Starting phenix.real_space_refine on Sat Jun 21 03:01:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0m_37982/06_2025/8x0m_37982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0m_37982/06_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_37982/06_2025/8x0m_37982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0m_37982/06_2025/8x0m_37982.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0m_37982/06_2025/8x0m_37982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0m_37982/06_2025/8x0m_37982.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 189 5.16 5 C 15278 2.51 5 N 4200 2.21 5 O 4605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.40, per 1000 atoms: 0.63 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: 5.62 Conformation dependent library (CDL) restraints added in 2.9 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: 3.74 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: 10.30 Time building geometry restraints manager: 6.74 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 57.310 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 24964 Z= 0.161 Angle : 0.724 17.530 34036 Z= 0.377 Chirality : 0.046 0.626 3804 Planarity : 0.005 0.120 4362 Dihedral : 16.788 89.911 9233 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.68 % Allowed : 32.73 % Favored : 66.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3106 helix: 2.85 (0.28), residues: 327 sheet: 0.44 (0.17), residues: 972 loop : -1.04 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 251 HIS 0.005 0.001 HIS F 623 PHE 0.034 0.002 PHE B 339 TYR 0.031 0.002 TYR K 861 ARG 0.012 0.001 ARG G 949 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 9) link_NAG-ASN : angle 5.49814 ( 27) link_BETA1-4 : bond 0.00727 ( 6) link_BETA1-4 : angle 1.72960 ( 18) hydrogen bonds : bond 0.11436 ( 943) hydrogen bonds : angle 5.29821 ( 2466) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.40664 ( 96) covalent geometry : bond 0.00358 (24901) covalent geometry : angle 0.70328 (33895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 694 time to evaluate : 2.900 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: 0.3779 time to fit residues: 402.9534 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 : 2.589 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110145 restraints weight = 40319.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113356 restraints weight = 17049.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115404 restraints weight = 9139.474| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24964 Z= 0.216 Angle : 0.666 16.860 34036 Z= 0.339 Chirality : 0.048 0.542 3804 Planarity : 0.005 0.066 4362 Dihedral : 5.184 51.869 3706 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.68 % Allowed : 27.41 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3106 helix: 2.76 (0.28), residues: 324 sheet: 0.40 (0.17), residues: 960 loop : -1.14 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 251 HIS 0.007 0.001 HIS F 395 PHE 0.021 0.002 PHE C 910 TYR 0.022 0.002 TYR C 896 ARG 0.008 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01100 ( 9) link_NAG-ASN : angle 5.35548 ( 27) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 1.16901 ( 18) hydrogen bonds : bond 0.04619 ( 943) hydrogen bonds : angle 4.67016 ( 2466) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.23498 ( 96) covalent geometry : bond 0.00495 (24901) covalent geometry : angle 0.64629 (33895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 762 time to evaluate : 2.636 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: 0.6926 (mmmt) REVERT: A 211 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7804 (p) REVERT: B 395 HIS cc_start: 0.7564 (t-90) cc_final: 0.7238 (t-90) REVERT: B 396 ASP cc_start: 0.7710 (t0) cc_final: 0.7230 (t0) REVERT: B 462 TYR cc_start: 0.7987 (t80) cc_final: 0.7635 (t80) REVERT: B 484 ILE cc_start: 0.8225 (mm) cc_final: 0.7952 (mt) REVERT: B 498 GLU cc_start: 0.7048 (pm20) cc_final: 0.6846 (pm20) REVERT: B 566 LYS cc_start: 0.7440 (mmmm) cc_final: 0.7233 (mmmm) REVERT: B 677 GLU cc_start: 0.7683 (pm20) cc_final: 0.7280 (pm20) REVERT: C 818 HIS cc_start: 0.6015 (t-90) cc_final: 0.5720 (t-90) REVERT: C 930 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8239 (ttp-110) REVERT: C 1024 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 1095 MET cc_start: 0.7111 (ppp) cc_final: 0.6632 (ppp) REVERT: E 113 MET cc_start: 0.5033 (mmp) cc_final: 0.4660 (mmp) REVERT: E 165 LYS cc_start: 0.8626 (tptp) cc_final: 0.8421 (tptp) REVERT: E 252 ASN cc_start: 0.7916 (t0) cc_final: 0.7668 (t0) REVERT: F 394 ASN cc_start: 0.7699 (t0) cc_final: 0.7177 (t0) REVERT: F 399 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7576 (mtpp) REVERT: F 589 ILE cc_start: 0.8581 (tt) cc_final: 0.8369 (tt) REVERT: F 638 TYR cc_start: 0.8508 (p90) cc_final: 0.8158 (p90) REVERT: F 659 GLU cc_start: 0.7435 (tt0) cc_final: 0.7105 (tt0) REVERT: F 686 GLN cc_start: 0.7893 (mt0) cc_final: 0.7670 (mt0) REVERT: F 694 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7871 (mp) REVERT: G 914 GLU cc_start: 0.7642 (mp0) cc_final: 0.7125 (mp0) REVERT: G 945 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7804 (mtpp) REVERT: G 954 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7529 (t0) REVERT: G 1019 GLN cc_start: 0.7799 (mm-40) cc_final: 0.6880 (mm-40) REVERT: G 1082 ARG cc_start: 0.8342 (ptt-90) cc_final: 0.8141 (ptt-90) REVERT: G 1144 SER cc_start: 0.8622 (t) cc_final: 0.8306 (m) REVERT: I 113 MET cc_start: 0.7246 (mmm) cc_final: 0.6956 (mmm) REVERT: I 142 LYS cc_start: 0.7703 (tmmt) cc_final: 0.7361 (tmtt) REVERT: I 193 TYR cc_start: 0.8107 (m-80) cc_final: 0.7649 (m-80) REVERT: J 363 SER cc_start: 0.8507 (t) cc_final: 0.8155 (p) REVERT: J 467 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7131 (mm-40) REVERT: J 473 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8058 (mmtp) REVERT: J 496 THR cc_start: 0.7905 (p) cc_final: 0.7600 (p) REVERT: J 529 LYS cc_start: 0.8229 (tppt) cc_final: 0.7517 (tppt) REVERT: J 547 ASP cc_start: 0.7755 (p0) cc_final: 0.7470 (p0) REVERT: J 567 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7261 (mmtt) REVERT: J 600 VAL cc_start: 0.8562 (p) cc_final: 0.8240 (t) REVERT: J 713 SER cc_start: 0.8180 (t) cc_final: 0.7942 (t) REVERT: K 876 LYS cc_start: 0.7787 (tttp) cc_final: 0.7466 (tttm) REVERT: K 960 ASP cc_start: 0.7697 (p0) cc_final: 0.7400 (p0) REVERT: K 970 THR cc_start: 0.8509 (t) cc_final: 0.8257 (m) REVERT: K 997 ASP cc_start: 0.7641 (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: 0.7763 (mt0) REVERT: K 1115 THR cc_start: 0.8631 (t) cc_final: 0.8327 (p) REVERT: K 1223 SER cc_start: 0.8049 (t) cc_final: 0.7839 (t) outliers start: 124 outliers final: 67 residues processed: 821 average time/residue: 0.3671 time to fit residues: 462.3155 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 : 2.786 ------------------------------------------------------------------------------- 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: 0.6980 chunk 275 optimal weight: 1.9990 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: 1.9990 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 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 = 0.3620 r_free = 0.3620 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109460 restraints weight = 40422.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112767 restraints weight = 17312.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114858 restraints weight = 9376.010| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24964 Z= 0.133 Angle : 0.600 17.808 34036 Z= 0.302 Chirality : 0.045 0.535 3804 Planarity : 0.005 0.061 4362 Dihedral : 4.716 54.640 3695 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.00 % Allowed : 28.58 % 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: -0.25 (0.15), residues: 3106 helix: 2.83 (0.28), residues: 324 sheet: 0.41 (0.17), residues: 969 loop : -1.10 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 642 HIS 0.018 0.001 HIS B 685 PHE 0.022 0.001 PHE C1235 TYR 0.028 0.001 TYR B 397 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 9) link_NAG-ASN : angle 4.92577 ( 27) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 1.14958 ( 18) hydrogen bonds : bond 0.03898 ( 943) hydrogen bonds : angle 4.54801 ( 2466) SS BOND : bond 0.00276 ( 48) SS BOND : angle 1.18969 ( 96) covalent geometry : bond 0.00307 (24901) covalent geometry : angle 0.58072 (33895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 743 time to evaluate : 2.739 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: 0.7551 (mmmt) cc_final: 0.7020 (mmmt) REVERT: A 211 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7742 (p) REVERT: B 395 HIS cc_start: 0.7503 (t-90) cc_final: 0.7130 (t-90) REVERT: B 396 ASP cc_start: 0.7655 (t0) cc_final: 0.7102 (t0) REVERT: B 462 TYR cc_start: 0.7986 (t80) cc_final: 0.7630 (t80) REVERT: B 484 ILE cc_start: 0.8192 (mm) cc_final: 0.7923 (mt) REVERT: B 517 GLN cc_start: 0.7833 (mm110) cc_final: 0.7594 (mm-40) REVERT: B 586 LYS cc_start: 0.8227 (mmmm) cc_final: 0.8012 (mtpt) REVERT: B 679 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7871 (mtpp) REVERT: B 711 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (mp) REVERT: C 818 HIS cc_start: 0.6067 (t-90) cc_final: 0.5842 (t-90) REVERT: C 930 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8227 (ttp-110) REVERT: C 1018 ILE cc_start: 0.8015 (pt) cc_final: 0.7788 (pt) REVERT: C 1021 ARG cc_start: 0.8844 (tpp-160) cc_final: 0.8554 (tpt170) REVERT: C 1024 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6968 (mm-30) REVERT: C 1095 MET cc_start: 0.7069 (ppp) cc_final: 0.6554 (ppp) REVERT: C 1117 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8222 (p) REVERT: E 113 MET cc_start: 0.5192 (mmp) cc_final: 0.4799 (mmp) REVERT: F 394 ASN cc_start: 0.7755 (t0) cc_final: 0.7216 (t0) REVERT: F 399 LYS cc_start: 0.8373 (mtpp) cc_final: 0.7589 (mtpp) REVERT: F 511 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8265 (mmm160) REVERT: F 659 GLU cc_start: 0.7371 (tt0) cc_final: 0.7126 (tt0) REVERT: F 686 GLN cc_start: 0.7823 (mt0) cc_final: 0.7622 (mt0) REVERT: F 694 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7869 (mp) REVERT: G 836 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7636 (ttp80) REVERT: G 925 ARG cc_start: 0.8279 (ptp90) cc_final: 0.8078 (ptp90) REVERT: G 945 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7755 (mtpp) REVERT: G 954 ASN cc_start: 0.7895 (t0) cc_final: 0.7484 (t0) REVERT: G 1019 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7087 (mm-40) REVERT: G 1038 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8271 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8480 (tp) cc_final: 0.8224 (mt) REVERT: G 1061 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6793 (tm-30) REVERT: G 1144 SER cc_start: 0.8659 (t) cc_final: 0.8226 (m) REVERT: G 1160 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6298 (tttm) REVERT: I 113 MET cc_start: 0.7350 (mmm) cc_final: 0.6990 (mmm) REVERT: I 142 LYS cc_start: 0.7664 (tmmt) cc_final: 0.7363 (tmtt) REVERT: I 172 GLN cc_start: 0.3542 (mm110) cc_final: 0.3267 (mm110) REVERT: I 193 TYR cc_start: 0.8028 (m-80) cc_final: 0.7664 (m-80) REVERT: J 467 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7178 (mm-40) REVERT: J 496 THR cc_start: 0.7821 (p) cc_final: 0.7541 (p) REVERT: J 498 GLU cc_start: 0.6921 (pm20) cc_final: 0.6559 (pm20) REVERT: J 529 LYS cc_start: 0.8179 (tppt) cc_final: 0.7467 (tppt) REVERT: J 547 ASP cc_start: 0.7779 (p0) cc_final: 0.7467 (p0) REVERT: J 567 LYS cc_start: 0.7479 (mmtp) cc_final: 0.7246 (mmtt) REVERT: J 586 LYS cc_start: 0.7111 (mptt) cc_final: 0.6505 (mmtp) REVERT: J 634 GLU cc_start: 0.7359 (tp30) cc_final: 0.7132 (tp30) REVERT: J 713 SER cc_start: 0.8180 (t) cc_final: 0.7957 (t) REVERT: K 876 LYS cc_start: 0.7746 (tttp) cc_final: 0.7400 (tttm) REVERT: K 960 ASP cc_start: 0.7701 (p0) cc_final: 0.7493 (p0) REVERT: K 970 THR cc_start: 0.8492 (t) cc_final: 0.8155 (p) REVERT: K 1019 GLN cc_start: 0.8047 (mt0) cc_final: 0.7748 (mt0) REVERT: K 1115 THR cc_start: 0.8608 (t) cc_final: 0.8270 (p) REVERT: K 1130 VAL cc_start: 0.8062 (p) cc_final: 0.7760 (t) REVERT: K 1223 SER cc_start: 0.8014 (t) cc_final: 0.7807 (t) outliers start: 106 outliers final: 64 residues processed: 793 average time/residue: 0.3829 time to fit residues: 464.1874 Evaluate side-chains 794 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 725 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 547 ASP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 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 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 231 VAL 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 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 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: 5.9990 chunk 196 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 202 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 143 optimal weight: 0.0030 chunk 274 optimal weight: 2.9990 overall best weight: 1.1552 ------------------------------------------------------------------------------- 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 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 K1079 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109775 restraints weight = 40723.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113124 restraints weight = 17381.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115267 restraints weight = 9388.022| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24964 Z= 0.117 Angle : 0.589 17.104 34036 Z= 0.293 Chirality : 0.044 0.541 3804 Planarity : 0.004 0.059 4362 Dihedral : 4.533 57.208 3695 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.56 % Allowed : 28.54 % Favored : 66.89 % 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: 0.49 (0.16), residues: 978 loop : -1.10 (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 0.029 0.001 TYR B 397 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 4.83591 ( 27) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 1.14184 ( 18) hydrogen bonds : bond 0.03640 ( 943) hydrogen bonds : angle 4.44753 ( 2466) SS BOND : bond 0.00253 ( 48) SS BOND : angle 0.98363 ( 96) covalent geometry : bond 0.00272 (24901) covalent geometry : angle 0.57131 (33895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 743 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7120 (mmmt) REVERT: A 211 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7734 (p) REVERT: B 395 HIS cc_start: 0.7481 (t-90) cc_final: 0.7095 (t-90) REVERT: B 462 TYR cc_start: 0.7970 (t80) cc_final: 0.7609 (t80) REVERT: B 484 ILE cc_start: 0.8186 (mm) cc_final: 0.7903 (mt) REVERT: B 532 TYR cc_start: 0.8201 (p90) cc_final: 0.7969 (p90) REVERT: B 586 LYS cc_start: 0.8223 (mmmm) cc_final: 0.8012 (mtpt) REVERT: B 679 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7867 (mtpp) REVERT: B 711 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 818 HIS cc_start: 0.6183 (t-90) cc_final: 0.5943 (t-90) REVERT: C 930 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8213 (ttp-110) REVERT: C 954 ASN cc_start: 0.7576 (p0) cc_final: 0.7240 (p0) REVERT: C 983 SER cc_start: 0.8791 (t) cc_final: 0.8235 (p) REVERT: C 1014 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8192 (mmt180) REVERT: C 1018 ILE cc_start: 0.8009 (pt) cc_final: 0.7755 (pt) REVERT: C 1021 ARG cc_start: 0.8885 (tpp-160) cc_final: 0.8531 (tpt170) REVERT: C 1024 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 1059 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 1095 MET cc_start: 0.7062 (ppp) cc_final: 0.6512 (ppp) REVERT: C 1117 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 1214 PHE cc_start: 0.8173 (t80) cc_final: 0.7896 (t80) REVERT: C 1227 LYS cc_start: 0.8251 (mttt) cc_final: 0.7791 (mttt) REVERT: E 113 MET cc_start: 0.5251 (mmp) cc_final: 0.4858 (mmp) REVERT: F 394 ASN cc_start: 0.7755 (t0) cc_final: 0.7246 (t0) REVERT: F 459 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8449 (ttm170) REVERT: F 511 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8242 (mmm160) REVERT: F 516 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: F 586 LYS cc_start: 0.7296 (pttt) cc_final: 0.7005 (pptt) REVERT: F 593 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8277 (tt) REVERT: F 638 TYR cc_start: 0.8510 (p90) cc_final: 0.8163 (p90) REVERT: F 659 GLU cc_start: 0.7197 (tt0) cc_final: 0.6978 (tt0) REVERT: F 686 GLN cc_start: 0.7813 (mt0) cc_final: 0.7603 (mt0) REVERT: G 914 GLU cc_start: 0.7608 (mp0) cc_final: 0.6966 (mp0) REVERT: G 945 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7633 (mtpp) REVERT: G 1019 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7324 (mm-40) REVERT: G 1038 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8361 (ttt-90) REVERT: G 1059 LEU cc_start: 0.8458 (tp) cc_final: 0.8208 (mt) REVERT: G 1061 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6787 (tm-30) REVERT: G 1144 SER cc_start: 0.8558 (t) cc_final: 0.8167 (m) REVERT: G 1150 ASN cc_start: 0.8303 (p0) cc_final: 0.7867 (p0) REVERT: G 1160 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6317 (tttm) REVERT: I 142 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7513 (tmtt) REVERT: I 160 PHE cc_start: 0.6919 (m-10) cc_final: 0.6717 (m-10) REVERT: I 193 TYR cc_start: 0.8156 (m-80) cc_final: 0.7705 (m-80) REVERT: I 265 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7110 (tm-30) REVERT: J 467 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7160 (mm-40) REVERT: J 496 THR cc_start: 0.7812 (p) cc_final: 0.7508 (p) REVERT: J 498 GLU cc_start: 0.6897 (pm20) cc_final: 0.6529 (pm20) REVERT: J 529 LYS cc_start: 0.8214 (tppt) cc_final: 0.7452 (tppt) REVERT: J 544 THR cc_start: 0.7695 (p) cc_final: 0.7446 (t) REVERT: J 547 ASP cc_start: 0.7768 (p0) cc_final: 0.7475 (p0) REVERT: J 567 LYS cc_start: 0.7465 (mmtp) cc_final: 0.7247 (mmtt) REVERT: J 586 LYS cc_start: 0.7030 (mptt) cc_final: 0.6473 (mmtp) REVERT: J 713 SER cc_start: 0.8254 (t) cc_final: 0.8035 (t) REVERT: K 876 LYS cc_start: 0.7725 (tttp) cc_final: 0.7379 (tttm) REVERT: K 970 THR cc_start: 0.8496 (t) cc_final: 0.8144 (p) REVERT: K 1019 GLN cc_start: 0.7961 (mt0) cc_final: 0.7695 (mt0) REVERT: K 1029 TYR cc_start: 0.8339 (t80) cc_final: 0.8129 (t80) REVERT: K 1115 THR cc_start: 0.8600 (t) cc_final: 0.8297 (p) REVERT: K 1130 VAL cc_start: 0.8033 (p) cc_final: 0.7742 (t) REVERT: K 1223 SER cc_start: 0.7996 (t) cc_final: 0.7790 (t) outliers start: 121 outliers final: 76 residues processed: 804 average time/residue: 0.4189 time to fit residues: 518.3430 Evaluate side-chains 813 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 728 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain 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 496 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 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 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1160 LYS 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 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 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 1059 LEU 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: 0.7980 chunk 255 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 195 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108257 restraints weight = 40245.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111455 restraints weight = 16901.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113480 restraints weight = 9026.501| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24964 Z= 0.169 Angle : 0.624 17.560 34036 Z= 0.312 Chirality : 0.045 0.552 3804 Planarity : 0.005 0.060 4362 Dihedral : 4.650 57.791 3695 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.24 % Allowed : 28.24 % Favored : 66.52 % 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: -0.19 (0.15), residues: 3106 helix: 2.80 (0.27), residues: 324 sheet: 0.46 (0.17), residues: 969 loop : -1.05 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 642 HIS 0.013 0.001 HIS B 685 PHE 0.014 0.002 PHE B 383 TYR 0.026 0.002 TYR B 397 ARG 0.005 0.000 ARG E 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 9) link_NAG-ASN : angle 4.95584 ( 27) link_BETA1-4 : bond 0.00396 ( 6) link_BETA1-4 : angle 1.21719 ( 18) hydrogen bonds : bond 0.04053 ( 943) hydrogen bonds : angle 4.51360 ( 2466) SS BOND : bond 0.00415 ( 48) SS BOND : angle 1.42632 ( 96) covalent geometry : bond 0.00388 (24901) covalent geometry : angle 0.60388 (33895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 756 time to evaluate : 2.941 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: 0.7592 (mmmt) cc_final: 0.7139 (mmmt) REVERT: A 160 PHE cc_start: 0.7893 (m-80) cc_final: 0.7671 (m-80) REVERT: B 343 LYS cc_start: 0.8684 (mptt) cc_final: 0.8408 (mptt) REVERT: B 395 HIS cc_start: 0.7541 (t-90) cc_final: 0.7048 (t-90) REVERT: B 396 ASP cc_start: 0.7751 (t0) cc_final: 0.7161 (t0) REVERT: B 462 TYR cc_start: 0.8007 (t80) cc_final: 0.7565 (t80) REVERT: B 484 ILE cc_start: 0.8202 (mm) cc_final: 0.7926 (mt) REVERT: B 532 TYR cc_start: 0.8282 (p90) cc_final: 0.8035 (p90) REVERT: B 711 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8057 (mp) REVERT: C 818 HIS cc_start: 0.6452 (t-90) cc_final: 0.6197 (t-90) REVERT: C 819 SER cc_start: 0.8274 (m) cc_final: 0.7946 (p) REVERT: C 857 LEU cc_start: 0.8468 (mt) cc_final: 0.8250 (mt) REVERT: C 930 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8208 (ttp-110) REVERT: C 954 ASN cc_start: 0.7599 (p0) cc_final: 0.7253 (p0) REVERT: C 983 SER cc_start: 0.8825 (t) cc_final: 0.8296 (p) REVERT: C 1014 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8206 (mmt180) REVERT: C 1021 ARG cc_start: 0.8946 (tpp-160) cc_final: 0.8601 (tpt170) REVERT: C 1024 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6885 (mm-30) REVERT: C 1059 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 1095 MET cc_start: 0.7039 (ppp) cc_final: 0.6442 (ppp) REVERT: C 1117 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 1227 LYS cc_start: 0.8263 (mttt) cc_final: 0.7807 (mttt) REVERT: E 113 MET cc_start: 0.5170 (mmp) cc_final: 0.4796 (mmp) REVERT: F 394 ASN cc_start: 0.7753 (t0) cc_final: 0.7254 (t0) REVERT: F 459 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8471 (ttm170) REVERT: F 511 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8210 (mmm160) REVERT: F 570 PHE cc_start: 0.8249 (t80) cc_final: 0.8033 (t80) REVERT: F 586 LYS cc_start: 0.7316 (pttt) cc_final: 0.7046 (pptt) REVERT: F 638 TYR cc_start: 0.8518 (p90) cc_final: 0.8151 (p90) REVERT: F 659 GLU cc_start: 0.7208 (tt0) cc_final: 0.6999 (tt0) REVERT: F 686 GLN cc_start: 0.7872 (mt0) cc_final: 0.7648 (mt0) REVERT: F 694 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7747 (mp) REVERT: G 914 GLU cc_start: 0.7625 (mp0) cc_final: 0.6924 (mp0) REVERT: G 945 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7681 (mtpp) REVERT: G 977 ILE cc_start: 0.8815 (tp) cc_final: 0.8523 (mm) REVERT: G 989 ASP cc_start: 0.7180 (m-30) cc_final: 0.6894 (m-30) REVERT: G 1019 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7245 (mm-40) REVERT: G 1059 LEU cc_start: 0.8486 (tp) cc_final: 0.8249 (mt) REVERT: G 1061 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6836 (tm-30) REVERT: G 1144 SER cc_start: 0.8582 (t) cc_final: 0.8245 (m) REVERT: G 1150 ASN cc_start: 0.8293 (p0) cc_final: 0.7824 (p0) REVERT: I 142 LYS cc_start: 0.8021 (tmmt) cc_final: 0.7731 (tmtt) REVERT: I 177 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3678 (mpp) REVERT: I 193 TYR cc_start: 0.8300 (m-80) cc_final: 0.7930 (m-80) REVERT: I 265 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7247 (tm-30) REVERT: J 373 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7398 (mm-30) REVERT: J 387 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7323 (mt) REVERT: J 467 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7188 (mm-40) REVERT: J 496 THR cc_start: 0.7882 (p) cc_final: 0.7600 (p) REVERT: J 498 GLU cc_start: 0.6928 (pm20) cc_final: 0.6583 (pm20) REVERT: J 522 LYS cc_start: 0.8196 (tttp) cc_final: 0.7586 (tttp) REVERT: J 529 LYS cc_start: 0.8281 (tppt) cc_final: 0.7326 (tppt) REVERT: J 533 ASN cc_start: 0.8315 (t0) cc_final: 0.7381 (t0) REVERT: J 544 THR cc_start: 0.7731 (p) cc_final: 0.6997 (t) REVERT: J 586 LYS cc_start: 0.7028 (mptt) cc_final: 0.6471 (mmtp) REVERT: K 876 LYS cc_start: 0.7848 (tttp) cc_final: 0.7480 (tttm) REVERT: K 960 ASP cc_start: 0.7598 (p0) cc_final: 0.7395 (p0) REVERT: K 970 THR cc_start: 0.8470 (t) cc_final: 0.8133 (p) REVERT: K 1001 ASN cc_start: 0.7941 (m-40) cc_final: 0.7450 (m-40) REVERT: K 1019 GLN cc_start: 0.8127 (mt0) cc_final: 0.7894 (mt0) REVERT: K 1079 ASN cc_start: 0.8502 (t0) cc_final: 0.8280 (t0) REVERT: K 1084 MET cc_start: 0.7755 (mtm) cc_final: 0.7548 (mtp) REVERT: K 1115 THR cc_start: 0.8623 (t) cc_final: 0.8298 (p) REVERT: K 1130 VAL cc_start: 0.8082 (p) cc_final: 0.7781 (t) REVERT: K 1156 GLU cc_start: 0.7299 (pm20) cc_final: 0.7065 (pm20) outliers start: 139 outliers final: 93 residues processed: 814 average time/residue: 0.3729 time to fit residues: 464.5709 Evaluate side-chains 841 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 740 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 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 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 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 467 GLN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 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 1137 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 MET 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 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 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1213 VAL Chi-restraints excluded: chain K residue 1227 LYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN G 847 GLN G 954 ASN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 545 ASN J 559 HIS J 623 HIS J 686 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104889 restraints weight = 40378.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108139 restraints weight = 17066.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110237 restraints weight = 9232.515| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24964 Z= 0.237 Angle : 0.676 17.880 34036 Z= 0.340 Chirality : 0.047 0.510 3804 Planarity : 0.005 0.061 4362 Dihedral : 4.946 59.718 3695 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.47 % Allowed : 28.54 % Favored : 65.99 % 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: -0.36 (0.15), residues: 3106 helix: 2.73 (0.27), residues: 324 sheet: 0.37 (0.17), residues: 969 loop : -1.20 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 102 HIS 0.036 0.001 HIS F 559 PHE 0.022 0.002 PHE C1235 TYR 0.024 0.002 TYR B 397 ARG 0.005 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01040 ( 9) link_NAG-ASN : angle 5.46147 ( 27) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 1.31577 ( 18) hydrogen bonds : bond 0.04688 ( 943) hydrogen bonds : angle 4.68840 ( 2466) SS BOND : bond 0.00382 ( 48) SS BOND : angle 1.44767 ( 96) covalent geometry : bond 0.00537 (24901) covalent geometry : angle 0.65412 (33895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 781 time to evaluate : 2.829 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: A 123 VAL cc_start: 0.7216 (t) cc_final: 0.6987 (t) REVERT: A 139 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7114 (mmmt) REVERT: B 395 HIS cc_start: 0.7471 (t70) cc_final: 0.6851 (t70) REVERT: B 396 ASP cc_start: 0.7842 (t0) cc_final: 0.7236 (t0) REVERT: B 462 TYR cc_start: 0.8083 (t80) cc_final: 0.7633 (t80) REVERT: B 467 GLN cc_start: 0.7624 (mm110) cc_final: 0.7367 (mm110) REVERT: B 484 ILE cc_start: 0.8201 (mm) cc_final: 0.7915 (mt) REVERT: B 711 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 818 HIS cc_start: 0.6797 (t-90) cc_final: 0.6578 (t70) REVERT: C 819 SER cc_start: 0.8211 (m) cc_final: 0.7984 (p) REVERT: C 857 LEU cc_start: 0.8471 (mt) cc_final: 0.8262 (mt) REVERT: C 930 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: C 954 ASN cc_start: 0.7658 (p0) cc_final: 0.7330 (p0) REVERT: C 983 SER cc_start: 0.8834 (t) cc_final: 0.8264 (p) REVERT: C 998 GLU cc_start: 0.6449 (mp0) cc_final: 0.6066 (mp0) REVERT: C 1014 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8187 (mmt180) REVERT: C 1018 ILE cc_start: 0.8047 (pt) cc_final: 0.7838 (pt) REVERT: C 1021 ARG cc_start: 0.9012 (tpp-160) cc_final: 0.8431 (tpt170) REVERT: C 1024 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 1059 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 1095 MET cc_start: 0.7050 (ppp) cc_final: 0.6341 (ppp) REVERT: C 1117 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8273 (p) REVERT: C 1227 LYS cc_start: 0.8293 (mttt) cc_final: 0.7901 (mttt) REVERT: E 113 MET cc_start: 0.5410 (mmp) cc_final: 0.5046 (mmp) REVERT: F 370 VAL cc_start: 0.8642 (t) cc_final: 0.8413 (m) REVERT: F 394 ASN cc_start: 0.7701 (t0) cc_final: 0.7242 (t0) REVERT: F 399 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8217 (mtpp) REVERT: F 430 MET cc_start: 0.7463 (ttp) cc_final: 0.7204 (ttp) REVERT: F 459 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8433 (ttm170) REVERT: F 484 ILE cc_start: 0.8371 (mm) cc_final: 0.8123 (mm) REVERT: F 511 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8250 (mmm160) REVERT: F 548 MET cc_start: 0.7263 (mpp) cc_final: 0.6837 (mpp) REVERT: F 570 PHE cc_start: 0.8334 (t80) cc_final: 0.8110 (t80) REVERT: F 586 LYS cc_start: 0.7430 (pttt) cc_final: 0.7129 (pptt) REVERT: F 638 TYR cc_start: 0.8562 (p90) cc_final: 0.8215 (p90) REVERT: F 685 HIS cc_start: 0.7790 (p90) cc_final: 0.7572 (p90) REVERT: F 694 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7832 (mp) REVERT: G 844 LEU cc_start: 0.7300 (mm) cc_final: 0.7095 (mt) REVERT: G 914 GLU cc_start: 0.7620 (mp0) cc_final: 0.6925 (mp0) REVERT: G 945 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7718 (mtpp) REVERT: G 954 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7541 (t0) REVERT: G 1019 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7338 (mm-40) REVERT: G 1059 LEU cc_start: 0.8516 (tp) cc_final: 0.8293 (mt) REVERT: G 1061 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6916 (tm-30) REVERT: G 1144 SER cc_start: 0.8632 (t) cc_final: 0.8338 (m) REVERT: G 1213 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8448 (t) REVERT: I 124 LYS cc_start: 0.7852 (tppt) cc_final: 0.7607 (tppt) REVERT: I 126 GLU cc_start: 0.6341 (tp30) cc_final: 0.5804 (tp30) REVERT: I 142 LYS cc_start: 0.8256 (tmmt) cc_final: 0.8052 (tttt) REVERT: I 172 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6899 (tm-30) REVERT: I 177 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.3931 (mpp) REVERT: I 193 TYR cc_start: 0.8487 (m-80) cc_final: 0.8045 (m-80) REVERT: I 221 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7447 (mtt180) REVERT: I 252 ASN cc_start: 0.7722 (t0) cc_final: 0.7420 (t0) REVERT: J 373 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7432 (mm-30) REVERT: J 387 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7397 (mt) REVERT: J 396 ASP cc_start: 0.7178 (t0) cc_final: 0.6887 (t0) REVERT: J 402 TYR cc_start: 0.8268 (p90) cc_final: 0.7972 (p90) REVERT: J 467 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7220 (mm-40) REVERT: J 510 ASP cc_start: 0.8083 (t0) cc_final: 0.7778 (t70) REVERT: J 522 LYS cc_start: 0.8161 (tttp) cc_final: 0.7480 (tttp) REVERT: J 529 LYS cc_start: 0.8288 (tppt) cc_final: 0.7323 (tppt) REVERT: J 533 ASN cc_start: 0.8300 (t0) cc_final: 0.7362 (t0) REVERT: J 544 THR cc_start: 0.7827 (p) cc_final: 0.7200 (p) REVERT: J 586 LYS cc_start: 0.7153 (mptt) cc_final: 0.6427 (mmtp) REVERT: J 692 TYR cc_start: 0.8351 (t80) cc_final: 0.8087 (t80) REVERT: K 876 LYS cc_start: 0.7959 (tttp) cc_final: 0.7572 (tttm) REVERT: K 938 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8158 (mtmm) REVERT: K 970 THR cc_start: 0.8462 (t) cc_final: 0.8165 (p) REVERT: K 1014 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7272 (mmt90) REVERT: K 1019 GLN cc_start: 0.8281 (mt0) cc_final: 0.8000 (mt0) REVERT: K 1084 MET cc_start: 0.7786 (mtm) cc_final: 0.7574 (mtp) REVERT: K 1115 THR cc_start: 0.8625 (t) cc_final: 0.8310 (p) REVERT: K 1130 VAL cc_start: 0.8070 (p) cc_final: 0.7785 (t) outliers start: 145 outliers final: 102 residues processed: 848 average time/residue: 0.3836 time to fit residues: 496.8555 Evaluate side-chains 867 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 753 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET 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 383 PHE 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 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 711 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 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 111 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 561 SER 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 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 207 optimal weight: 0.0970 chunk 304 optimal weight: 50.0000 chunk 228 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 177 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 337 GLN B 340 ASN B 461 GLN C1209 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 GLN G 954 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108020 restraints weight = 40120.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111212 restraints weight = 16625.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113248 restraints weight = 8848.609| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24964 Z= 0.119 Angle : 0.639 17.895 34036 Z= 0.319 Chirality : 0.045 0.533 3804 Planarity : 0.004 0.047 4362 Dihedral : 4.712 55.937 3695 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 4.41 % Allowed : 30.02 % Favored : 65.57 % 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: 2.87 (0.27), residues: 324 sheet: 0.44 (0.16), residues: 978 loop : -1.07 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 102 HIS 0.011 0.001 HIS A 196 PHE 0.026 0.001 PHE C1235 TYR 0.031 0.001 TYR B 397 ARG 0.004 0.000 ARG G 836 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 9) link_NAG-ASN : angle 5.00368 ( 27) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 1.18124 ( 18) hydrogen bonds : bond 0.03811 ( 943) hydrogen bonds : angle 4.57448 ( 2466) SS BOND : bond 0.00318 ( 48) SS BOND : angle 1.21088 ( 96) covalent geometry : bond 0.00272 (24901) covalent geometry : angle 0.62013 (33895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 768 time to evaluate : 2.908 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: 0.7667 (mmmt) cc_final: 0.7114 (mmmt) REVERT: B 395 HIS cc_start: 0.7500 (t70) cc_final: 0.7047 (t70) REVERT: B 396 ASP cc_start: 0.7766 (t0) cc_final: 0.7215 (t0) REVERT: B 462 TYR cc_start: 0.8035 (t80) cc_final: 0.7576 (t80) REVERT: B 467 GLN cc_start: 0.7586 (mm110) cc_final: 0.7336 (mm110) REVERT: B 484 ILE cc_start: 0.8171 (mm) cc_final: 0.7899 (mt) REVERT: B 517 GLN cc_start: 0.8034 (mm110) cc_final: 0.7754 (mm-40) REVERT: C 819 SER cc_start: 0.8188 (m) cc_final: 0.7882 (p) REVERT: C 954 ASN cc_start: 0.7601 (p0) cc_final: 0.7243 (p0) REVERT: C 983 SER cc_start: 0.8801 (t) cc_final: 0.8264 (p) REVERT: C 998 GLU cc_start: 0.6337 (mp0) cc_final: 0.6002 (mp0) REVERT: C 1014 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8107 (mmt180) REVERT: C 1018 ILE cc_start: 0.8080 (pt) cc_final: 0.7869 (pt) REVERT: C 1021 ARG cc_start: 0.8916 (tpp-160) cc_final: 0.8412 (tpt170) REVERT: C 1024 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6911 (mm-30) REVERT: C 1059 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7956 (mp) REVERT: C 1095 MET cc_start: 0.7034 (ppp) cc_final: 0.6360 (ppp) REVERT: C 1117 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 1160 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7199 (mmtp) REVERT: C 1227 LYS cc_start: 0.8256 (mttt) cc_final: 0.7830 (mttt) REVERT: E 113 MET cc_start: 0.5260 (mmp) cc_final: 0.4920 (mmp) REVERT: F 394 ASN cc_start: 0.7740 (t0) cc_final: 0.7255 (t0) REVERT: F 399 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8186 (mtpp) REVERT: F 430 MET cc_start: 0.7339 (ttp) cc_final: 0.6957 (ttp) REVERT: F 459 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (ttm170) REVERT: F 548 MET cc_start: 0.7021 (mpp) cc_final: 0.6592 (mpp) REVERT: F 566 LYS cc_start: 0.7013 (mmmt) cc_final: 0.6799 (mmmt) REVERT: F 570 PHE cc_start: 0.8246 (t80) cc_final: 0.8032 (t80) REVERT: F 586 LYS cc_start: 0.7388 (pttt) cc_final: 0.7075 (pptt) REVERT: F 594 ASP cc_start: 0.7611 (t0) cc_final: 0.7335 (t0) REVERT: F 638 TYR cc_start: 0.8553 (p90) cc_final: 0.8220 (p90) REVERT: G 910 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: G 912 ASP cc_start: 0.7796 (m-30) cc_final: 0.7336 (t0) REVERT: G 914 GLU cc_start: 0.7617 (mp0) cc_final: 0.6977 (mp0) REVERT: G 930 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7916 (ttp-110) REVERT: G 945 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7667 (mtpp) REVERT: G 954 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7451 (t0) REVERT: G 1019 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7326 (mm-40) REVERT: G 1059 LEU cc_start: 0.8460 (tp) cc_final: 0.8238 (mt) REVERT: G 1061 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6924 (tm-30) REVERT: G 1082 ARG cc_start: 0.8326 (ptt90) cc_final: 0.8031 (ptt-90) REVERT: G 1144 SER cc_start: 0.8473 (t) cc_final: 0.8152 (m) REVERT: I 124 LYS cc_start: 0.7782 (tppt) cc_final: 0.7491 (tppt) REVERT: I 126 GLU cc_start: 0.6327 (tp30) cc_final: 0.5767 (tp30) REVERT: I 142 LYS cc_start: 0.8184 (tmmt) cc_final: 0.7963 (tttt) REVERT: I 187 GLU cc_start: 0.7292 (pm20) cc_final: 0.7023 (pm20) REVERT: I 193 TYR cc_start: 0.8490 (m-80) cc_final: 0.8052 (m-80) REVERT: I 221 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: I 252 ASN cc_start: 0.7621 (t0) cc_final: 0.7353 (t0) REVERT: J 363 SER cc_start: 0.8385 (t) cc_final: 0.8029 (p) REVERT: J 387 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7322 (mt) REVERT: J 402 TYR cc_start: 0.8087 (p90) cc_final: 0.7810 (p90) REVERT: J 467 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7253 (mm-40) REVERT: J 510 ASP cc_start: 0.8009 (t0) cc_final: 0.7662 (t70) REVERT: J 522 LYS cc_start: 0.8196 (tttp) cc_final: 0.7522 (tttp) REVERT: J 529 LYS cc_start: 0.8249 (tppt) cc_final: 0.7404 (tppt) REVERT: J 533 ASN cc_start: 0.8331 (t0) cc_final: 0.7521 (t0) REVERT: J 544 THR cc_start: 0.7802 (p) cc_final: 0.7231 (t) REVERT: J 586 LYS cc_start: 0.6954 (mptt) cc_final: 0.6400 (mmtp) REVERT: J 692 TYR cc_start: 0.8268 (t80) cc_final: 0.7983 (t80) REVERT: J 735 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7063 (p) REVERT: K 876 LYS cc_start: 0.7868 (tttp) cc_final: 0.7494 (tttm) REVERT: K 903 MET cc_start: 0.7685 (mtm) cc_final: 0.7438 (mtp) REVERT: K 917 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8371 (tp40) REVERT: K 938 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8131 (mtmm) REVERT: K 970 THR cc_start: 0.8459 (t) cc_final: 0.8138 (p) REVERT: K 986 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 1014 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7759 (mmt90) REVERT: K 1019 GLN cc_start: 0.8109 (mt0) cc_final: 0.7814 (mt0) REVERT: K 1022 THR cc_start: 0.8529 (t) cc_final: 0.8146 (p) REVERT: K 1084 MET cc_start: 0.7741 (mtm) cc_final: 0.7534 (mtp) REVERT: K 1115 THR cc_start: 0.8607 (t) cc_final: 0.8300 (p) REVERT: K 1130 VAL cc_start: 0.8030 (p) cc_final: 0.7765 (t) outliers start: 117 outliers final: 84 residues processed: 819 average time/residue: 0.4910 time to fit residues: 625.3130 Evaluate side-chains 852 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 756 time to evaluate : 3.243 ------------------------------------------------------------------------------- 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 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 833 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 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 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 459 ARG Chi-restraints excluded: chain F residue 469 VAL 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 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 954 ASN Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain I residue 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 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 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 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 735 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 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 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 1240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 160 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 303 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 300 optimal weight: 0.0980 chunk 257 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 C1019 GLN F 517 GLN F 559 HIS G 847 GLN G 954 ASN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107477 restraints weight = 40200.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110623 restraints weight = 16876.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112625 restraints weight = 9040.959| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24964 Z= 0.129 Angle : 0.641 17.923 34036 Z= 0.319 Chirality : 0.045 0.529 3804 Planarity : 0.004 0.047 4362 Dihedral : 4.647 54.804 3695 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.64 % Allowed : 30.02 % Favored : 65.35 % 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: 2.87 (0.27), residues: 324 sheet: 0.48 (0.16), residues: 978 loop : -1.10 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 251 HIS 0.009 0.001 HIS A 196 PHE 0.013 0.001 PHE C 910 TYR 0.029 0.001 TYR B 397 ARG 0.005 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 9) link_NAG-ASN : angle 5.08382 ( 27) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 1.19455 ( 18) hydrogen bonds : bond 0.03796 ( 943) hydrogen bonds : angle 4.52198 ( 2466) SS BOND : bond 0.00380 ( 48) SS BOND : angle 1.20032 ( 96) covalent geometry : bond 0.00299 (24901) covalent geometry : angle 0.62181 (33895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 767 time to evaluate : 3.626 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: 0.7632 (mmmt) cc_final: 0.7092 (mmmt) REVERT: B 343 LYS cc_start: 0.8785 (mptt) cc_final: 0.8463 (mptt) REVERT: B 395 HIS cc_start: 0.7454 (t70) cc_final: 0.7000 (t70) REVERT: B 396 ASP cc_start: 0.7811 (t0) cc_final: 0.7225 (t0) REVERT: B 462 TYR cc_start: 0.8038 (t80) cc_final: 0.7595 (t80) REVERT: B 467 GLN cc_start: 0.7596 (mm110) cc_final: 0.7338 (mm110) REVERT: B 517 GLN cc_start: 0.8060 (mm110) cc_final: 0.7752 (mm-40) REVERT: B 532 TYR cc_start: 0.8341 (p90) cc_final: 0.8040 (p90) REVERT: B 714 ILE cc_start: 0.8508 (tp) cc_final: 0.8289 (tt) REVERT: C 819 SER cc_start: 0.8199 (m) cc_final: 0.7895 (p) REVERT: C 950 VAL cc_start: 0.7970 (t) cc_final: 0.7372 (m) REVERT: C 954 ASN cc_start: 0.7585 (p0) cc_final: 0.7224 (p0) REVERT: C 983 SER cc_start: 0.8787 (t) cc_final: 0.8268 (p) REVERT: C 998 GLU cc_start: 0.6335 (mp0) cc_final: 0.5978 (mp0) REVERT: C 1014 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8238 (mmt180) REVERT: C 1018 ILE cc_start: 0.8093 (pt) cc_final: 0.7861 (pt) REVERT: C 1021 ARG cc_start: 0.8910 (tpp-160) cc_final: 0.8414 (tpt170) REVERT: C 1024 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6950 (mm-30) REVERT: C 1059 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 1095 MET cc_start: 0.7053 (ppp) cc_final: 0.6364 (ppp) REVERT: C 1117 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 1160 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7187 (mmtp) REVERT: C 1227 LYS cc_start: 0.8276 (mttt) cc_final: 0.7854 (mttt) REVERT: E 113 MET cc_start: 0.5231 (mmp) cc_final: 0.4905 (mmp) REVERT: E 178 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.4439 (pmt170) REVERT: F 370 VAL cc_start: 0.8646 (t) cc_final: 0.8416 (m) REVERT: F 394 ASN cc_start: 0.7770 (t0) cc_final: 0.7357 (t0) REVERT: F 399 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8181 (mtpp) REVERT: F 430 MET cc_start: 0.7343 (ttp) cc_final: 0.6948 (ttp) REVERT: F 459 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8485 (ttm170) REVERT: F 548 MET cc_start: 0.7159 (mpp) cc_final: 0.6717 (mpp) REVERT: F 570 PHE cc_start: 0.8219 (t80) cc_final: 0.8000 (t80) REVERT: F 586 LYS cc_start: 0.7408 (pttt) cc_final: 0.7080 (pptt) REVERT: F 594 ASP cc_start: 0.7606 (t0) cc_final: 0.7352 (t0) REVERT: F 638 TYR cc_start: 0.8533 (p90) cc_final: 0.8214 (p90) REVERT: G 910 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: G 914 GLU cc_start: 0.7612 (mp0) cc_final: 0.6900 (mp0) REVERT: G 930 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7888 (ttp-110) REVERT: G 945 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7637 (mtpp) REVERT: G 954 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7430 (t0) REVERT: G 1019 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7326 (mm-40) REVERT: G 1059 LEU cc_start: 0.8468 (tp) cc_final: 0.8252 (mt) REVERT: G 1061 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6941 (tm-30) REVERT: G 1082 ARG cc_start: 0.8365 (ptt90) cc_final: 0.8078 (ptt-90) REVERT: G 1144 SER cc_start: 0.8428 (t) cc_final: 0.8114 (m) REVERT: I 126 GLU cc_start: 0.6290 (tp30) cc_final: 0.5763 (tp30) REVERT: I 132 TYR cc_start: 0.8435 (m-80) cc_final: 0.8228 (m-10) REVERT: I 142 LYS cc_start: 0.8161 (tmmt) cc_final: 0.7852 (ttpt) REVERT: I 187 GLU cc_start: 0.7319 (pm20) cc_final: 0.6948 (pm20) REVERT: I 193 TYR cc_start: 0.8506 (m-80) cc_final: 0.8038 (m-80) REVERT: I 221 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7352 (mtt180) REVERT: I 252 ASN cc_start: 0.7711 (t0) cc_final: 0.7428 (t0) REVERT: J 387 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7336 (mt) REVERT: J 402 TYR cc_start: 0.8149 (p90) cc_final: 0.7884 (p90) REVERT: J 467 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7232 (mm-40) REVERT: J 486 CYS cc_start: 0.5420 (p) cc_final: 0.5068 (p) REVERT: J 510 ASP cc_start: 0.7992 (t0) cc_final: 0.7700 (t70) REVERT: J 522 LYS cc_start: 0.8218 (tttp) cc_final: 0.7537 (tttp) REVERT: J 529 LYS cc_start: 0.8295 (tppt) cc_final: 0.7471 (tppt) REVERT: J 533 ASN cc_start: 0.8379 (t0) cc_final: 0.7597 (t0) REVERT: J 544 THR cc_start: 0.7781 (p) cc_final: 0.7291 (p) REVERT: J 545 ASN cc_start: 0.8710 (t0) cc_final: 0.8502 (t0) REVERT: J 577 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7789 (ptp-170) REVERT: J 586 LYS cc_start: 0.6969 (mptt) cc_final: 0.6351 (mttm) REVERT: J 692 TYR cc_start: 0.8264 (t80) cc_final: 0.7957 (t80) REVERT: K 876 LYS cc_start: 0.7886 (tttp) cc_final: 0.7516 (tttm) REVERT: K 903 MET cc_start: 0.7687 (mtm) cc_final: 0.7482 (mtp) REVERT: K 970 THR cc_start: 0.8456 (t) cc_final: 0.8118 (p) REVERT: K 986 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8385 (p) REVERT: K 1014 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7723 (mmt90) REVERT: K 1019 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: K 1115 THR cc_start: 0.8619 (t) cc_final: 0.8313 (p) REVERT: K 1130 VAL cc_start: 0.8068 (p) cc_final: 0.7781 (t) REVERT: K 1229 SER cc_start: 0.8341 (t) cc_final: 0.7772 (p) outliers start: 123 outliers final: 89 residues processed: 821 average time/residue: 0.4531 time to fit residues: 571.4311 Evaluate side-chains 858 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 757 time to evaluate : 2.885 ------------------------------------------------------------------------------- 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 496 THR Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 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 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 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 709 LEU Chi-restraints excluded: chain G residue 817 GLU 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 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 954 ASN 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 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 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1019 GLN Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 233 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 545 ASN B 557 GLN ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS G 847 GLN G 954 ASN G1002 GLN G1050 GLN J 559 HIS J 686 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107650 restraints weight = 40175.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110844 restraints weight = 16755.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112861 restraints weight = 8925.172| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24964 Z= 0.124 Angle : 0.649 17.808 34036 Z= 0.321 Chirality : 0.045 0.528 3804 Planarity : 0.004 0.047 4362 Dihedral : 4.596 54.093 3695 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.34 % Allowed : 30.54 % Favored : 65.12 % 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: -0.15 (0.15), residues: 3106 helix: 2.86 (0.28), residues: 324 sheet: 0.53 (0.17), residues: 993 loop : -1.08 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 251 HIS 0.010 0.001 HIS F 559 PHE 0.013 0.001 PHE C 910 TYR 0.028 0.001 TYR B 397 ARG 0.006 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 9) link_NAG-ASN : angle 4.98753 ( 27) link_BETA1-4 : bond 0.00439 ( 6) link_BETA1-4 : angle 1.20565 ( 18) hydrogen bonds : bond 0.03651 ( 943) hydrogen bonds : angle 4.48844 ( 2466) SS BOND : bond 0.00379 ( 48) SS BOND : angle 1.52169 ( 96) covalent geometry : bond 0.00289 (24901) covalent geometry : angle 0.62930 (33895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 763 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7266 (mmmt) REVERT: B 343 LYS cc_start: 0.8773 (mptt) cc_final: 0.8485 (mptt) REVERT: B 395 HIS cc_start: 0.7472 (t70) cc_final: 0.6982 (t70) REVERT: B 396 ASP cc_start: 0.7819 (t0) cc_final: 0.7207 (t0) REVERT: B 462 TYR cc_start: 0.8044 (t80) cc_final: 0.7572 (t80) REVERT: B 467 GLN cc_start: 0.7592 (mm110) cc_final: 0.7336 (mm110) REVERT: B 511 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7275 (ttm-80) REVERT: B 517 GLN cc_start: 0.8106 (mm110) cc_final: 0.7834 (mm-40) REVERT: B 714 ILE cc_start: 0.8501 (tp) cc_final: 0.8286 (tt) REVERT: C 950 VAL cc_start: 0.7910 (t) cc_final: 0.7243 (m) REVERT: C 954 ASN cc_start: 0.7582 (p0) cc_final: 0.7222 (p0) REVERT: C 983 SER cc_start: 0.8788 (t) cc_final: 0.8270 (p) REVERT: C 998 GLU cc_start: 0.6367 (mp0) cc_final: 0.6078 (mp0) REVERT: C 1018 ILE cc_start: 0.8082 (pt) cc_final: 0.7850 (pt) REVERT: C 1021 ARG cc_start: 0.8900 (tpp-160) cc_final: 0.8443 (tpt170) REVERT: C 1024 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6944 (mm-30) REVERT: C 1059 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8010 (mp) REVERT: C 1095 MET cc_start: 0.7043 (ppp) cc_final: 0.6381 (ppp) REVERT: C 1117 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (p) REVERT: C 1227 LYS cc_start: 0.8294 (mttt) cc_final: 0.7864 (mttt) REVERT: E 113 MET cc_start: 0.5239 (mmp) cc_final: 0.4920 (mmp) REVERT: E 178 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.4345 (pmt170) REVERT: F 370 VAL cc_start: 0.8652 (t) cc_final: 0.8429 (m) REVERT: F 394 ASN cc_start: 0.7790 (t0) cc_final: 0.7315 (t0) REVERT: F 399 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8196 (mtpp) REVERT: F 430 MET cc_start: 0.7354 (ttp) cc_final: 0.6821 (ttp) REVERT: F 459 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8368 (ptp-170) REVERT: F 548 MET cc_start: 0.7097 (mpp) cc_final: 0.6703 (mpp) REVERT: F 584 LYS cc_start: 0.5494 (OUTLIER) cc_final: 0.5112 (ttmm) REVERT: F 586 LYS cc_start: 0.7424 (pttt) cc_final: 0.7099 (pptt) REVERT: F 594 ASP cc_start: 0.7648 (t0) cc_final: 0.7372 (t0) REVERT: F 638 TYR cc_start: 0.8516 (p90) cc_final: 0.8202 (p90) REVERT: G 910 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: G 914 GLU cc_start: 0.7604 (mp0) cc_final: 0.6907 (mp0) REVERT: G 930 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7878 (ttp-110) REVERT: G 945 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7625 (mtpp) REVERT: G 1019 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7315 (mm-40) REVERT: G 1023 VAL cc_start: 0.8757 (t) cc_final: 0.8497 (p) REVERT: G 1059 LEU cc_start: 0.8457 (tp) cc_final: 0.8253 (mt) REVERT: G 1061 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6946 (tm-30) REVERT: G 1082 ARG cc_start: 0.8359 (ptt90) cc_final: 0.8084 (ptt-90) REVERT: G 1095 MET cc_start: 0.7947 (ptp) cc_final: 0.7706 (ptp) REVERT: G 1144 SER cc_start: 0.8426 (t) cc_final: 0.8102 (m) REVERT: I 113 MET cc_start: 0.7335 (mmm) cc_final: 0.6957 (mmm) REVERT: I 126 GLU cc_start: 0.6195 (tp30) cc_final: 0.5646 (tp30) REVERT: I 142 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7857 (ttpt) REVERT: I 187 GLU cc_start: 0.7292 (pm20) cc_final: 0.6922 (pm20) REVERT: I 193 TYR cc_start: 0.8522 (m-80) cc_final: 0.8030 (m-80) REVERT: I 221 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7397 (mtt180) REVERT: I 252 ASN cc_start: 0.7790 (t0) cc_final: 0.7546 (t0) REVERT: J 387 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7313 (mt) REVERT: J 402 TYR cc_start: 0.8136 (p90) cc_final: 0.7882 (p90) REVERT: J 467 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7256 (mm-40) REVERT: J 486 CYS cc_start: 0.5437 (p) cc_final: 0.5017 (p) REVERT: J 510 ASP cc_start: 0.7976 (t0) cc_final: 0.7649 (t70) REVERT: J 522 LYS cc_start: 0.8218 (tttp) cc_final: 0.7534 (tttp) REVERT: J 529 LYS cc_start: 0.8306 (tppt) cc_final: 0.7508 (tppt) REVERT: J 533 ASN cc_start: 0.8352 (t0) cc_final: 0.7553 (t0) REVERT: J 544 THR cc_start: 0.7774 (p) cc_final: 0.7374 (p) REVERT: J 545 ASN cc_start: 0.8714 (t0) cc_final: 0.8493 (t0) REVERT: J 577 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7773 (ptp-170) REVERT: J 586 LYS cc_start: 0.6962 (mptt) cc_final: 0.6328 (mttm) REVERT: J 692 TYR cc_start: 0.8225 (t80) cc_final: 0.7909 (t80) REVERT: K 876 LYS cc_start: 0.7861 (tttp) cc_final: 0.7475 (tttm) REVERT: K 903 MET cc_start: 0.7690 (mtm) cc_final: 0.7480 (mtp) REVERT: K 970 THR cc_start: 0.8459 (t) cc_final: 0.8124 (p) REVERT: K 986 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 1014 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7713 (mmt90) REVERT: K 1019 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: K 1022 THR cc_start: 0.8558 (t) cc_final: 0.8156 (p) REVERT: K 1029 TYR cc_start: 0.8262 (t80) cc_final: 0.8036 (t80) REVERT: K 1115 THR cc_start: 0.8609 (t) cc_final: 0.8300 (p) REVERT: K 1130 VAL cc_start: 0.8040 (p) cc_final: 0.7759 (t) outliers start: 115 outliers final: 87 residues processed: 811 average time/residue: 0.4365 time to fit residues: 539.3386 Evaluate side-chains 856 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 757 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 833 HIS Chi-restraints excluded: chain C residue 834 ILE 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 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 178 ARG 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 584 LYS 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 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 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 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 I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1019 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 65 optimal weight: 0.0370 chunk 303 optimal weight: 40.0000 chunk 214 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 295 optimal weight: 0.3980 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS ** G 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 GLN J 559 HIS J 618 HIS J 686 GLN ** K1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106888 restraints weight = 40721.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110175 restraints weight = 17282.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112273 restraints weight = 9310.771| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24964 Z= 0.113 Angle : 0.650 17.603 34036 Z= 0.321 Chirality : 0.045 0.516 3804 Planarity : 0.004 0.048 4362 Dihedral : 4.509 53.381 3695 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.81 % Allowed : 31.37 % Favored : 64.82 % 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: -0.08 (0.15), residues: 3106 helix: 2.86 (0.27), residues: 324 sheet: 0.59 (0.17), residues: 987 loop : -1.02 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 251 HIS 0.011 0.001 HIS F 559 PHE 0.026 0.001 PHE C1235 TYR 0.027 0.001 TYR B 397 ARG 0.008 0.000 ARG E 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 9) link_NAG-ASN : angle 4.90725 ( 27) link_BETA1-4 : bond 0.00409 ( 6) link_BETA1-4 : angle 1.18088 ( 18) hydrogen bonds : bond 0.03412 ( 943) hydrogen bonds : angle 4.42934 ( 2466) SS BOND : bond 0.00396 ( 48) SS BOND : angle 1.66126 ( 96) covalent geometry : bond 0.00262 (24901) covalent geometry : angle 0.62934 (33895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 777 time to evaluate : 3.853 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: 0.7641 (mmmt) cc_final: 0.7306 (mmmt) REVERT: B 343 LYS cc_start: 0.8770 (mptt) cc_final: 0.8487 (mptt) REVERT: B 395 HIS cc_start: 0.7484 (t70) cc_final: 0.6977 (t70) REVERT: B 396 ASP cc_start: 0.7785 (t0) cc_final: 0.7143 (t0) REVERT: B 462 TYR cc_start: 0.8030 (t80) cc_final: 0.7555 (t80) REVERT: B 467 GLN cc_start: 0.7589 (mm110) cc_final: 0.7350 (mm110) REVERT: B 511 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7225 (ttm-80) REVERT: B 517 GLN cc_start: 0.8091 (mm110) cc_final: 0.7805 (mm-40) REVERT: B 714 ILE cc_start: 0.8467 (tp) cc_final: 0.8256 (tt) REVERT: C 950 VAL cc_start: 0.7798 (t) cc_final: 0.7136 (m) REVERT: C 954 ASN cc_start: 0.7539 (p0) cc_final: 0.7175 (p0) REVERT: C 983 SER cc_start: 0.8801 (t) cc_final: 0.8277 (p) REVERT: C 998 GLU cc_start: 0.6343 (mp0) cc_final: 0.6035 (mp0) REVERT: C 1018 ILE cc_start: 0.8059 (pt) cc_final: 0.7818 (pt) REVERT: C 1021 ARG cc_start: 0.8899 (tpp-160) cc_final: 0.8450 (tpt170) REVERT: C 1024 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6940 (mm-30) REVERT: C 1059 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 1095 MET cc_start: 0.7049 (ppp) cc_final: 0.6365 (ppp) REVERT: C 1160 LYS cc_start: 0.7733 (mmtp) cc_final: 0.7116 (mmtp) REVERT: C 1227 LYS cc_start: 0.8279 (mttt) cc_final: 0.7862 (mttt) REVERT: E 113 MET cc_start: 0.5319 (mmp) cc_final: 0.4991 (mmp) REVERT: E 178 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.5217 (ppt170) REVERT: F 370 VAL cc_start: 0.8645 (t) cc_final: 0.8415 (m) REVERT: F 394 ASN cc_start: 0.7796 (t0) cc_final: 0.7310 (t0) REVERT: F 430 MET cc_start: 0.7278 (ttp) cc_final: 0.6747 (ttp) REVERT: F 459 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8451 (ttm170) REVERT: F 548 MET cc_start: 0.7019 (mpp) cc_final: 0.6671 (mpp) REVERT: F 584 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.5063 (ttmm) REVERT: F 586 LYS cc_start: 0.7417 (pttt) cc_final: 0.7082 (pptt) REVERT: F 594 ASP cc_start: 0.7657 (t0) cc_final: 0.7390 (t0) REVERT: F 638 TYR cc_start: 0.8518 (p90) cc_final: 0.8214 (p90) REVERT: G 910 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: G 914 GLU cc_start: 0.7593 (mp0) cc_final: 0.6877 (mp0) REVERT: G 930 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: G 945 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7612 (mtpp) REVERT: G 1019 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7328 (mm-40) REVERT: G 1059 LEU cc_start: 0.8436 (tp) cc_final: 0.8234 (mt) REVERT: G 1061 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6957 (tm-30) REVERT: G 1082 ARG cc_start: 0.8340 (ptt90) cc_final: 0.8102 (ptt-90) REVERT: G 1095 MET cc_start: 0.7936 (ptp) cc_final: 0.7717 (ptp) REVERT: G 1138 ASP cc_start: 0.7736 (m-30) cc_final: 0.7286 (p0) REVERT: G 1144 SER cc_start: 0.8300 (t) cc_final: 0.7975 (m) REVERT: G 1213 VAL cc_start: 0.8562 (p) cc_final: 0.8361 (t) REVERT: I 126 GLU cc_start: 0.6061 (tp30) cc_final: 0.5526 (tp30) REVERT: I 142 LYS cc_start: 0.8202 (tmmt) cc_final: 0.7864 (ttpt) REVERT: I 187 GLU cc_start: 0.7273 (pm20) cc_final: 0.6906 (pm20) REVERT: I 193 TYR cc_start: 0.8508 (m-80) cc_final: 0.7925 (m-80) REVERT: I 221 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7419 (mtt180) REVERT: I 240 GLU cc_start: 0.2281 (tp30) cc_final: 0.1945 (tp30) REVERT: I 252 ASN cc_start: 0.7808 (t0) cc_final: 0.7575 (t0) REVERT: J 387 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (mt) REVERT: J 402 TYR cc_start: 0.8074 (p90) cc_final: 0.7812 (p90) REVERT: J 467 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7239 (mm-40) REVERT: J 486 CYS cc_start: 0.5475 (p) cc_final: 0.5043 (p) REVERT: J 510 ASP cc_start: 0.7908 (t0) cc_final: 0.7646 (t70) REVERT: J 529 LYS cc_start: 0.8334 (tppt) cc_final: 0.7549 (tppt) REVERT: J 533 ASN cc_start: 0.8364 (t0) cc_final: 0.7564 (t0) REVERT: J 544 THR cc_start: 0.7784 (p) cc_final: 0.7410 (p) REVERT: J 545 ASN cc_start: 0.8695 (t0) cc_final: 0.8489 (t0) REVERT: J 577 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7759 (ptp-170) REVERT: J 692 TYR cc_start: 0.8158 (t80) cc_final: 0.7824 (t80) REVERT: K 822 MET cc_start: 0.7966 (ptt) cc_final: 0.7741 (ptp) REVERT: K 876 LYS cc_start: 0.7795 (tttp) cc_final: 0.7401 (tttm) REVERT: K 903 MET cc_start: 0.7588 (mtm) cc_final: 0.7379 (mtp) REVERT: K 970 THR cc_start: 0.8483 (t) cc_final: 0.8120 (p) REVERT: K 986 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8410 (p) REVERT: K 1019 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: K 1022 THR cc_start: 0.8552 (t) cc_final: 0.8152 (p) REVERT: K 1029 TYR cc_start: 0.8281 (t80) cc_final: 0.8017 (t80) REVERT: K 1115 THR cc_start: 0.8596 (t) cc_final: 0.8286 (p) REVERT: K 1130 VAL cc_start: 0.8036 (p) cc_final: 0.7751 (t) outliers start: 101 outliers final: 82 residues processed: 817 average time/residue: 0.4264 time to fit residues: 526.8171 Evaluate side-chains 857 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 765 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 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 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 584 LYS Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 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 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 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 I residue 242 SER Chi-restraints excluded: chain J residue 359 HIS Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 473 LYS Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 659 GLU Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 935 SER Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1019 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 181 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 100 optimal weight: 60.0000 chunk 272 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS J 686 GLN ** K1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103967 restraints weight = 40366.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107199 restraints weight = 17124.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109269 restraints weight = 9249.217| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24964 Z= 0.248 Angle : 0.739 18.661 34036 Z= 0.373 Chirality : 0.048 0.560 3804 Planarity : 0.005 0.049 4362 Dihedral : 4.998 54.775 3695 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.03 % Allowed : 30.88 % 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: 2.74 (0.27), residues: 324 sheet: 0.45 (0.17), residues: 996 loop : -1.17 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 251 HIS 0.020 0.002 HIS G1146 PHE 0.027 0.002 PHE C1235 TYR 0.028 0.002 TYR B 397 ARG 0.009 0.001 ARG E 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 9) link_NAG-ASN : angle 5.39035 ( 27) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 1.36707 ( 18) hydrogen bonds : bond 0.04807 ( 943) hydrogen bonds : angle 4.71552 ( 2466) SS BOND : bond 0.00547 ( 48) SS BOND : angle 1.94576 ( 96) covalent geometry : bond 0.00564 (24901) covalent geometry : angle 0.71675 (33895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13754.77 seconds wall clock time: 246 minutes 28.39 seconds (14788.39 seconds total)