Starting phenix.real_space_refine on Sun Jan 26 05:08:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0m_37982/01_2025/8x0m_37982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0m_37982/01_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_37982/01_2025/8x0m_37982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0m_37982/01_2025/8x0m_37982.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0m_37982/01_2025/8x0m_37982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0m_37982/01_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 15.03, per 1000 atoms: 0.62 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: 6.21 Conformation dependent library (CDL) restraints added in 3.1 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: 3.53 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: 12.03 Time building geometry restraints manager: 7.03 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: 3.590 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: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.050 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.150 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.260 ------------------------------------------------------------------------------- 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 24901 Z= 0.240 Angle : 0.703 15.737 33895 Z= 0.372 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 *********************** 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 : 3.161 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: 0.3917 time to fit residues: 417.9736 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 : 2.613 ------------------------------------------------------------------------------- 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 24901 Z= 0.332 Angle : 0.646 11.988 33895 Z= 0.335 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 *********************** 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 : 2.549 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: 0.3836 time to fit residues: 483.8049 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 : 2.665 ------------------------------------------------------------------------------- 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: 0.8980 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3614 r_free = 0.3614 target = 0.127678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109107 restraints weight = 40405.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112413 restraints weight = 17269.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114520 restraints weight = 9353.559| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24901 Z= 0.224 Angle : 0.585 12.994 33895 Z= 0.300 Chirality : 0.045 0.544 3804 Planarity : 0.005 0.062 4362 Dihedral : 4.737 54.523 3695 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.19 % Allowed : 28.39 % Favored : 67.42 % 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: -0.26 (0.15), residues: 3106 helix: 2.82 (0.28), residues: 324 sheet: 0.41 (0.17), residues: 969 loop : -1.11 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 642 HIS 0.018 0.001 HIS B 685 PHE 0.022 0.002 PHE C1235 TYR 0.028 0.001 TYR B 397 ARG 0.005 0.000 ARG A 243 *********************** 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 855 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 744 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7042 (mmmt) REVERT: A 211 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 395 HIS cc_start: 0.7514 (t-90) cc_final: 0.7143 (t-90) REVERT: B 396 ASP cc_start: 0.7676 (t0) cc_final: 0.7121 (t0) REVERT: B 462 TYR cc_start: 0.7988 (t80) cc_final: 0.7640 (t80) REVERT: B 484 ILE cc_start: 0.8189 (mm) cc_final: 0.7892 (mt) REVERT: B 517 GLN cc_start: 0.7832 (mm110) cc_final: 0.7596 (mm-40) REVERT: B 586 LYS cc_start: 0.8232 (mmmm) cc_final: 0.8017 (mtpt) REVERT: B 679 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7880 (mtpp) REVERT: B 711 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 818 HIS cc_start: 0.6105 (t-90) cc_final: 0.5801 (t-90) REVERT: C 930 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8227 (ttp-110) REVERT: C 997 ASP cc_start: 0.7850 (p0) cc_final: 0.6907 (p0) REVERT: C 1018 ILE cc_start: 0.8013 (pt) cc_final: 0.7773 (pt) REVERT: C 1021 ARG cc_start: 0.8855 (tpp-160) cc_final: 0.8554 (tpt170) REVERT: C 1024 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6964 (mm-30) REVERT: C 1095 MET cc_start: 0.7076 (ppp) cc_final: 0.6560 (ppp) REVERT: C 1117 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8232 (p) REVERT: E 113 MET cc_start: 0.5155 (mmp) cc_final: 0.4762 (mmp) REVERT: E 165 LYS cc_start: 0.8604 (tptp) cc_final: 0.8402 (tptp) REVERT: F 394 ASN cc_start: 0.7751 (t0) cc_final: 0.7210 (t0) REVERT: F 399 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7598 (mtpp) REVERT: F 511 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8264 (mmm160) REVERT: F 659 GLU cc_start: 0.7370 (tt0) cc_final: 0.7137 (tt0) REVERT: F 694 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7888 (mp) REVERT: G 836 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7660 (ttp80) REVERT: G 925 ARG cc_start: 0.8293 (ptp90) cc_final: 0.8091 (ptp90) REVERT: G 945 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7778 (mtpp) REVERT: G 954 ASN cc_start: 0.7918 (t0) cc_final: 0.7514 (t0) REVERT: G 1019 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7084 (mm-40) REVERT: G 1059 LEU cc_start: 0.8485 (tp) cc_final: 0.8230 (mt) REVERT: G 1061 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6803 (tm-30) REVERT: G 1144 SER cc_start: 0.8667 (t) cc_final: 0.8247 (m) REVERT: G 1160 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6317 (tttm) REVERT: I 113 MET cc_start: 0.7338 (mmm) cc_final: 0.6996 (mmm) REVERT: I 142 LYS cc_start: 0.7724 (tmmt) cc_final: 0.7429 (tmtt) REVERT: I 193 TYR cc_start: 0.8045 (m-80) cc_final: 0.7677 (m-80) REVERT: J 467 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7186 (mm-40) REVERT: J 496 THR cc_start: 0.7846 (p) cc_final: 0.7576 (p) REVERT: J 498 GLU cc_start: 0.6916 (pm20) cc_final: 0.6563 (pm20) REVERT: J 529 LYS cc_start: 0.8185 (tppt) cc_final: 0.7471 (tppt) REVERT: J 547 ASP cc_start: 0.7775 (p0) cc_final: 0.7463 (p0) REVERT: J 567 LYS cc_start: 0.7509 (mmtp) cc_final: 0.7283 (mmtt) REVERT: J 586 LYS cc_start: 0.7131 (mptt) cc_final: 0.6533 (mmtp) REVERT: J 634 GLU cc_start: 0.7330 (tp30) cc_final: 0.7104 (tp30) REVERT: J 713 SER cc_start: 0.8183 (t) cc_final: 0.7960 (t) REVERT: K 876 LYS cc_start: 0.7770 (tttp) cc_final: 0.7420 (tttm) REVERT: K 960 ASP cc_start: 0.7696 (p0) cc_final: 0.7441 (p0) REVERT: K 970 THR cc_start: 0.8492 (t) cc_final: 0.8157 (p) REVERT: K 1019 GLN cc_start: 0.8077 (mt0) cc_final: 0.7791 (mt0) REVERT: K 1115 THR cc_start: 0.8617 (t) cc_final: 0.8276 (p) REVERT: K 1130 VAL cc_start: 0.8064 (p) cc_final: 0.7763 (t) REVERT: K 1223 SER cc_start: 0.8035 (t) cc_final: 0.7827 (t) outliers start: 111 outliers final: 69 residues processed: 795 average time/residue: 0.3986 time to fit residues: 485.7416 Evaluate side-chains 799 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 725 time to evaluate : 3.222 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain B residue 444 LEU 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 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 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 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 1024 GLU Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1160 LYS 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 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 359 HIS 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 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: 0.7980 chunk 196 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 143 optimal weight: 0.0060 chunk 274 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** B 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS F 516 GLN F 565 HIS F 661 HIS G 847 GLN G1075 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 686 GLN J 689 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109444 restraints weight = 40725.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112770 restraints weight = 17351.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114882 restraints weight = 9401.441| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24901 Z= 0.182 Angle : 0.576 14.549 33895 Z= 0.291 Chirality : 0.044 0.541 3804 Planarity : 0.004 0.060 4362 Dihedral : 4.556 57.416 3695 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.52 % Allowed : 28.43 % Favored : 67.04 % 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: 2.84 (0.28), residues: 324 sheet: 0.48 (0.16), residues: 978 loop : -1.09 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 642 HIS 0.015 0.001 HIS B 685 PHE 0.016 0.001 PHE C1235 TYR 0.028 0.001 TYR B 397 ARG 0.006 0.000 ARG A 178 *********************** 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 862 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 742 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7123 (mmmt) REVERT: A 211 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7739 (p) REVERT: B 395 HIS cc_start: 0.7492 (t-90) cc_final: 0.7105 (t-90) REVERT: B 462 TYR cc_start: 0.7976 (t80) cc_final: 0.7612 (t80) REVERT: B 484 ILE cc_start: 0.8170 (mm) cc_final: 0.7885 (mt) REVERT: B 532 TYR cc_start: 0.8211 (p90) cc_final: 0.7983 (p90) REVERT: B 679 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7870 (mtpp) REVERT: B 711 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (mp) REVERT: C 818 HIS cc_start: 0.6208 (t-90) cc_final: 0.5961 (t-90) REVERT: C 930 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8214 (ttp-110) REVERT: C 954 ASN cc_start: 0.7589 (p0) cc_final: 0.7254 (p0) REVERT: C 983 SER cc_start: 0.8791 (t) cc_final: 0.8240 (p) REVERT: C 1014 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8169 (mmt180) REVERT: C 1018 ILE cc_start: 0.8016 (pt) cc_final: 0.7761 (pt) REVERT: C 1021 ARG cc_start: 0.8870 (tpp-160) cc_final: 0.8480 (tpt170) REVERT: C 1024 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 1059 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7941 (mp) REVERT: C 1095 MET cc_start: 0.7064 (ppp) cc_final: 0.6512 (ppp) REVERT: C 1117 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 1214 PHE cc_start: 0.8174 (t80) cc_final: 0.7938 (t80) REVERT: C 1227 LYS cc_start: 0.8246 (mttt) cc_final: 0.7787 (mttt) REVERT: E 113 MET cc_start: 0.5210 (mmp) cc_final: 0.4814 (mmp) REVERT: E 165 LYS cc_start: 0.8642 (tptp) cc_final: 0.8395 (tptp) REVERT: F 394 ASN cc_start: 0.7744 (t0) cc_final: 0.7235 (t0) REVERT: F 459 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8449 (ttm170) REVERT: F 511 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8245 (mmm160) REVERT: F 516 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: F 586 LYS cc_start: 0.7299 (pttt) cc_final: 0.7007 (pptt) REVERT: F 593 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8279 (tt) REVERT: F 638 TYR cc_start: 0.8512 (p90) cc_final: 0.8164 (p90) REVERT: F 659 GLU cc_start: 0.7197 (tt0) cc_final: 0.6981 (tt0) REVERT: F 686 GLN cc_start: 0.7796 (mt0) cc_final: 0.7518 (mt0) REVERT: F 694 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7749 (mp) REVERT: G 914 GLU cc_start: 0.7615 (mp0) cc_final: 0.6973 (mp0) REVERT: G 945 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7637 (mtpp) REVERT: G 1019 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7319 (mm-40) REVERT: G 1038 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8360 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8457 (tp) cc_final: 0.8209 (mt) REVERT: G 1061 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6808 (tm-30) REVERT: G 1082 ARG cc_start: 0.8343 (ptt90) cc_final: 0.8067 (ptt-90) REVERT: G 1144 SER cc_start: 0.8574 (t) cc_final: 0.8194 (m) REVERT: G 1150 ASN cc_start: 0.8312 (p0) cc_final: 0.7838 (p0) REVERT: I 142 LYS cc_start: 0.7821 (tmmt) cc_final: 0.7549 (tmtt) REVERT: I 193 TYR cc_start: 0.8168 (m-80) cc_final: 0.7714 (m-80) REVERT: I 265 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7099 (tm-30) REVERT: J 467 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7184 (mm-40) REVERT: J 496 THR cc_start: 0.7824 (p) cc_final: 0.7514 (p) REVERT: J 498 GLU cc_start: 0.6891 (pm20) cc_final: 0.6511 (pm20) REVERT: J 529 LYS cc_start: 0.8218 (tppt) cc_final: 0.7434 (tppt) REVERT: J 544 THR cc_start: 0.7697 (p) cc_final: 0.7430 (t) REVERT: J 547 ASP cc_start: 0.7778 (p0) cc_final: 0.7495 (p0) REVERT: J 567 LYS cc_start: 0.7477 (mmtp) cc_final: 0.7261 (mmtt) REVERT: J 586 LYS cc_start: 0.7040 (mptt) cc_final: 0.6484 (mmtp) REVERT: J 713 SER cc_start: 0.8250 (t) cc_final: 0.8033 (t) REVERT: K 876 LYS cc_start: 0.7751 (tttp) cc_final: 0.7390 (tttm) REVERT: K 970 THR cc_start: 0.8493 (t) cc_final: 0.8145 (p) REVERT: K 1019 GLN cc_start: 0.7978 (mt0) cc_final: 0.7733 (mt0) REVERT: K 1029 TYR cc_start: 0.8329 (t80) cc_final: 0.8123 (t80) REVERT: K 1115 THR cc_start: 0.8598 (t) cc_final: 0.8291 (p) REVERT: K 1130 VAL cc_start: 0.8062 (p) cc_final: 0.7765 (t) REVERT: K 1223 SER cc_start: 0.7961 (t) cc_final: 0.7758 (t) outliers start: 120 outliers final: 76 residues processed: 801 average time/residue: 0.3855 time to fit residues: 470.0683 Evaluate side-chains 810 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 725 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 200 VAL 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 551 ASN Chi-restraints excluded: chain B residue 588 HIS 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 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 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 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 1043 MET 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 359 HIS 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 1090 ASN 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 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: 4.9990 chunk 102 optimal weight: 20.0000 chunk 219 optimal weight: 0.8980 chunk 255 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 F 559 HIS F 685 HIS G 847 GLN G 954 ASN 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 ** 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 = 0.3596 r_free = 0.3596 target = 0.126433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108719 restraints weight = 40242.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111900 restraints weight = 16893.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113941 restraints weight = 9049.805| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24901 Z= 0.238 Angle : 0.595 15.799 33895 Z= 0.303 Chirality : 0.045 0.548 3804 Planarity : 0.004 0.059 4362 Dihedral : 4.616 57.774 3695 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.98 % Allowed : 28.47 % Favored : 66.55 % 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: 2.82 (0.27), residues: 324 sheet: 0.46 (0.17), residues: 969 loop : -1.02 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 642 HIS 0.013 0.001 HIS B 685 PHE 0.023 0.001 PHE C1235 TYR 0.025 0.002 TYR B 397 ARG 0.005 0.000 ARG C1014 *********************** 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 892 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 760 time to evaluate : 2.595 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: 0.7587 (mmmt) cc_final: 0.7136 (mmmt) REVERT: A 160 PHE cc_start: 0.7881 (m-80) cc_final: 0.7663 (m-80) REVERT: A 211 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7782 (p) REVERT: B 343 LYS cc_start: 0.8678 (mptt) cc_final: 0.8407 (mptt) REVERT: B 395 HIS cc_start: 0.7529 (t-90) cc_final: 0.7096 (t-90) REVERT: B 396 ASP cc_start: 0.7750 (t0) cc_final: 0.7132 (t0) REVERT: B 435 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7848 (tp) REVERT: B 462 TYR cc_start: 0.7998 (t80) cc_final: 0.7559 (t80) REVERT: B 484 ILE cc_start: 0.8235 (mm) cc_final: 0.7963 (mt) REVERT: B 532 TYR cc_start: 0.8282 (p90) cc_final: 0.8031 (p90) REVERT: B 586 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7588 (mtpp) REVERT: B 711 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8056 (mp) REVERT: C 818 HIS cc_start: 0.6448 (t-90) cc_final: 0.6209 (t-90) REVERT: C 819 SER cc_start: 0.8273 (m) cc_final: 0.7932 (p) REVERT: C 930 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: C 954 ASN cc_start: 0.7591 (p0) cc_final: 0.7243 (p0) REVERT: C 983 SER cc_start: 0.8823 (t) cc_final: 0.8297 (p) REVERT: C 1014 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8159 (mmt180) REVERT: C 1021 ARG cc_start: 0.8908 (tpp-160) cc_final: 0.8530 (tpt170) REVERT: C 1024 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 1059 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 1095 MET cc_start: 0.7046 (ppp) cc_final: 0.6451 (ppp) REVERT: C 1117 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8190 (p) REVERT: C 1227 LYS cc_start: 0.8234 (mttt) cc_final: 0.7788 (mttt) REVERT: E 113 MET cc_start: 0.5189 (mmp) cc_final: 0.4813 (mmp) REVERT: E 165 LYS cc_start: 0.8654 (tptp) cc_final: 0.8336 (tptp) REVERT: F 394 ASN cc_start: 0.7760 (t0) cc_final: 0.7254 (t0) REVERT: F 430 MET cc_start: 0.7368 (ttp) cc_final: 0.7074 (ttp) REVERT: F 459 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8466 (ttm170) REVERT: F 504 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6883 (tpt) REVERT: F 511 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8215 (mmm160) REVERT: F 570 PHE cc_start: 0.8222 (t80) cc_final: 0.7988 (t80) REVERT: F 586 LYS cc_start: 0.7310 (pttt) cc_final: 0.7040 (pptt) REVERT: F 638 TYR cc_start: 0.8515 (p90) cc_final: 0.8147 (p90) REVERT: F 659 GLU cc_start: 0.7207 (tt0) cc_final: 0.7001 (tt0) REVERT: F 685 HIS cc_start: 0.7740 (p90) cc_final: 0.7434 (p90) REVERT: F 686 GLN cc_start: 0.7907 (mt0) cc_final: 0.7623 (mt0) REVERT: G 914 GLU cc_start: 0.7624 (mp0) cc_final: 0.6916 (mp0) REVERT: G 945 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7678 (mtpp) REVERT: G 977 ILE cc_start: 0.8807 (tp) cc_final: 0.8520 (mm) REVERT: G 1019 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7362 (mm-40) REVERT: G 1038 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8384 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8481 (tp) cc_final: 0.8247 (mt) REVERT: G 1061 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6836 (tm-30) REVERT: G 1144 SER cc_start: 0.8556 (t) cc_final: 0.8217 (m) REVERT: G 1150 ASN cc_start: 0.8293 (p0) cc_final: 0.7806 (p0) REVERT: I 142 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7708 (tmtt) REVERT: I 193 TYR cc_start: 0.8289 (m-80) cc_final: 0.7846 (m-80) REVERT: I 221 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7369 (mtt180) REVERT: I 265 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7230 (tm-30) REVERT: J 373 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7387 (mm-30) REVERT: J 467 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7237 (mm-40) REVERT: J 496 THR cc_start: 0.7874 (p) cc_final: 0.7588 (p) REVERT: J 498 GLU cc_start: 0.6914 (pm20) cc_final: 0.6566 (pm20) REVERT: J 529 LYS cc_start: 0.8285 (tppt) cc_final: 0.7311 (tppt) REVERT: J 533 ASN cc_start: 0.8312 (t0) cc_final: 0.7378 (t0) REVERT: J 544 THR cc_start: 0.7739 (p) cc_final: 0.6996 (t) REVERT: J 547 ASP cc_start: 0.7800 (p0) cc_final: 0.7539 (p0) REVERT: J 586 LYS cc_start: 0.7022 (mptt) cc_final: 0.6467 (mmtp) REVERT: K 876 LYS cc_start: 0.7832 (tttp) cc_final: 0.7470 (tttm) REVERT: K 970 THR cc_start: 0.8469 (t) cc_final: 0.8134 (p) REVERT: K 1001 ASN cc_start: 0.7926 (m-40) cc_final: 0.7435 (m-40) REVERT: K 1019 GLN cc_start: 0.8073 (mt0) cc_final: 0.7848 (mt0) REVERT: K 1079 ASN cc_start: 0.8488 (t0) cc_final: 0.8264 (t0) REVERT: K 1084 MET cc_start: 0.7739 (mtm) cc_final: 0.7536 (mtp) REVERT: K 1115 THR cc_start: 0.8620 (t) cc_final: 0.8301 (p) REVERT: K 1130 VAL cc_start: 0.8078 (p) cc_final: 0.7780 (t) outliers start: 132 outliers final: 89 residues processed: 817 average time/residue: 0.3936 time to fit residues: 491.4116 Evaluate side-chains 836 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 738 time to evaluate : 2.920 ------------------------------------------------------------------------------- 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 200 VAL 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 435 LEU 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 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 349 ILE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 504 MET 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 850 GLU 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 1043 MET Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 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 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 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1095 MET Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 623 HIS ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS F 337 GLN F 340 ASN F 386 GLN G 847 GLN G 954 ASN G1075 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 545 ASN J 559 HIS J 686 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107136 restraints weight = 40101.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110302 restraints weight = 16743.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112320 restraints weight = 8959.311| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24901 Z= 0.288 Angle : 0.620 15.683 33895 Z= 0.315 Chirality : 0.046 0.517 3804 Planarity : 0.005 0.060 4362 Dihedral : 4.752 59.821 3695 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.20 % Allowed : 28.51 % 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: -0.22 (0.15), residues: 3106 helix: 2.79 (0.27), residues: 324 sheet: 0.41 (0.17), residues: 972 loop : -1.06 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 662 HIS 0.024 0.001 HIS F 559 PHE 0.020 0.002 PHE C1235 TYR 0.023 0.002 TYR B 397 ARG 0.006 0.000 ARG G1082 *********************** 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 901 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 763 time to evaluate : 2.731 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: 0.7636 (mmmt) cc_final: 0.7124 (mmmt) REVERT: B 395 HIS cc_start: 0.7559 (t-90) cc_final: 0.7029 (t-90) REVERT: B 396 ASP cc_start: 0.7856 (t0) cc_final: 0.7245 (t0) REVERT: B 462 TYR cc_start: 0.8041 (t80) cc_final: 0.7580 (t80) REVERT: B 484 ILE cc_start: 0.8273 (mm) cc_final: 0.8016 (mt) REVERT: B 517 GLN cc_start: 0.7985 (mm110) cc_final: 0.7727 (mm-40) REVERT: B 711 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 818 HIS cc_start: 0.6596 (t-90) cc_final: 0.6332 (t-90) REVERT: C 819 SER cc_start: 0.8194 (m) cc_final: 0.7797 (p) REVERT: C 857 LEU cc_start: 0.8455 (mt) cc_final: 0.8250 (mt) REVERT: C 930 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8195 (ttp-110) REVERT: C 954 ASN cc_start: 0.7619 (p0) cc_final: 0.7278 (p0) REVERT: C 983 SER cc_start: 0.8816 (t) cc_final: 0.8274 (p) REVERT: C 998 GLU cc_start: 0.6392 (mp0) cc_final: 0.5928 (mp0) REVERT: C 1014 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8137 (mmt180) REVERT: C 1018 ILE cc_start: 0.8058 (pt) cc_final: 0.7851 (pt) REVERT: C 1021 ARG cc_start: 0.8943 (tpp-160) cc_final: 0.8365 (tpt170) REVERT: C 1024 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6845 (mm-30) REVERT: C 1059 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7996 (mp) REVERT: C 1095 MET cc_start: 0.7062 (ppp) cc_final: 0.6394 (ppp) REVERT: C 1117 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 1227 LYS cc_start: 0.8271 (mttt) cc_final: 0.7864 (mttt) REVERT: E 113 MET cc_start: 0.5334 (mmp) cc_final: 0.4961 (mmp) REVERT: E 165 LYS cc_start: 0.8665 (tptp) cc_final: 0.8358 (tptp) REVERT: E 195 TRP cc_start: 0.8299 (t60) cc_final: 0.7990 (t60) REVERT: E 209 ILE cc_start: 0.8454 (tp) cc_final: 0.8221 (tp) REVERT: F 394 ASN cc_start: 0.7735 (t0) cc_final: 0.7248 (t0) REVERT: F 399 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8176 (mtpp) REVERT: F 430 MET cc_start: 0.7421 (ttp) cc_final: 0.7167 (ttp) REVERT: F 459 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8283 (ttm170) REVERT: F 511 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8215 (mmm160) REVERT: F 548 MET cc_start: 0.7311 (mpp) cc_final: 0.6886 (mpp) REVERT: F 570 PHE cc_start: 0.8268 (t80) cc_final: 0.8034 (t80) REVERT: F 586 LYS cc_start: 0.7376 (pttt) cc_final: 0.7082 (pptt) REVERT: F 638 TYR cc_start: 0.8559 (p90) cc_final: 0.8241 (p90) REVERT: F 686 GLN cc_start: 0.7872 (mt0) cc_final: 0.7625 (mt0) REVERT: F 694 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7737 (mp) REVERT: F 720 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7220 (ppp) REVERT: G 914 GLU cc_start: 0.7617 (mp0) cc_final: 0.6899 (mp0) REVERT: G 945 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7706 (mtpp) REVERT: G 954 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7489 (t0) REVERT: G 1019 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7313 (mm-40) REVERT: G 1038 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8402 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8495 (tp) cc_final: 0.8263 (mt) REVERT: G 1061 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 1144 SER cc_start: 0.8598 (t) cc_final: 0.8289 (m) REVERT: G 1150 ASN cc_start: 0.8289 (p0) cc_final: 0.7792 (p0) REVERT: G 1213 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (t) REVERT: I 126 GLU cc_start: 0.6413 (tp30) cc_final: 0.5905 (tp30) REVERT: I 142 LYS cc_start: 0.8154 (tmmt) cc_final: 0.7867 (tmtt) REVERT: I 149 VAL cc_start: 0.8290 (m) cc_final: 0.8027 (t) REVERT: I 177 MET cc_start: 0.4192 (OUTLIER) cc_final: 0.3967 (mpp) REVERT: I 193 TYR cc_start: 0.8423 (m-80) cc_final: 0.7971 (m-80) REVERT: I 221 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7308 (mtt180) REVERT: J 373 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7395 (mm-30) REVERT: J 387 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (mt) REVERT: J 402 TYR cc_start: 0.8224 (p90) cc_final: 0.7955 (p90) REVERT: J 467 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7248 (mm-40) REVERT: J 522 LYS cc_start: 0.8235 (tttp) cc_final: 0.7602 (tttp) REVERT: J 529 LYS cc_start: 0.8297 (tppt) cc_final: 0.7373 (tppt) REVERT: J 533 ASN cc_start: 0.8322 (t0) cc_final: 0.7400 (t0) REVERT: J 544 THR cc_start: 0.7744 (p) cc_final: 0.7066 (t) REVERT: J 547 ASP cc_start: 0.7813 (p0) cc_final: 0.7586 (p0) REVERT: J 586 LYS cc_start: 0.7021 (mptt) cc_final: 0.6448 (mmtp) REVERT: J 692 TYR cc_start: 0.8351 (t80) cc_final: 0.8062 (t80) REVERT: K 876 LYS cc_start: 0.7909 (tttp) cc_final: 0.7530 (tttm) REVERT: K 938 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8182 (mtmm) REVERT: K 970 THR cc_start: 0.8472 (t) cc_final: 0.8146 (p) REVERT: K 1014 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8105 (mmt90) REVERT: K 1019 GLN cc_start: 0.8208 (mt0) cc_final: 0.7954 (mt0) REVERT: K 1079 ASN cc_start: 0.8547 (t0) cc_final: 0.8336 (t0) REVERT: K 1084 MET cc_start: 0.7755 (mtm) cc_final: 0.7545 (mtp) REVERT: K 1115 THR cc_start: 0.8628 (t) cc_final: 0.8304 (p) REVERT: K 1130 VAL cc_start: 0.8078 (p) cc_final: 0.7789 (t) outliers start: 138 outliers final: 96 residues processed: 827 average time/residue: 0.4036 time to fit residues: 509.0296 Evaluate side-chains 851 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 742 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 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 951 MET 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 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 378 MET Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 608 VAL 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 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 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 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 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 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 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL 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 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- 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 337 GLN B 340 ASN B 395 HIS C1019 GLN C1209 HIS E 125 HIS F 340 ASN ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 686 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106732 restraints weight = 40297.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109932 restraints weight = 16760.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111950 restraints weight = 8885.618| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24901 Z= 0.228 Angle : 0.614 15.718 33895 Z= 0.312 Chirality : 0.045 0.538 3804 Planarity : 0.004 0.058 4362 Dihedral : 4.687 57.342 3695 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.17 % Allowed : 28.70 % Favored : 66.14 % 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: -0.21 (0.15), residues: 3106 helix: 2.82 (0.27), residues: 324 sheet: 0.40 (0.17), residues: 969 loop : -1.05 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 662 HIS 0.010 0.001 HIS B 685 PHE 0.019 0.001 PHE C1235 TYR 0.032 0.002 TYR B 397 ARG 0.006 0.000 ARG E 258 *********************** 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 896 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 759 time to evaluate : 2.662 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: 0.7651 (mmmt) cc_final: 0.7123 (mmmt) REVERT: B 343 LYS cc_start: 0.8702 (mptt) cc_final: 0.8495 (mptt) REVERT: B 395 HIS cc_start: 0.7427 (t70) cc_final: 0.6858 (t70) REVERT: B 396 ASP cc_start: 0.7766 (t0) cc_final: 0.7178 (t0) REVERT: B 462 TYR cc_start: 0.8035 (t80) cc_final: 0.7575 (t80) REVERT: B 467 GLN cc_start: 0.7591 (mm110) cc_final: 0.7329 (mm110) REVERT: B 484 ILE cc_start: 0.8263 (mm) cc_final: 0.8010 (mt) REVERT: B 517 GLN cc_start: 0.7998 (mm110) cc_final: 0.7702 (mm-40) REVERT: B 711 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8096 (mp) REVERT: C 818 HIS cc_start: 0.6701 (t-90) cc_final: 0.6449 (t-90) REVERT: C 819 SER cc_start: 0.8180 (m) cc_final: 0.7783 (p) REVERT: C 857 LEU cc_start: 0.8456 (mt) cc_final: 0.8251 (mt) REVERT: C 930 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8184 (ttp-110) REVERT: C 954 ASN cc_start: 0.7588 (p0) cc_final: 0.7237 (p0) REVERT: C 983 SER cc_start: 0.8818 (t) cc_final: 0.8284 (p) REVERT: C 998 GLU cc_start: 0.6390 (mp0) cc_final: 0.5920 (mp0) REVERT: C 1014 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8091 (mmt180) REVERT: C 1018 ILE cc_start: 0.8066 (pt) cc_final: 0.7836 (pt) REVERT: C 1021 ARG cc_start: 0.8921 (tpp-160) cc_final: 0.8386 (tpt170) REVERT: C 1024 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6934 (mm-30) REVERT: C 1059 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7985 (mp) REVERT: C 1095 MET cc_start: 0.7041 (ppp) cc_final: 0.6352 (ppp) REVERT: C 1117 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (p) REVERT: C 1227 LYS cc_start: 0.8297 (mttt) cc_final: 0.7862 (mttt) REVERT: E 113 MET cc_start: 0.5285 (mmp) cc_final: 0.4923 (mmp) REVERT: E 165 LYS cc_start: 0.8676 (tptp) cc_final: 0.8319 (tptp) REVERT: F 370 VAL cc_start: 0.8646 (t) cc_final: 0.8426 (m) REVERT: F 394 ASN cc_start: 0.7789 (t0) cc_final: 0.7315 (t0) REVERT: F 399 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8195 (mtpp) REVERT: F 430 MET cc_start: 0.7394 (ttp) cc_final: 0.7036 (ttp) REVERT: F 459 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: F 514 LEU cc_start: 0.8824 (mm) cc_final: 0.8618 (mt) REVERT: F 548 MET cc_start: 0.7130 (mpp) cc_final: 0.6673 (mpp) REVERT: F 566 LYS cc_start: 0.7097 (mmmt) cc_final: 0.6862 (mmmt) REVERT: F 570 PHE cc_start: 0.8250 (t80) cc_final: 0.8038 (t80) REVERT: F 586 LYS cc_start: 0.7392 (pttt) cc_final: 0.7083 (pptt) REVERT: F 638 TYR cc_start: 0.8554 (p90) cc_final: 0.8236 (p90) REVERT: F 686 GLN cc_start: 0.7758 (mt0) cc_final: 0.7483 (mt0) REVERT: G 910 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: G 912 ASP cc_start: 0.7793 (m-30) cc_final: 0.7398 (t0) REVERT: G 914 GLU cc_start: 0.7610 (mp0) cc_final: 0.6957 (mp0) REVERT: G 945 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7672 (mtpp) REVERT: G 1019 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7319 (mm-40) REVERT: G 1038 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8276 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8468 (tp) cc_final: 0.8247 (mt) REVERT: G 1061 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6908 (tm-30) REVERT: G 1082 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8118 (ptt-90) REVERT: G 1139 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8169 (ptmt) REVERT: G 1144 SER cc_start: 0.8515 (t) cc_final: 0.8198 (m) REVERT: G 1213 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8409 (t) REVERT: I 126 GLU cc_start: 0.6311 (tp30) cc_final: 0.5750 (tp30) REVERT: I 142 LYS cc_start: 0.8199 (tmmt) cc_final: 0.7948 (tmtt) REVERT: I 187 GLU cc_start: 0.7164 (pm20) cc_final: 0.6899 (pm20) REVERT: I 193 TYR cc_start: 0.8451 (m-80) cc_final: 0.8006 (m-80) REVERT: I 221 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7406 (mtt180) REVERT: I 252 ASN cc_start: 0.7619 (t0) cc_final: 0.7377 (t0) REVERT: J 363 SER cc_start: 0.8420 (t) cc_final: 0.8049 (p) REVERT: J 373 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7389 (mm-30) REVERT: J 387 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7355 (mt) REVERT: J 402 TYR cc_start: 0.8142 (p90) cc_final: 0.7894 (p90) REVERT: J 467 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7269 (mm-40) REVERT: J 510 ASP cc_start: 0.8022 (t0) cc_final: 0.7728 (t70) REVERT: J 522 LYS cc_start: 0.8238 (tttp) cc_final: 0.7603 (tttp) REVERT: J 529 LYS cc_start: 0.8254 (tppt) cc_final: 0.7402 (tppt) REVERT: J 533 ASN cc_start: 0.8352 (t0) cc_final: 0.7527 (t0) REVERT: J 544 THR cc_start: 0.7734 (p) cc_final: 0.7160 (t) REVERT: J 547 ASP cc_start: 0.7810 (p0) cc_final: 0.7584 (p0) REVERT: J 586 LYS cc_start: 0.6976 (mptt) cc_final: 0.6436 (mmtp) REVERT: J 692 TYR cc_start: 0.8313 (t80) cc_final: 0.8015 (t80) REVERT: K 876 LYS cc_start: 0.7882 (tttp) cc_final: 0.7508 (tttm) REVERT: K 917 GLN cc_start: 0.8671 (tt0) cc_final: 0.8465 (tp40) REVERT: K 938 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8173 (mtmm) REVERT: K 970 THR cc_start: 0.8464 (t) cc_final: 0.8139 (p) REVERT: K 986 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8377 (p) REVERT: K 1014 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7776 (mmt90) REVERT: K 1019 GLN cc_start: 0.8140 (mt0) cc_final: 0.7851 (mt0) REVERT: K 1079 ASN cc_start: 0.8546 (t0) cc_final: 0.8339 (t0) REVERT: K 1115 THR cc_start: 0.8612 (t) cc_final: 0.8304 (p) REVERT: K 1130 VAL cc_start: 0.8058 (p) cc_final: 0.7777 (t) REVERT: K 1156 GLU cc_start: 0.7279 (pm20) cc_final: 0.7065 (pm20) outliers start: 137 outliers final: 105 residues processed: 822 average time/residue: 0.4017 time to fit residues: 501.4517 Evaluate side-chains 867 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 751 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 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 951 MET 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 208 THR 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 378 MET Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL 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 608 VAL 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 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 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 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1213 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 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 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 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 687 ILE 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 975 GLN Chi-restraints excluded: chain K residue 986 THR 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 1186 SER 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: 0.0040 chunk 182 optimal weight: 0.0010 chunk 291 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- 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 545 ASN B 551 ASN F 340 ASN F 559 HIS ** F 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 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 = 0.3543 r_free = 0.3543 target = 0.122701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104501 restraints weight = 40540.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107745 restraints weight = 17144.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109827 restraints weight = 9250.492| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24901 Z= 0.336 Angle : 0.671 15.736 33895 Z= 0.344 Chirality : 0.047 0.544 3804 Planarity : 0.005 0.061 4362 Dihedral : 4.937 56.399 3695 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.05 % Allowed : 28.51 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.15), residues: 3106 helix: 2.77 (0.27), residues: 324 sheet: 0.38 (0.17), residues: 981 loop : -1.13 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 102 HIS 0.011 0.001 HIS F 559 PHE 0.026 0.002 PHE C1235 TYR 0.029 0.002 TYR B 397 ARG 0.006 0.001 ARG G1082 *********************** 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 922 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 788 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7089 (mmmt) REVERT: B 343 LYS cc_start: 0.8724 (mptt) cc_final: 0.8453 (mptt) REVERT: B 395 HIS cc_start: 0.7523 (t70) cc_final: 0.7055 (t70) REVERT: B 396 ASP cc_start: 0.7877 (t0) cc_final: 0.7272 (t0) REVERT: B 462 TYR cc_start: 0.8082 (t80) cc_final: 0.7543 (t80) REVERT: B 467 GLN cc_start: 0.7613 (mm110) cc_final: 0.7331 (mm110) REVERT: B 484 ILE cc_start: 0.8228 (mm) cc_final: 0.7986 (mt) REVERT: B 517 GLN cc_start: 0.8091 (mm110) cc_final: 0.7841 (mm-40) REVERT: B 634 GLU cc_start: 0.7233 (tp30) cc_final: 0.6979 (tp30) REVERT: B 714 ILE cc_start: 0.8508 (tp) cc_final: 0.8289 (tt) REVERT: C 819 SER cc_start: 0.8206 (m) cc_final: 0.7978 (p) REVERT: C 920 GLU cc_start: 0.7506 (pm20) cc_final: 0.7305 (pm20) REVERT: C 930 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.8211 (ttp-110) REVERT: C 954 ASN cc_start: 0.7644 (p0) cc_final: 0.7306 (p0) REVERT: C 983 SER cc_start: 0.8816 (t) cc_final: 0.8285 (p) REVERT: C 998 GLU cc_start: 0.6463 (mp0) cc_final: 0.6073 (mp0) REVERT: C 1001 ASN cc_start: 0.7935 (m-40) cc_final: 0.7642 (m110) REVERT: C 1014 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8111 (mmt180) REVERT: C 1018 ILE cc_start: 0.8074 (pt) cc_final: 0.7857 (pt) REVERT: C 1021 ARG cc_start: 0.8912 (tpp-160) cc_final: 0.8416 (tpt170) REVERT: C 1059 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8060 (mp) REVERT: C 1095 MET cc_start: 0.7066 (ppp) cc_final: 0.6367 (ppp) REVERT: C 1117 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 1160 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7109 (mmtp) REVERT: C 1227 LYS cc_start: 0.8291 (mttt) cc_final: 0.7923 (mttt) REVERT: E 113 MET cc_start: 0.5299 (mmp) cc_final: 0.4959 (mmp) REVERT: E 165 LYS cc_start: 0.8677 (tptp) cc_final: 0.8370 (tptp) REVERT: E 178 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.4640 (pmt170) REVERT: F 370 VAL cc_start: 0.8644 (t) cc_final: 0.8415 (m) REVERT: F 394 ASN cc_start: 0.7724 (t0) cc_final: 0.7272 (t0) REVERT: F 399 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8221 (mtpp) REVERT: F 430 MET cc_start: 0.7478 (ttp) cc_final: 0.7209 (ttp) REVERT: F 459 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8352 (ttm170) REVERT: F 484 ILE cc_start: 0.8402 (mm) cc_final: 0.8151 (mm) REVERT: F 514 LEU cc_start: 0.8763 (mm) cc_final: 0.8548 (mp) REVERT: F 548 MET cc_start: 0.7377 (mpp) cc_final: 0.6946 (mpp) REVERT: F 570 PHE cc_start: 0.8329 (t80) cc_final: 0.8113 (t80) REVERT: F 586 LYS cc_start: 0.7461 (pttt) cc_final: 0.7149 (pptt) REVERT: F 594 ASP cc_start: 0.7639 (t0) cc_final: 0.7381 (t0) REVERT: F 638 TYR cc_start: 0.8547 (p90) cc_final: 0.8265 (p90) REVERT: F 686 GLN cc_start: 0.7810 (mt0) cc_final: 0.7566 (mt0) REVERT: F 694 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7843 (mp) REVERT: G 914 GLU cc_start: 0.7603 (mp0) cc_final: 0.6869 (mp0) REVERT: G 945 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7714 (mtpp) REVERT: G 1019 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7284 (mm-40) REVERT: G 1023 VAL cc_start: 0.8796 (t) cc_final: 0.8541 (p) REVERT: G 1038 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8349 (ttt-90) REVERT: G 1061 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6957 (tm-30) REVERT: G 1144 SER cc_start: 0.8608 (t) cc_final: 0.8318 (m) REVERT: G 1213 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8432 (t) REVERT: G 1227 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8038 (mtmm) REVERT: I 126 GLU cc_start: 0.6333 (tp30) cc_final: 0.5810 (tp30) REVERT: I 142 LYS cc_start: 0.8317 (tmmt) cc_final: 0.8049 (ttpt) REVERT: I 172 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: I 177 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.4217 (mpp) REVERT: I 187 GLU cc_start: 0.7283 (pm20) cc_final: 0.6908 (pm20) REVERT: I 193 TYR cc_start: 0.8573 (m-80) cc_final: 0.8106 (m-80) REVERT: I 252 ASN cc_start: 0.7878 (t0) cc_final: 0.7655 (t0) REVERT: J 387 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7420 (mt) REVERT: J 402 TYR cc_start: 0.8241 (p90) cc_final: 0.8011 (p90) REVERT: J 467 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7230 (mm-40) REVERT: J 486 CYS cc_start: 0.5455 (p) cc_final: 0.5029 (p) REVERT: J 522 LYS cc_start: 0.8231 (tttp) cc_final: 0.7594 (tttp) REVERT: J 529 LYS cc_start: 0.8284 (tppt) cc_final: 0.7417 (tppt) REVERT: J 533 ASN cc_start: 0.8297 (t0) cc_final: 0.7495 (t0) REVERT: J 544 THR cc_start: 0.7772 (p) cc_final: 0.7251 (p) REVERT: J 577 ARG cc_start: 0.8060 (ptp-170) cc_final: 0.7818 (ptp-170) REVERT: J 586 LYS cc_start: 0.7172 (mptt) cc_final: 0.6517 (mmtp) REVERT: J 692 TYR cc_start: 0.8384 (t80) cc_final: 0.8107 (t80) REVERT: K 822 MET cc_start: 0.7971 (ptp) cc_final: 0.7743 (ptt) REVERT: K 876 LYS cc_start: 0.7963 (tttp) cc_final: 0.7509 (tttm) REVERT: K 903 MET cc_start: 0.7665 (mtm) cc_final: 0.7422 (mtp) REVERT: K 917 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8448 (tp40) REVERT: K 970 THR cc_start: 0.8465 (t) cc_final: 0.8165 (p) REVERT: K 986 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (p) REVERT: K 1014 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7256 (mmt90) REVERT: K 1019 GLN cc_start: 0.8221 (mt0) cc_final: 0.7918 (mt0) REVERT: K 1115 THR cc_start: 0.8623 (t) cc_final: 0.8313 (p) REVERT: K 1130 VAL cc_start: 0.8074 (p) cc_final: 0.7791 (t) outliers start: 134 outliers final: 100 residues processed: 844 average time/residue: 0.4019 time to fit residues: 518.0324 Evaluate side-chains 868 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 755 time to evaluate : 2.957 ------------------------------------------------------------------------------- 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 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 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 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 111 MET 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 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain F residue 608 VAL 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 833 HIS Chi-restraints excluded: chain G residue 846 MET 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 930 ARG Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1190 THR 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 172 GLN 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 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 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 917 GLN 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 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 1213 VAL 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: 6.9990 chunk 15 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 268 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 557 GLN F 340 ASN ** F 664 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 545 ASN 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 = 0.3556 r_free = 0.3556 target = 0.123429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105194 restraints weight = 40554.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108441 restraints weight = 17139.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110527 restraints weight = 9269.686| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24901 Z= 0.255 Angle : 0.662 16.303 33895 Z= 0.337 Chirality : 0.046 0.545 3804 Planarity : 0.005 0.048 4362 Dihedral : 4.840 56.699 3695 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.64 % Allowed : 30.28 % Favored : 65.08 % 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: 2.78 (0.27), residues: 324 sheet: 0.44 (0.16), residues: 993 loop : -1.16 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 251 HIS 0.022 0.001 HIS F 559 PHE 0.025 0.002 PHE C1235 TYR 0.030 0.002 TYR B 397 ARG 0.007 0.000 ARG E 258 *********************** 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 893 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 770 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7290 (mmmt) REVERT: B 343 LYS cc_start: 0.8706 (mptt) cc_final: 0.8424 (mptt) REVERT: B 395 HIS cc_start: 0.7510 (t70) cc_final: 0.6992 (t70) REVERT: B 396 ASP cc_start: 0.7844 (t0) cc_final: 0.7287 (t0) REVERT: B 462 TYR cc_start: 0.8082 (t80) cc_final: 0.7627 (t80) REVERT: B 467 GLN cc_start: 0.7597 (mm110) cc_final: 0.7322 (mm110) REVERT: B 484 ILE cc_start: 0.8234 (mm) cc_final: 0.7988 (mt) REVERT: B 517 GLN cc_start: 0.8079 (mm110) cc_final: 0.7847 (mm-40) REVERT: B 529 LYS cc_start: 0.8147 (tttp) cc_final: 0.7735 (tttp) REVERT: B 634 GLU cc_start: 0.7216 (tp30) cc_final: 0.6977 (tp30) REVERT: B 714 ILE cc_start: 0.8523 (tp) cc_final: 0.8303 (tt) REVERT: C 930 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8222 (ttp-110) REVERT: C 954 ASN cc_start: 0.7680 (p0) cc_final: 0.7336 (p0) REVERT: C 983 SER cc_start: 0.8816 (t) cc_final: 0.8288 (p) REVERT: C 998 GLU cc_start: 0.6417 (mp0) cc_final: 0.6020 (mp0) REVERT: C 1018 ILE cc_start: 0.8111 (pt) cc_final: 0.7895 (pt) REVERT: C 1021 ARG cc_start: 0.8903 (tpp-160) cc_final: 0.8419 (tpt170) REVERT: C 1035 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7693 (ttmm) REVERT: C 1059 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 1095 MET cc_start: 0.7031 (ppp) cc_final: 0.6364 (ppp) REVERT: C 1117 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 1227 LYS cc_start: 0.8315 (mttt) cc_final: 0.7944 (mttt) REVERT: E 113 MET cc_start: 0.5307 (mmp) cc_final: 0.4971 (mmp) REVERT: E 165 LYS cc_start: 0.8664 (tptp) cc_final: 0.8316 (tptp) REVERT: E 178 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.4438 (pmt170) REVERT: F 370 VAL cc_start: 0.8644 (t) cc_final: 0.8422 (m) REVERT: F 394 ASN cc_start: 0.7762 (t0) cc_final: 0.7315 (t0) REVERT: F 399 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8220 (mtpp) REVERT: F 430 MET cc_start: 0.7407 (ttp) cc_final: 0.7071 (ttp) REVERT: F 459 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8295 (ttm170) REVERT: F 484 ILE cc_start: 0.8328 (mm) cc_final: 0.8080 (mm) REVERT: F 548 MET cc_start: 0.7298 (mpp) cc_final: 0.6922 (mpp) REVERT: F 570 PHE cc_start: 0.8295 (t80) cc_final: 0.8074 (t80) REVERT: F 586 LYS cc_start: 0.7459 (pttt) cc_final: 0.7135 (pptt) REVERT: F 594 ASP cc_start: 0.7639 (t0) cc_final: 0.7382 (t0) REVERT: F 638 TYR cc_start: 0.8548 (p90) cc_final: 0.8257 (p90) REVERT: F 686 GLN cc_start: 0.7757 (mt0) cc_final: 0.7514 (mt0) REVERT: F 694 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7752 (mp) REVERT: G 914 GLU cc_start: 0.7591 (mp0) cc_final: 0.6902 (mp0) REVERT: G 930 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: G 945 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7705 (mtpp) REVERT: G 1019 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7355 (mm-40) REVERT: G 1023 VAL cc_start: 0.8788 (t) cc_final: 0.8514 (p) REVERT: G 1061 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6901 (tm-30) REVERT: G 1144 SER cc_start: 0.8496 (t) cc_final: 0.8175 (m) REVERT: G 1213 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8416 (t) REVERT: G 1227 LYS cc_start: 0.8303 (mtmm) cc_final: 0.8028 (mtmm) REVERT: I 113 MET cc_start: 0.7410 (mmm) cc_final: 0.7026 (mmm) REVERT: I 126 GLU cc_start: 0.6220 (tp30) cc_final: 0.5672 (tp30) REVERT: I 142 LYS cc_start: 0.8371 (tmmt) cc_final: 0.8109 (ttpt) REVERT: I 177 MET cc_start: 0.4545 (OUTLIER) cc_final: 0.4114 (mpp) REVERT: I 187 GLU cc_start: 0.7236 (pm20) cc_final: 0.6849 (pm20) REVERT: I 193 TYR cc_start: 0.8597 (m-80) cc_final: 0.8357 (m-10) REVERT: I 221 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7443 (mtt180) REVERT: I 252 ASN cc_start: 0.7947 (t0) cc_final: 0.7723 (t0) REVERT: J 387 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7359 (mt) REVERT: J 402 TYR cc_start: 0.8155 (p90) cc_final: 0.7881 (p90) REVERT: J 467 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7281 (mm-40) REVERT: J 486 CYS cc_start: 0.5440 (p) cc_final: 0.5041 (p) REVERT: J 522 LYS cc_start: 0.8231 (tttp) cc_final: 0.7594 (tttp) REVERT: J 529 LYS cc_start: 0.8307 (tppt) cc_final: 0.7494 (tppt) REVERT: J 533 ASN cc_start: 0.8347 (t0) cc_final: 0.7520 (t0) REVERT: J 544 THR cc_start: 0.7796 (p) cc_final: 0.7307 (p) REVERT: J 577 ARG cc_start: 0.8022 (ptp-170) cc_final: 0.7800 (ptp-170) REVERT: J 586 LYS cc_start: 0.7136 (mptt) cc_final: 0.6567 (mmtp) REVERT: J 692 TYR cc_start: 0.8296 (t80) cc_final: 0.8007 (t80) REVERT: K 822 MET cc_start: 0.7984 (ptp) cc_final: 0.7758 (ptt) REVERT: K 876 LYS cc_start: 0.7942 (tttp) cc_final: 0.7504 (tttm) REVERT: K 970 THR cc_start: 0.8461 (t) cc_final: 0.8158 (p) REVERT: K 986 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8400 (p) REVERT: K 1014 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7820 (mmt90) REVERT: K 1019 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: K 1022 THR cc_start: 0.8525 (t) cc_final: 0.8156 (p) REVERT: K 1115 THR cc_start: 0.8614 (t) cc_final: 0.8323 (p) REVERT: K 1130 VAL cc_start: 0.8053 (p) cc_final: 0.7800 (t) REVERT: K 1229 SER cc_start: 0.8358 (t) cc_final: 0.7821 (p) outliers start: 123 outliers final: 98 residues processed: 825 average time/residue: 0.4255 time to fit residues: 537.5382 Evaluate side-chains 874 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 764 time to evaluate : 3.442 ------------------------------------------------------------------------------- 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 B residue 412 VAL 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 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 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 951 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 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 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 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL 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 597 THR Chi-restraints excluded: chain F residue 608 VAL 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 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 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1190 THR 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 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 221 ARG 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 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 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: 5.9990 chunk 303 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 223 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 131 optimal weight: 0.0370 chunk 295 optimal weight: 4.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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 545 ASN B 557 GLN C1140 ASN F 340 ASN ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS ** F 664 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 J 673 GLN J 686 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107439 restraints weight = 40227.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110586 restraints weight = 16733.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112572 restraints weight = 8925.999| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24901 Z= 0.189 Angle : 0.645 16.738 33895 Z= 0.327 Chirality : 0.045 0.526 3804 Planarity : 0.004 0.046 4362 Dihedral : 4.643 55.467 3695 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.70 % Allowed : 31.56 % Favored : 64.74 % 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 (0.27), residues: 324 sheet: 0.42 (0.16), residues: 1011 loop : -1.07 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 251 HIS 0.009 0.001 HIS A 196 PHE 0.026 0.001 PHE C1235 TYR 0.030 0.001 TYR B 397 ARG 0.006 0.000 ARG E 258 ********************** 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 869 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 771 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7313 (mmmt) REVERT: B 343 LYS cc_start: 0.8703 (mptt) cc_final: 0.8398 (mptt) REVERT: B 395 HIS cc_start: 0.7460 (t70) cc_final: 0.6951 (t70) REVERT: B 396 ASP cc_start: 0.7749 (t0) cc_final: 0.7166 (t0) REVERT: B 462 TYR cc_start: 0.8052 (t80) cc_final: 0.7586 (t80) REVERT: B 467 GLN cc_start: 0.7581 (mm110) cc_final: 0.7327 (mm110) REVERT: B 511 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7405 (ttm-80) REVERT: B 517 GLN cc_start: 0.8068 (mm110) cc_final: 0.7804 (mm-40) REVERT: B 529 LYS cc_start: 0.8123 (tttp) cc_final: 0.7708 (tttp) REVERT: B 634 GLU cc_start: 0.7205 (tp30) cc_final: 0.6980 (tp30) REVERT: B 714 ILE cc_start: 0.8538 (tp) cc_final: 0.8314 (tt) REVERT: C 917 GLN cc_start: 0.8534 (tt0) cc_final: 0.8297 (tt0) REVERT: C 930 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8190 (ttp-110) REVERT: C 950 VAL cc_start: 0.7884 (t) cc_final: 0.7216 (m) REVERT: C 954 ASN cc_start: 0.7613 (p0) cc_final: 0.7263 (p0) REVERT: C 983 SER cc_start: 0.8791 (t) cc_final: 0.8281 (p) REVERT: C 998 GLU cc_start: 0.6358 (mp0) cc_final: 0.6064 (mp0) REVERT: C 1018 ILE cc_start: 0.8109 (pt) cc_final: 0.7883 (pt) REVERT: C 1021 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8435 (tpt170) REVERT: C 1035 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7682 (ttmm) REVERT: C 1059 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7991 (mp) REVERT: C 1095 MET cc_start: 0.7023 (ppp) cc_final: 0.6330 (ppp) REVERT: C 1227 LYS cc_start: 0.8298 (mttt) cc_final: 0.7903 (mttt) REVERT: E 113 MET cc_start: 0.5250 (mmp) cc_final: 0.4935 (mmp) REVERT: E 165 LYS cc_start: 0.8640 (tptp) cc_final: 0.8263 (tptp) REVERT: E 208 THR cc_start: 0.8336 (m) cc_final: 0.7824 (t) REVERT: F 394 ASN cc_start: 0.7779 (t0) cc_final: 0.7319 (t0) REVERT: F 430 MET cc_start: 0.7320 (ttp) cc_final: 0.6817 (ttp) REVERT: F 459 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8384 (ptp-170) REVERT: F 548 MET cc_start: 0.7285 (mpp) cc_final: 0.6916 (mpp) REVERT: F 586 LYS cc_start: 0.7451 (pttt) cc_final: 0.7108 (pptt) REVERT: F 594 ASP cc_start: 0.7613 (t0) cc_final: 0.7360 (t0) REVERT: F 638 TYR cc_start: 0.8540 (p90) cc_final: 0.8204 (p90) REVERT: F 686 GLN cc_start: 0.7729 (mt0) cc_final: 0.7491 (mt0) REVERT: G 910 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: G 914 GLU cc_start: 0.7595 (mp0) cc_final: 0.6905 (mp0) REVERT: G 930 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7914 (ttp-110) REVERT: G 945 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7642 (mtpp) REVERT: G 1019 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7343 (mm-40) REVERT: G 1023 VAL cc_start: 0.8767 (t) cc_final: 0.8532 (p) REVERT: G 1061 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6940 (tm-30) REVERT: G 1082 ARG cc_start: 0.8401 (ptt90) cc_final: 0.8170 (ptt-90) REVERT: G 1138 ASP cc_start: 0.7728 (m-30) cc_final: 0.7315 (p0) REVERT: G 1144 SER cc_start: 0.8356 (t) cc_final: 0.8015 (m) REVERT: G 1213 VAL cc_start: 0.8587 (p) cc_final: 0.8365 (t) REVERT: I 113 MET cc_start: 0.7369 (mmm) cc_final: 0.6997 (mmm) REVERT: I 126 GLU cc_start: 0.6087 (tp30) cc_final: 0.5612 (tp30) REVERT: I 142 LYS cc_start: 0.8401 (tmmt) cc_final: 0.8142 (ttpt) REVERT: I 187 GLU cc_start: 0.7157 (pm20) cc_final: 0.6760 (pm20) REVERT: I 193 TYR cc_start: 0.8589 (m-80) cc_final: 0.8372 (m-10) REVERT: I 221 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7429 (mtt180) REVERT: I 240 GLU cc_start: 0.2501 (tp30) cc_final: 0.2053 (tp30) REVERT: J 387 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7308 (mt) REVERT: J 402 TYR cc_start: 0.8095 (p90) cc_final: 0.7811 (p90) REVERT: J 435 LEU cc_start: 0.8096 (tp) cc_final: 0.7835 (tp) REVERT: J 467 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7289 (mm-40) REVERT: J 486 CYS cc_start: 0.5436 (p) cc_final: 0.5018 (p) REVERT: J 511 ARG cc_start: 0.8456 (mmt90) cc_final: 0.8205 (tpt-90) REVERT: J 522 LYS cc_start: 0.8228 (tttp) cc_final: 0.7553 (tttp) REVERT: J 529 LYS cc_start: 0.8302 (tppt) cc_final: 0.7507 (tppt) REVERT: J 533 ASN cc_start: 0.8373 (t0) cc_final: 0.7573 (t0) REVERT: J 544 THR cc_start: 0.7557 (p) cc_final: 0.7208 (p) REVERT: J 692 TYR cc_start: 0.8221 (t80) cc_final: 0.7919 (t80) REVERT: K 876 LYS cc_start: 0.7897 (tttp) cc_final: 0.7526 (tttm) REVERT: K 970 THR cc_start: 0.8452 (t) cc_final: 0.8136 (p) REVERT: K 986 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8395 (p) REVERT: K 1014 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7775 (mmt90) REVERT: K 1019 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: K 1022 THR cc_start: 0.8485 (t) cc_final: 0.8104 (p) REVERT: K 1115 THR cc_start: 0.8606 (t) cc_final: 0.8307 (p) REVERT: K 1130 VAL cc_start: 0.8037 (p) cc_final: 0.7779 (t) outliers start: 98 outliers final: 76 residues processed: 812 average time/residue: 0.4038 time to fit residues: 496.3407 Evaluate side-chains 847 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 762 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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 B residue 412 VAL 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 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 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 111 MET Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 608 VAL 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 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE 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 1190 THR 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 221 ARG 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 575 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 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 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 181 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 0.0980 chunk 269 optimal weight: 8.9990 chunk 100 optimal weight: 60.0000 chunk 272 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 461 GLN B 545 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN ** F 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G1002 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106088 restraints weight = 40084.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109217 restraints weight = 16771.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111214 restraints weight = 8944.277| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24901 Z= 0.260 Angle : 0.664 17.121 33895 Z= 0.337 Chirality : 0.046 0.533 3804 Planarity : 0.005 0.048 4362 Dihedral : 4.709 55.941 3695 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.62 % Allowed : 31.67 % Favored : 64.71 % 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: -0.23 (0.15), residues: 3106 helix: 2.78 (0.27), residues: 324 sheet: 0.45 (0.17), residues: 993 loop : -1.11 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 251 HIS 0.025 0.001 HIS G1146 PHE 0.016 0.002 PHE C 910 TYR 0.034 0.002 TYR K1029 ARG 0.007 0.000 ARG E 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9871.60 seconds wall clock time: 180 minutes 25.60 seconds (10825.60 seconds total)