B 395 HIS cc_start: 0.7427 (t70) cc_final: 0.6804 (t70) REVERT: B 396 ASP cc_start: 0.7789 (t0) cc_final: 0.7186 (t0) REVERT: B 462 TYR cc_start: 0.8020 (t80) cc_final: 0.7552 (t80) REVERT: B 484 ILE cc_start: 0.8270 (mm) cc_final: 0.8007 (mt) REVERT: B 517 GLN cc_start: 0.7964 (mm110) cc_final: 0.7663 (mm-40) REVERT: B 532 TYR cc_start: 0.8381 (p90) cc_final: 0.8027 (p90) REVERT: B 635 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7286 (t0) REVERT: B 711 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (mp) REVERT: C 818 HIS cc_start: 0.6706 (t-90) cc_final: 0.6454 (t-90) REVERT: C 819 SER cc_start: 0.8185 (m) cc_final: 0.7792 (p) REVERT: C 857 LEU cc_start: 0.8453 (mt) cc_final: 0.8248 (mt) REVERT: C 954 ASN cc_start: 0.7608 (p0) cc_final: 0.7258 (p0) REVERT: C 983 SER cc_start: 0.8814 (t) cc_final: 0.8282 (p) REVERT: C 997 ASP cc_start: 0.8051 (p0) cc_final: 0.6991 (p0) REVERT: C 998 GLU cc_start: 0.6380 (mp0) cc_final: 0.5844 (mp0) REVERT: C 1014 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8293 (mmt180) REVERT: C 1018 ILE cc_start: 0.8057 (pt) cc_final: 0.7829 (pt) REVERT: C 1021 ARG cc_start: 0.8913 (tpp-160) cc_final: 0.8399 (tpt170) REVERT: C 1024 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6929 (mm-30) REVERT: C 1059 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 1095 MET cc_start: 0.7047 (ppp) cc_final: 0.6359 (ppp) REVERT: C 1117 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8200 (p) REVERT: C 1166 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8167 (mmtp) REVERT: C 1227 LYS cc_start: 0.8300 (mttt) cc_final: 0.7864 (mttt) REVERT: E 113 MET cc_start: 0.5295 (mmp) cc_final: 0.4937 (mmp) REVERT: E 165 LYS cc_start: 0.8732 (tptp) cc_final: 0.8517 (tptp) REVERT: F 370 VAL cc_start: 0.8644 (t) cc_final: 0.8422 (m) REVERT: F 394 ASN cc_start: 0.7738 (t0) cc_final: 0.7255 (t0) REVERT: F 399 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8202 (mtpp) REVERT: F 430 MET cc_start: 0.7410 (ttp) cc_final: 0.7078 (ttp) REVERT: F 459 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8458 (ttm170) REVERT: F 548 MET cc_start: 0.7040 (mpp) cc_final: 0.6613 (mpp) REVERT: F 570 PHE cc_start: 0.8253 (t80) cc_final: 0.8040 (t80) REVERT: F 586 LYS cc_start: 0.7396 (pttt) cc_final: 0.7091 (pptt) REVERT: F 638 TYR cc_start: 0.8553 (p90) cc_final: 0.8239 (p90) REVERT: F 686 GLN cc_start: 0.7869 (mt0) cc_final: 0.7662 (mt0) REVERT: F 694 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7787 (mp) REVERT: F 699 THR cc_start: 0.7898 (t) cc_final: 0.7695 (p) REVERT: G 912 ASP cc_start: 0.7811 (m-30) cc_final: 0.7395 (t0) REVERT: G 914 GLU cc_start: 0.7616 (mp0) cc_final: 0.6962 (mp0) REVERT: G 945 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7658 (mtpp) REVERT: G 954 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7399 (t0) REVERT: G 982 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (p) REVERT: G 1019 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7353 (mm-40) REVERT: G 1059 LEU cc_start: 0.8466 (tp) cc_final: 0.8261 (mt) REVERT: G 1061 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6932 (tm-30) REVERT: G 1144 SER cc_start: 0.8539 (t) cc_final: 0.8226 (m) REVERT: G 1213 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8393 (t) REVERT: I 113 MET cc_start: 0.7336 (mmm) cc_final: 0.6926 (mmm) REVERT: I 126 GLU cc_start: 0.6333 (tp30) cc_final: 0.5735 (tp30) REVERT: I 141 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6216 (ptt) REVERT: I 142 LYS cc_start: 0.8187 (tmmt) cc_final: 0.7947 (tmtt) REVERT: I 177 MET cc_start: 0.4158 (OUTLIER) cc_final: 0.3831 (mpp) REVERT: I 187 GLU cc_start: 0.7171 (pm20) cc_final: 0.6903 (pm20) REVERT: I 193 TYR cc_start: 0.8449 (m-80) cc_final: 0.8001 (m-80) REVERT: I 221 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: I 252 ASN cc_start: 0.7639 (t0) cc_final: 0.7381 (t0) REVERT: J 373 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7386 (mm-30) REVERT: J 387 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7365 (mt) REVERT: J 402 TYR cc_start: 0.8150 (p90) cc_final: 0.7891 (p90) REVERT: J 467 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7236 (mm-40) REVERT: J 510 ASP cc_start: 0.8024 (t0) cc_final: 0.7712 (t70) REVERT: J 522 LYS cc_start: 0.8228 (tttp) cc_final: 0.7588 (tttp) REVERT: J 529 LYS cc_start: 0.8246 (tppt) cc_final: 0.7390 (tppt) REVERT: J 533 ASN cc_start: 0.8348 (t0) cc_final: 0.7531 (t0) REVERT: J 544 THR cc_start: 0.7742 (p) cc_final: 0.7122 (t) REVERT: J 586 LYS cc_start: 0.6982 (mptt) cc_final: 0.6429 (mmtp) REVERT: J 692 TYR cc_start: 0.8299 (t80) cc_final: 0.7990 (t80) REVERT: J 735 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.6875 (p) REVERT: K 876 LYS cc_start: 0.7881 (tttp) cc_final: 0.7506 (tttm) REVERT: K 917 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8362 (tp40) REVERT: K 938 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8175 (mtmm) REVERT: K 970 THR cc_start: 0.8465 (t) cc_final: 0.8141 (p) REVERT: K 1014 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7868 (mmt90) REVERT: K 1019 GLN cc_start: 0.8158 (mt0) cc_final: 0.7868 (mt0) REVERT: K 1079 ASN cc_start: 0.8545 (t0) cc_final: 0.8336 (t0) REVERT: K 1115 THR cc_start: 0.8619 (t) cc_final: 0.8298 (p) REVERT: K 1130 VAL cc_start: 0.8054 (p) cc_final: 0.7768 (t) REVERT: K 1156 GLU cc_start: 0.7291 (pm20) cc_final: 0.7072 (pm20) outliers start: 133 outliers final: 96 residues processed: 832 average time/residue: 0.3891 time to fit residues: 494.3471 Evaluate side-chains 867 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 754 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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 230 VAL 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 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 635 ASP 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 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 1014 ARG 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 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS 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 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET 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 870 VAL 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 954 ASN Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 982 SER 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 1190 THR Chi-restraints excluded: chain G residue 1213 VAL Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU 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 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS 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 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 735 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 917 GLN Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1014 ARG 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 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 160 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 303 optimal weight: 50.0000 chunk 137 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 845 GLN F 559 HIS G 847 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 623 HIS J 686 GLN J 689 GLN K1146 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104062 restraints weight = 40250.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107166 restraints weight = 16753.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109126 restraints weight = 8968.906| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 24964 Z= 0.342 Angle : 0.777 19.286 34036 Z= 0.398 Chirality : 0.050 0.561 3804 Planarity : 0.006 0.063 4362 Dihedral : 5.312 57.505 3695 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 5.47 % Allowed : 28.66 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3106 helix: 2.59 (0.27), residues: 324 sheet: 0.29 (0.17), residues: 963 loop : -1.33 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 102 HIS 0.010 0.002 HIS B 685 PHE 0.028 0.003 PHE B 383 TYR 0.031 0.003 TYR B 397 ARG 0.008 0.001 ARG E 258 Details of bonding type rmsd link_NAG-ASN : bond 0.01065 ( 9) link_NAG-ASN : angle 5.72873 ( 27) link_BETA1-4 : bond 0.00409 ( 6) link_BETA1-4 : angle 1.48184 ( 18) hydrogen bonds : bond 0.05606 ( 943) hydrogen bonds : angle 4.90579 ( 2466) SS BOND : bond 0.00618 ( 48) SS BOND : angle 1.94473 ( 96) covalent geometry : bond 0.00773 (24901) covalent geometry : angle 0.75333 (33895) *********************** 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 961 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 816 time to evaluate : 2.641 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: 0.7708 (mmmt) cc_final: 0.7118 (mmmt) REVERT: A 189 PRO cc_start: 0.8173 (Cg_exo) cc_final: 0.7890 (Cg_endo) REVERT: B 343 LYS cc_start: 0.8721 (mptt) cc_final: 0.8519 (mptt) REVERT: B 395 HIS cc_start: 0.7565 (t70) cc_final: 0.7005 (t70) REVERT: B 396 ASP cc_start: 0.8010 (t0) cc_final: 0.7441 (t0) REVERT: B 462 TYR cc_start: 0.8123 (t80) cc_final: 0.7633 (t80) REVERT: B 467 GLN cc_start: 0.7650 (mm110) cc_final: 0.7344 (mm110) REVERT: B 484 ILE cc_start: 0.8175 (mm) cc_final: 0.7942 (mt) REVERT: B 517 GLN cc_start: 0.8055 (mm110) cc_final: 0.7834 (mm-40) REVERT: B 634 GLU cc_start: 0.7232 (tp30) cc_final: 0.6942 (tp30) REVERT: B 635 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7267 (t0) REVERT: B 711 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 819 SER cc_start: 0.8242 (m) cc_final: 0.7989 (p) REVERT: C 913 SER cc_start: 0.8338 (p) cc_final: 0.8021 (t) REVERT: C 920 GLU cc_start: 0.7526 (pm20) cc_final: 0.7242 (pm20) REVERT: C 954 ASN cc_start: 0.7741 (p0) cc_final: 0.7419 (p0) REVERT: C 983 SER cc_start: 0.8817 (t) cc_final: 0.8301 (p) REVERT: C 997 ASP cc_start: 0.8082 (p0) cc_final: 0.7116 (p0) REVERT: C 998 GLU cc_start: 0.6467 (mp0) cc_final: 0.5892 (mp0) REVERT: C 1018 ILE cc_start: 0.8111 (pt) cc_final: 0.7891 (pt) REVERT: C 1021 ARG cc_start: 0.8893 (tpp-160) cc_final: 0.8429 (tpt170) REVERT: C 1059 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8092 (mp) REVERT: C 1095 MET cc_start: 0.7065 (ppp) cc_final: 0.6362 (ppp) REVERT: C 1166 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8179 (mmtp) REVERT: C 1227 LYS cc_start: 0.8328 (mttt) cc_final: 0.7984 (mttt) REVERT: E 113 MET cc_start: 0.5303 (mmp) cc_final: 0.4938 (mmp) REVERT: E 178 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.4663 (pmt170) REVERT: F 370 VAL cc_start: 0.8638 (t) cc_final: 0.8416 (m) REVERT: F 394 ASN cc_start: 0.7707 (t0) cc_final: 0.7295 (t0) REVERT: F 404 ASP cc_start: 0.8609 (t0) cc_final: 0.8394 (t0) REVERT: F 430 MET cc_start: 0.7554 (ttp) cc_final: 0.7324 (ttp) REVERT: F 484 ILE cc_start: 0.8441 (mm) cc_final: 0.8188 (mm) REVERT: F 548 MET cc_start: 0.7365 (mpp) cc_final: 0.6946 (mpp) REVERT: F 570 PHE cc_start: 0.8388 (t80) cc_final: 0.8146 (t80) REVERT: F 586 LYS cc_start: 0.7507 (pttt) cc_final: 0.7206 (pptt) REVERT: F 594 ASP cc_start: 0.7621 (t0) cc_final: 0.7370 (t0) REVERT: F 638 TYR cc_start: 0.8545 (p90) cc_final: 0.8310 (p90) REVERT: F 679 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8237 (mtpp) REVERT: F 694 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8130 (mp) REVERT: F 699 THR cc_start: 0.8237 (t) cc_final: 0.7994 (p) REVERT: G 914 GLU cc_start: 0.7582 (mp0) cc_final: 0.6908 (mp0) REVERT: G 930 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7956 (ttp-110) REVERT: G 945 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7724 (mtpp) REVERT: G 954 ASN cc_start: 0.8161 (t0) cc_final: 0.7745 (t0) REVERT: G 982 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8651 (p) REVERT: G 1019 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7370 (mm-40) REVERT: G 1023 VAL cc_start: 0.8803 (t) cc_final: 0.8544 (p) REVERT: G 1056 LYS cc_start: 0.8278 (mmmm) cc_final: 0.8040 (mmtp) REVERT: G 1059 LEU cc_start: 0.8559 (tp) cc_final: 0.8345 (mt) REVERT: G 1061 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6981 (tm-30) REVERT: G 1144 SER cc_start: 0.8666 (t) cc_final: 0.8419 (m) REVERT: G 1213 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (t) REVERT: G 1227 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8083 (mtmm) REVERT: I 113 MET cc_start: 0.7355 (mmm) cc_final: 0.6993 (mmm) REVERT: I 126 GLU cc_start: 0.6190 (tp30) cc_final: 0.5715 (tp30) REVERT: I 142 LYS cc_start: 0.8318 (tmmt) cc_final: 0.8044 (ttpt) REVERT: I 172 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7452 (mm-40) REVERT: I 177 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4306 (mpp) REVERT: I 187 GLU cc_start: 0.7319 (pm20) cc_final: 0.7081 (pm20) REVERT: I 193 TYR cc_start: 0.8630 (m-80) cc_final: 0.8390 (m-10) REVERT: J 386 GLN cc_start: 0.7599 (mt0) cc_final: 0.7316 (mt0) REVERT: J 387 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7480 (mt) REVERT: J 402 TYR cc_start: 0.8240 (p90) cc_final: 0.8003 (p90) REVERT: J 409 GLU cc_start: 0.7198 (mp0) cc_final: 0.6799 (mp0) REVERT: J 467 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7164 (mm-40) REVERT: J 486 CYS cc_start: 0.5412 (p) cc_final: 0.5001 (p) REVERT: J 496 THR cc_start: 0.7909 (p) cc_final: 0.7628 (p) REVERT: J 510 ASP cc_start: 0.8079 (t0) cc_final: 0.7826 (t70) REVERT: J 522 LYS cc_start: 0.8241 (tttp) cc_final: 0.7586 (tttp) REVERT: J 529 LYS cc_start: 0.8317 (tppt) cc_final: 0.7407 (tppt) REVERT: J 533 ASN cc_start: 0.8339 (t0) cc_final: 0.7521 (t0) REVERT: J 544 THR cc_start: 0.7847 (p) cc_final: 0.7258 (p) REVERT: J 545 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8430 (t0) REVERT: J 586 LYS cc_start: 0.7235 (mptt) cc_final: 0.6474 (mmtp) REVERT: J 692 TYR cc_start: 0.8495 (t80) cc_final: 0.8250 (t80) REVERT: J 719 TYR cc_start: 0.8103 (t80) cc_final: 0.7880 (t80) REVERT: K 822 MET cc_start: 0.8025 (ptp) cc_final: 0.7804 (ptt) REVERT: K 876 LYS cc_start: 0.8077 (tttp) cc_final: 0.7771 (tttm) REVERT: K 970 THR cc_start: 0.8502 (t) cc_final: 0.8245 (p) REVERT: K 986 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8373 (p) REVERT: K 997 ASP cc_start: 0.7638 (p0) cc_final: 0.7179 (p0) REVERT: K 1014 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7205 (mmt90) REVERT: K 1019 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: K 1115 THR cc_start: 0.8655 (t) cc_final: 0.8356 (p) REVERT: K 1130 VAL cc_start: 0.8195 (p) cc_final: 0.7906 (t) REVERT: K 1196 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6757 (mm-30) REVERT: K 1242 VAL cc_start: 0.8001 (t) cc_final: 0.7781 (p) outliers start: 145 outliers final: 104 residues processed: 881 average time/residue: 0.4006 time to fit residues: 533.8530 Evaluate side-chains 900 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 782 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 383 PHE 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 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 640 GLU 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 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE 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 1120 THR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1217 MET Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 523 ILE Chi-restraints excluded: chain F residue 524 THR 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 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 833 HIS Chi-restraints excluded: chain G residue 854 GLU 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 982 SER 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 1158 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1190 THR Chi-restraints excluded: chain G residue 1213 VAL Chi-restraints excluded: chain G residue 1218 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU 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 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 575 VAL 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 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 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 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1019 GLN 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 1186 SER Chi-restraints excluded: chain K residue 1228 ILE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN B 623 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G1002 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 618 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105298 restraints weight = 40415.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108572 restraints weight = 17030.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110677 restraints weight = 9210.441| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24964 Z= 0.143 Angle : 0.684 18.108 34036 Z= 0.344 Chirality : 0.046 0.545 3804 Planarity : 0.005 0.046 4362 Dihedral : 4.951 56.117 3695 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.00 % Allowed : 31.07 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3106 helix: 2.85 (0.28), residues: 324 sheet: 0.40 (0.16), residues: 993 loop : -1.24 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 251 HIS 0.031 0.001 HIS F 559 PHE 0.027 0.001 PHE C1235 TYR 0.031 0.002 TYR B 397 ARG 0.007 0.000 ARG E 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00937 ( 9) link_NAG-ASN : angle 5.18540 ( 27) link_BETA1-4 : bond 0.00414 ( 6) link_BETA1-4 : angle 1.27509 ( 18) hydrogen bonds : bond 0.04163 ( 943) hydrogen bonds : angle 4.69463 ( 2466) SS BOND : bond 0.00489 ( 48) SS BOND : angle 1.75477 ( 96) covalent geometry : bond 0.00331 (24901) covalent geometry : angle 0.66267 (33895) *********************** 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 879 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 773 time to evaluate : 2.425 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: 0.7677 (mmmt) cc_final: 0.7261 (mmmt) REVERT: A 189 PRO cc_start: 0.8050 (Cg_exo) cc_final: 0.7760 (Cg_endo) REVERT: B 343 LYS cc_start: 0.8714 (mptt) cc_final: 0.8491 (mptt) REVERT: B 395 HIS cc_start: 0.7508 (t70) cc_final: 0.6961 (t70) REVERT: B 396 ASP cc_start: 0.7852 (t0) cc_final: 0.7317 (t0) REVERT: B 417 LYS cc_start: 0.7882 (mttp) cc_final: 0.7607 (mttp) REVERT: B 462 TYR cc_start: 0.8083 (t80) cc_final: 0.7563 (t80) REVERT: B 467 GLN cc_start: 0.7607 (mm110) cc_final: 0.7329 (mm110) REVERT: B 484 ILE cc_start: 0.8235 (mm) cc_final: 0.7983 (mt) REVERT: B 517 GLN cc_start: 0.8094 (mm110) cc_final: 0.7860 (mm-40) REVERT: B 529 LYS cc_start: 0.8150 (tttp) cc_final: 0.7726 (tttp) REVERT: B 634 GLU cc_start: 0.7219 (tp30) cc_final: 0.6971 (tp30) REVERT: C 913 SER cc_start: 0.8179 (p) cc_final: 0.7900 (t) REVERT: C 920 GLU cc_start: 0.7545 (pm20) cc_final: 0.7261 (pm20) REVERT: C 954 ASN cc_start: 0.7846 (p0) cc_final: 0.7499 (p0) REVERT: C 983 SER cc_start: 0.8818 (t) cc_final: 0.8296 (p) REVERT: C 997 ASP cc_start: 0.8042 (p0) cc_final: 0.7094 (p0) REVERT: C 998 GLU cc_start: 0.6382 (mp0) cc_final: 0.5822 (mp0) REVERT: C 1021 ARG cc_start: 0.8886 (tpp-160) cc_final: 0.8408 (tpt170) REVERT: C 1035 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7686 (ttmm) REVERT: C 1059 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 1095 MET cc_start: 0.7045 (ppp) cc_final: 0.6366 (ppp) REVERT: C 1166 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8184 (mmtp) REVERT: C 1227 LYS cc_start: 0.8285 (mttt) cc_final: 0.7926 (mttt) REVERT: E 113 MET cc_start: 0.5340 (mmp) cc_final: 0.4996 (mmp) REVERT: E 178 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.4297 (pmt170) REVERT: F 394 ASN cc_start: 0.7682 (t0) cc_final: 0.7235 (t0) REVERT: F 399 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8309 (mttp) REVERT: F 430 MET cc_start: 0.7382 (ttp) cc_final: 0.7006 (ttp) REVERT: F 548 MET cc_start: 0.7089 (mpp) cc_final: 0.6667 (mpp) REVERT: F 570 PHE cc_start: 0.8308 (t80) cc_final: 0.8064 (t80) REVERT: F 586 LYS cc_start: 0.7456 (pttt) cc_final: 0.7121 (pptt) REVERT: F 594 ASP cc_start: 0.7649 (t0) cc_final: 0.7414 (t0) REVERT: F 604 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7597 (mtm-85) REVERT: F 638 TYR cc_start: 0.8553 (p90) cc_final: 0.8253 (p90) REVERT: F 679 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8365 (mmmm) REVERT: F 694 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7878 (mp) REVERT: F 699 THR cc_start: 0.8138 (t) cc_final: 0.7863 (p) REVERT: G 912 ASP cc_start: 0.7827 (m-30) cc_final: 0.7589 (t0) REVERT: G 914 GLU cc_start: 0.7602 (mp0) cc_final: 0.6936 (mp0) REVERT: G 945 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7670 (mtpp) REVERT: G 954 ASN cc_start: 0.7921 (t0) cc_final: 0.7527 (t0) REVERT: G 1019 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7358 (mm-40) REVERT: G 1023 VAL cc_start: 0.8790 (t) cc_final: 0.8511 (p) REVERT: G 1059 LEU cc_start: 0.8485 (tp) cc_final: 0.8253 (mt) REVERT: G 1061 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6898 (tm-30) REVERT: G 1082 ARG cc_start: 0.8376 (ptt90) cc_final: 0.8069 (ptt-90) REVERT: G 1144 SER cc_start: 0.8550 (t) cc_final: 0.8197 (m) REVERT: G 1227 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8050 (mtmm) REVERT: I 126 GLU cc_start: 0.6159 (tp30) cc_final: 0.5544 (tp30) REVERT: I 142 LYS cc_start: 0.8312 (tmmt) cc_final: 0.8047 (ttpt) REVERT: I 172 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7468 (mm-40) REVERT: I 177 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4321 (mpp) REVERT: I 187 GLU cc_start: 0.7248 (pm20) cc_final: 0.6849 (pm20) REVERT: I 193 TYR cc_start: 0.8586 (m-80) cc_final: 0.8079 (m-80) REVERT: I 221 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7426 (mtt180) REVERT: J 386 GLN cc_start: 0.7548 (mt0) cc_final: 0.7280 (mt0) REVERT: J 387 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7354 (mt) REVERT: J 396 ASP cc_start: 0.7235 (t0) cc_final: 0.6935 (t0) REVERT: J 402 TYR cc_start: 0.8130 (p90) cc_final: 0.7839 (p90) REVERT: J 467 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7203 (mm-40) REVERT: J 486 CYS cc_start: 0.5393 (p) cc_final: 0.4973 (p) REVERT: J 510 ASP cc_start: 0.8025 (t0) cc_final: 0.7717 (t70) REVERT: J 522 LYS cc_start: 0.8210 (tttp) cc_final: 0.7488 (tttp) REVERT: J 529 LYS cc_start: 0.8295 (tppt) cc_final: 0.7389 (tppt) REVERT: J 533 ASN cc_start: 0.8334 (t0) cc_final: 0.7506 (t0) REVERT: J 544 THR cc_start: 0.7718 (p) cc_final: 0.7262 (p) REVERT: J 577 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7740 (ptp-170) REVERT: J 586 LYS cc_start: 0.6971 (mptt) cc_final: 0.6458 (mmtp) REVERT: J 692 TYR cc_start: 0.8329 (t80) cc_final: 0.8069 (t80) REVERT: J 694 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8024 (mt) REVERT: J 719 TYR cc_start: 0.8056 (t80) cc_final: 0.7791 (t80) REVERT: K 876 LYS cc_start: 0.7955 (tttp) cc_final: 0.7663 (tttm) REVERT: K 970 THR cc_start: 0.8454 (t) cc_final: 0.8167 (p) REVERT: K 986 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8380 (p) REVERT: K 1014 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7816 (mmt90) REVERT: K 1019 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: K 1022 THR cc_start: 0.8516 (t) cc_final: 0.8148 (p) REVERT: K 1115 THR cc_start: 0.8610 (t) cc_final: 0.8349 (p) REVERT: K 1130 VAL cc_start: 0.8032 (p) cc_final: 0.7797 (t) REVERT: K 1229 SER cc_start: 0.8388 (t) cc_final: 0.7846 (p) REVERT: K 1242 VAL cc_start: 0.7913 (t) cc_final: 0.7705 (p) outliers start: 106 outliers final: 80 residues processed: 818 average time/residue: 0.3856 time to fit residues: 476.9124 Evaluate side-chains 847 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 756 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 589 ILE 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 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 834 ILE 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 1059 LEU 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 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 850 GLU 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 990 ASN 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 1218 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 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 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1019 GLN 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 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 65 optimal weight: 0.4980 chunk 303 optimal weight: 40.0000 chunk 214 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 295 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS F 569 GLN G 847 GLN G1002 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106617 restraints weight = 40198.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109811 restraints weight = 16648.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111824 restraints weight = 8830.732| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24964 Z= 0.131 Angle : 0.672 17.857 34036 Z= 0.336 Chirality : 0.045 0.518 3804 Planarity : 0.005 0.047 4362 Dihedral : 4.765 56.230 3695 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.43 % Allowed : 31.94 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3106 helix: 2.88 (0.28), residues: 324 sheet: 0.38 (0.16), residues: 1011 loop : -1.16 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 251 HIS 0.014 0.001 HIS F 559 PHE 0.014 0.001 PHE C 910 TYR 0.030 0.001 TYR B 397 ARG 0.009 0.000 ARG G 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00911 ( 9) link_NAG-ASN : angle 5.01605 ( 27) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 1.21766 ( 18) hydrogen bonds : bond 0.03819 ( 943) hydrogen bonds : angle 4.56151 ( 2466) SS BOND : bond 0.00484 ( 48) SS BOND : angle 1.87213 ( 96) covalent geometry : bond 0.00305 (24901) covalent geometry : angle 0.65007 (33895) ********************** 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 858 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 767 time to evaluate : 2.501 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 123 VAL cc_start: 0.7310 (t) cc_final: 0.6981 (p) REVERT: A 139 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7309 (mmmt) REVERT: B 343 LYS cc_start: 0.8733 (mptt) cc_final: 0.8472 (mptt) REVERT: B 395 HIS cc_start: 0.7467 (t70) cc_final: 0.6927 (t70) REVERT: B 396 ASP cc_start: 0.7814 (t0) cc_final: 0.7219 (t0) REVERT: B 462 TYR cc_start: 0.8087 (t80) cc_final: 0.7559 (t80) REVERT: B 467 GLN cc_start: 0.7592 (mm110) cc_final: 0.7322 (mm110) REVERT: B 517 GLN cc_start: 0.8168 (mm110) cc_final: 0.7899 (mm-40) REVERT: B 529 LYS cc_start: 0.8136 (tttp) cc_final: 0.7725 (tttp) REVERT: B 634 GLU cc_start: 0.7206 (tp30) cc_final: 0.6941 (tp30) REVERT: C 845 GLN cc_start: 0.7743 (mt0) cc_final: 0.7478 (mt0) REVERT: C 917 GLN cc_start: 0.8557 (tt0) cc_final: 0.8314 (tt0) REVERT: C 920 GLU cc_start: 0.7532 (pm20) cc_final: 0.7267 (pm20) REVERT: C 954 ASN cc_start: 0.7811 (p0) cc_final: 0.7454 (p0) REVERT: C 983 SER cc_start: 0.8787 (t) cc_final: 0.8273 (p) REVERT: C 997 ASP cc_start: 0.8011 (p0) cc_final: 0.7018 (p0) REVERT: C 998 GLU cc_start: 0.6366 (mp0) cc_final: 0.5821 (mp0) REVERT: C 1021 ARG cc_start: 0.8903 (tpp-160) cc_final: 0.8446 (tpt170) REVERT: C 1035 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7678 (ttmm) REVERT: C 1059 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7985 (mp) REVERT: C 1095 MET cc_start: 0.7027 (ppp) cc_final: 0.6366 (ppp) REVERT: C 1166 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8178 (mmtp) REVERT: C 1227 LYS cc_start: 0.8257 (mttt) cc_final: 0.7833 (mttt) REVERT: E 113 MET cc_start: 0.5301 (mmp) cc_final: 0.4975 (mmp) REVERT: E 139 LYS cc_start: 0.7968 (mptt) cc_final: 0.7456 (mptt) REVERT: E 178 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.4307 (pmt170) REVERT: F 370 VAL cc_start: 0.8649 (t) cc_final: 0.8417 (m) REVERT: F 394 ASN cc_start: 0.7676 (t0) cc_final: 0.7211 (t0) REVERT: F 430 MET cc_start: 0.7346 (ttp) cc_final: 0.6958 (ttp) REVERT: F 548 MET cc_start: 0.7048 (mpp) cc_final: 0.6711 (mpp) REVERT: F 584 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5202 (ttmm) REVERT: F 586 LYS cc_start: 0.7456 (pttt) cc_final: 0.7126 (pptt) REVERT: F 594 ASP cc_start: 0.7651 (t0) cc_final: 0.7387 (t0) REVERT: F 638 TYR cc_start: 0.8556 (p90) cc_final: 0.8274 (p90) REVERT: G 912 ASP cc_start: 0.7808 (m-30) cc_final: 0.7414 (t0) REVERT: G 914 GLU cc_start: 0.7604 (mp0) cc_final: 0.6942 (mp0) REVERT: G 924 ASP cc_start: 0.7971 (t0) cc_final: 0.7586 (t70) REVERT: G 945 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7637 (mtpp) REVERT: G 954 ASN cc_start: 0.7897 (t0) cc_final: 0.7604 (t0) REVERT: G 1019 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7374 (mm-40) REVERT: G 1023 VAL cc_start: 0.8782 (t) cc_final: 0.8538 (p) REVERT: G 1059 LEU cc_start: 0.8462 (tp) cc_final: 0.8261 (mt) REVERT: G 1061 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6949 (tm-30) REVERT: G 1082 ARG cc_start: 0.8372 (ptt90) cc_final: 0.8124 (ptt-90) REVERT: G 1144 SER cc_start: 0.8403 (t) cc_final: 0.8076 (m) REVERT: G 1227 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8026 (mtmm) REVERT: I 113 MET cc_start: 0.7384 (mmm) cc_final: 0.7009 (mmm) REVERT: I 126 GLU cc_start: 0.6096 (tp30) cc_final: 0.5821 (tp30) REVERT: I 142 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8172 (ttpt) REVERT: I 177 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4414 (mpp) REVERT: I 187 GLU cc_start: 0.7137 (pm20) cc_final: 0.6751 (pm20) REVERT: I 193 TYR cc_start: 0.8628 (m-80) cc_final: 0.8412 (m-10) REVERT: I 249 VAL cc_start: 0.8027 (m) cc_final: 0.7781 (p) REVERT: J 387 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7335 (mt) REVERT: J 402 TYR cc_start: 0.8122 (p90) cc_final: 0.7824 (p90) REVERT: J 435 LEU cc_start: 0.8103 (tp) cc_final: 0.7896 (tp) REVERT: J 467 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7177 (mm-40) REVERT: J 486 CYS cc_start: 0.5419 (p) cc_final: 0.5010 (p) REVERT: J 522 LYS cc_start: 0.8235 (tttp) cc_final: 0.7525 (tttp) REVERT: J 529 LYS cc_start: 0.8293 (tppt) cc_final: 0.7527 (tppt) REVERT: J 533 ASN cc_start: 0.8361 (t0) cc_final: 0.7534 (t0) REVERT: J 544 THR cc_start: 0.7764 (p) cc_final: 0.7285 (p) REVERT: J 577 ARG cc_start: 0.7961 (ptp-170) cc_final: 0.7745 (ptp-170) REVERT: J 692 TYR cc_start: 0.8240 (t80) cc_final: 0.7969 (t80) REVERT: J 717 SER cc_start: 0.8480 (m) cc_final: 0.7943 (p) REVERT: K 822 MET cc_start: 0.7954 (ptt) cc_final: 0.7723 (ptp) REVERT: K 876 LYS cc_start: 0.7918 (tttp) cc_final: 0.7462 (tttm) REVERT: K 928 VAL cc_start: 0.8954 (p) cc_final: 0.8679 (t) REVERT: K 970 THR cc_start: 0.8447 (t) cc_final: 0.8141 (p) REVERT: K 986 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8380 (p) REVERT: K 1014 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7654 (mmt90) REVERT: K 1019 GLN cc_start: 0.8141 (mt0) cc_final: 0.7896 (mt0) REVERT: K 1115 THR cc_start: 0.8606 (t) cc_final: 0.8329 (p) REVERT: K 1130 VAL cc_start: 0.8047 (p) cc_final: 0.7800 (t) outliers start: 91 outliers final: 78 residues processed: 806 average time/residue: 0.3672 time to fit residues: 448.6846 Evaluate side-chains 844 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 759 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 589 ILE 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 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE 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 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 524 THR 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 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 687 ILE Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET 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 990 ASN 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 1218 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU 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 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1040 SER 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 1240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 181 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 100 optimal weight: 60.0000 chunk 272 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN G 847 GLN G1002 GLN ** G1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN ** K1045 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.121913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104422 restraints weight = 40133.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107590 restraints weight = 16677.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109596 restraints weight = 8895.019| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24964 Z= 0.221 Angle : 0.726 18.478 34036 Z= 0.366 Chirality : 0.047 0.535 3804 Planarity : 0.005 0.049 4362 Dihedral : 4.947 59.318 3695 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.58 % Allowed : 32.01 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3106 helix: 2.72 (0.27), residues: 324 sheet: 0.37 (0.16), residues: 1011 loop : -1.23 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 251 HIS 0.024 0.001 HIS G1146 PHE 0.029 0.002 PHE C1235 TYR 0.029 0.002 TYR B 397 ARG 0.007 0.001 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 9) link_NAG-ASN : angle 5.26861 ( 27) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 1.34184 ( 18) hydrogen bonds : bond 0.04566 ( 943) hydrogen bonds : angle 4.71201 ( 2466) SS BOND : bond 0.00585 ( 48) SS BOND : angle 2.08118 ( 96) covalent geometry : bond 0.00508 (24901) covalent geometry : angle 0.70272 (33895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10092.96 seconds wall clock time: 177 minutes 0.55 seconds (10620.55 seconds total)