Starting phenix.real_space_refine on Sun Oct 12 12:46:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0m_37982/10_2025/8x0m_37982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0m_37982/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x0m_37982/10_2025/8x0m_37982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0m_37982/10_2025/8x0m_37982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0m_37982/10_2025/8x0m_37982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0m_37982/10_2025/8x0m_37982.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 189 5.16 5 C 15278 2.51 5 N 4200 2.21 5 O 4605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24274 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "F" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "G" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "I" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "J" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "K" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 6.18, per 1000 atoms: 0.25 Number of scatterers: 24274 At special positions: 0 Unit cell: (161.7, 162.8, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 189 16.00 O 4605 8.00 N 4200 7.00 C 15278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 929 " distance=2.03 Simple disulfide: pdb=" SG CYS C 877 " - pdb=" SG CYS C 909 " distance=2.03 Simple disulfide: pdb=" SG CYS C 878 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS C 893 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1086 " distance=2.04 Simple disulfide: pdb=" SG CYS C1116 " - pdb=" SG CYS C1191 " distance=2.03 Simple disulfide: pdb=" SG CYS C1121 " - pdb=" SG CYS C1195 " distance=2.03 Simple disulfide: pdb=" SG CYS C1143 " - pdb=" SG CYS C1185 " distance=2.03 Simple disulfide: pdb=" SG CYS F 352 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 355 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 424 " - pdb=" SG CYS F 438 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 598 " distance=2.04 Simple disulfide: pdb=" SG CYS F 534 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 536 " - pdb=" SG CYS F 553 " distance=2.03 Simple disulfide: pdb=" SG CYS G 864 " - pdb=" SG CYS G 929 " distance=2.03 Simple disulfide: pdb=" SG CYS G 877 " - pdb=" SG CYS G 909 " distance=2.03 Simple disulfide: pdb=" SG CYS G 878 " - pdb=" SG CYS G 911 " distance=2.03 Simple disulfide: pdb=" SG CYS G 883 " - pdb=" SG CYS G 893 " distance=2.03 Simple disulfide: pdb=" SG CYS G1074 " - pdb=" SG CYS G1086 " distance=2.03 Simple disulfide: pdb=" SG CYS G1116 " - pdb=" SG CYS G1191 " distance=2.03 Simple disulfide: pdb=" SG CYS G1121 " - pdb=" SG CYS G1195 " distance=2.03 Simple disulfide: pdb=" SG CYS G1143 " - pdb=" SG CYS G1185 " distance=2.03 Simple disulfide: pdb=" SG CYS J 352 " - pdb=" SG CYS J 458 " distance=2.03 Simple disulfide: pdb=" SG CYS J 355 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 424 " - pdb=" SG CYS J 438 " distance=2.03 Simple disulfide: pdb=" SG CYS J 486 " - pdb=" SG CYS J 598 " distance=2.03 Simple disulfide: pdb=" SG CYS J 534 " - pdb=" SG CYS J 558 " distance=2.03 Simple disulfide: pdb=" SG CYS J 536 " - pdb=" SG CYS J 553 " distance=2.03 Simple disulfide: pdb=" SG CYS K 864 " - pdb=" SG CYS K 929 " distance=2.03 Simple disulfide: pdb=" SG CYS K 877 " - pdb=" SG CYS K 909 " distance=2.03 Simple disulfide: pdb=" SG CYS K 878 " - pdb=" SG CYS K 911 " distance=2.03 Simple disulfide: pdb=" SG CYS K 883 " - pdb=" SG CYS K 893 " distance=2.03 Simple disulfide: pdb=" SG CYS K1074 " - pdb=" SG CYS K1086 " distance=2.04 Simple disulfide: pdb=" SG CYS K1116 " - pdb=" SG CYS K1191 " distance=2.03 Simple disulfide: pdb=" SG CYS K1121 " - pdb=" SG CYS K1195 " distance=2.03 Simple disulfide: pdb=" SG CYS K1143 " - pdb=" SG CYS K1185 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 90 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 83 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG C1701 " - " ASN C 956 " " NAG G1701 " - " ASN G 956 " " NAG K1701 " - " ASN K 956 " " NAG L 1 " - " ASN B 533 " " NAG M 1 " - " ASN B 595 " " NAG N 1 " - " ASN F 533 " " NAG O 1 " - " ASN F 595 " " NAG P 1 " - " ASN J 533 " " NAG Q 1 " - " ASN J 595 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 992.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 70 sheets defined 15.5% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.851A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.810A pdb=" N ARG A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.550A pdb=" N THR B 345 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 695 through 735 removed outlier: 3.614A pdb=" N THR B 699 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Proline residue: B 731 - end of helix removed outlier: 3.734A pdb=" N LEU B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 735 " --> pdb=" O PRO B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'C' and resid 1053 through 1061 removed outlier: 3.554A pdb=" N TYR C1057 " --> pdb=" O SER C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1069 Processing helix chain 'C' and resid 1070 through 1074 removed outlier: 3.948A pdb=" N GLY C1073 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C1074 " --> pdb=" O PRO C1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1070 through 1074' Processing helix chain 'C' and resid 1098 through 1102 Processing helix chain 'C' and resid 1219 through 1253 removed outlier: 3.640A pdb=" N ARG C1253 " --> pdb=" O ILE C1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.958A pdb=" N ASP E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.523A pdb=" N MET E 177 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.542A pdb=" N PHE F 339 " --> pdb=" O SER F 336 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL F 341 " --> pdb=" O HIS F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 695 through 735 Proline residue: F 731 - end of helix removed outlier: 3.619A pdb=" N LEU F 734 " --> pdb=" O THR F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 748 Processing helix chain 'G' and resid 1053 through 1062 removed outlier: 3.685A pdb=" N TYR G1057 " --> pdb=" O SER G1053 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1069 removed outlier: 3.605A pdb=" N THR G1068 " --> pdb=" O ALA G1065 " (cutoff:3.500A) Processing helix chain 'G' and resid 1070 through 1074 removed outlier: 4.024A pdb=" N GLY G1073 " --> pdb=" O ALA G1070 " (cutoff:3.500A) Processing helix chain 'G' and resid 1098 through 1102 removed outlier: 3.774A pdb=" N ALA G1101 " --> pdb=" O PRO G1098 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G1102 " --> pdb=" O ASP G1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1098 through 1102' Processing helix chain 'G' and resid 1219 through 1253 removed outlier: 3.750A pdb=" N ARG G1253 " --> pdb=" O ILE G1249 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.636A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 158 removed outlier: 3.979A pdb=" N LEU I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.759A pdb=" N ARG I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.581A pdb=" N ASN J 340 " --> pdb=" O GLN J 337 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL J 341 " --> pdb=" O HIS J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 554 through 556 No H-bonds generated for 'chain 'J' and resid 554 through 556' Processing helix chain 'J' and resid 683 through 695 Processing helix chain 'J' and resid 695 through 730 removed outlier: 3.607A pdb=" N THR J 699 " --> pdb=" O TYR J 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 731 through 735 removed outlier: 3.689A pdb=" N THR J 735 " --> pdb=" O TYR J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 748 Processing helix chain 'K' and resid 1053 through 1061 removed outlier: 3.642A pdb=" N TYR K1057 " --> pdb=" O SER K1053 " (cutoff:3.500A) Processing helix chain 'K' and resid 1065 through 1069 Processing helix chain 'K' and resid 1070 through 1074 removed outlier: 4.101A pdb=" N GLY K1073 " --> pdb=" O ALA K1070 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS K1074 " --> pdb=" O PRO K1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1070 through 1074' Processing helix chain 'K' and resid 1098 through 1102 removed outlier: 3.877A pdb=" N ALA K1101 " --> pdb=" O PRO K1098 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE K1102 " --> pdb=" O ASP K1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1098 through 1102' Processing helix chain 'K' and resid 1219 through 1253 removed outlier: 3.770A pdb=" N ARG K1253 " --> pdb=" O ILE K1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.872A pdb=" N GLY A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS A 125 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 193 removed outlier: 4.652A pdb=" N PHE A 207 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.836A pdb=" N ILE A 223 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AA5, first strand: chain 'B' and resid 367 through 371 removed outlier: 7.055A pdb=" N GLN B 382 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 370 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 380 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 437 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL B 426 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 389 removed outlier: 12.208A pdb=" N GLN B 386 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N THR B 398 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 388 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 417 through 419 removed outlier: 4.658A pdb=" N GLU B 442 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 481 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AB3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AB4, first strand: chain 'B' and resid 639 through 643 Processing sheet with id=AB5, first strand: chain 'C' and resid 818 through 823 Processing sheet with id=AB6, first strand: chain 'C' and resid 830 through 834 removed outlier: 5.430A pdb=" N MET C 846 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 951 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 848 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 949 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 850 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 856 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR C 941 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN C 858 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 939 " --> pdb=" O ASN C 858 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 860 " --> pdb=" O TYR C 937 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR C 937 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 862 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER C 935 " --> pdb=" O ILE C 862 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 955 through 962 removed outlier: 6.785A pdb=" N SER C 935 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 862 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR C 937 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 860 " --> pdb=" O TYR C 937 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 939 " --> pdb=" O ASN C 858 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN C 858 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR C 941 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 856 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 850 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 949 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 848 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 951 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET C 846 " --> pdb=" O MET C 951 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AB9, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AC1, first strand: chain 'C' and resid 1018 through 1019 Processing sheet with id=AC2, first strand: chain 'C' and resid 1035 through 1036 Processing sheet with id=AC3, first strand: chain 'C' and resid 1112 through 1121 removed outlier: 5.582A pdb=" N ASP C1113 " --> pdb=" O LYS C1136 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C1136 " --> pdb=" O ASP C1113 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1130 " --> pdb=" O ALA C1119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1158 through 1161 Processing sheet with id=AC5, first strand: chain 'E' and resid 149 through 150 removed outlier: 6.128A pdb=" N HIS E 125 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR E 132 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 191 through 193 removed outlier: 4.722A pdb=" N PHE E 207 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 222 through 224 removed outlier: 7.184A pdb=" N ILE E 223 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 350 through 352 Processing sheet with id=AC9, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.089A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 27.719A pdb=" N LYS F 380 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 22.981A pdb=" N ASP F 404 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 17.221A pdb=" N GLN F 382 " --> pdb=" O TYR F 402 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N TYR F 402 " --> pdb=" O GLN F 382 " (cutoff:3.500A) removed outlier: 11.839A pdb=" N SER F 384 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE F 400 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N GLN F 386 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N THR F 398 " --> pdb=" O GLN F 386 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 388 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.089A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N HIS F 432 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N ALA F 385 " --> pdb=" O MET F 430 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N MET F 430 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ILE F 387 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N GLY F 428 " --> pdb=" O ILE F 387 " (cutoff:3.500A) removed outlier: 16.728A pdb=" N ILE F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 19.112A pdb=" N VAL F 426 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 417 through 419 removed outlier: 4.473A pdb=" N GLU F 442 " --> pdb=" O TYR F 462 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 482 through 489 Processing sheet with id=AD4, first strand: chain 'F' and resid 569 through 570 Processing sheet with id=AD5, first strand: chain 'F' and resid 508 through 510 removed outlier: 4.625A pdb=" N VAL F 560 " --> pdb=" O ASP F 510 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD7, first strand: chain 'F' and resid 607 through 609 Processing sheet with id=AD8, first strand: chain 'F' and resid 639 through 643 Processing sheet with id=AD9, first strand: chain 'G' and resid 817 through 823 Processing sheet with id=AE1, first strand: chain 'G' and resid 830 through 834 removed outlier: 5.134A pdb=" N MET G 846 " --> pdb=" O MET G 951 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET G 951 " --> pdb=" O MET G 846 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL G 848 " --> pdb=" O ARG G 949 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG G 949 " --> pdb=" O VAL G 848 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 850 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 830 through 834 Processing sheet with id=AE3, first strand: chain 'G' and resid 858 through 863 removed outlier: 6.266A pdb=" N LEU G 859 " --> pdb=" O LYS G 938 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS G 938 " --> pdb=" O LEU G 859 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR G 861 " --> pdb=" O ALA G 936 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE5, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE6, first strand: chain 'G' and resid 1018 through 1019 Processing sheet with id=AE7, first strand: chain 'G' and resid 1035 through 1036 Processing sheet with id=AE8, first strand: chain 'G' and resid 1112 through 1121 removed outlier: 7.180A pdb=" N LEU G1114 " --> pdb=" O LYS G1136 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LYS G1136 " --> pdb=" O LEU G1114 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS G1116 " --> pdb=" O THR G1134 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR G1134 " --> pdb=" O CYS G1116 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL G1118 " --> pdb=" O THR G1132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR G1132 " --> pdb=" O VAL G1118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AF1, first strand: chain 'I' and resid 149 through 150 Processing sheet with id=AF2, first strand: chain 'I' and resid 257 through 259 removed outlier: 4.756A pdb=" N PHE I 207 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ALA I 199 " --> pdb=" O PRO I 210 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 257 through 259 removed outlier: 7.152A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 350 through 352 Processing sheet with id=AF5, first strand: chain 'J' and resid 367 through 371 removed outlier: 7.058A pdb=" N GLN J 382 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL J 370 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS J 380 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS J 437 " --> pdb=" O VAL J 426 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL J 426 " --> pdb=" O LYS J 437 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 386 through 389 removed outlier: 3.710A pdb=" N GLY J 388 " --> pdb=" O LYS J 399 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS J 399 " --> pdb=" O GLY J 388 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 417 through 419 removed outlier: 4.408A pdb=" N GLU J 442 " --> pdb=" O TYR J 462 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 482 through 489 Processing sheet with id=AF9, first strand: chain 'J' and resid 569 through 570 Processing sheet with id=AG1, first strand: chain 'J' and resid 514 through 517 Processing sheet with id=AG2, first strand: chain 'J' and resid 542 through 544 Processing sheet with id=AG3, first strand: chain 'J' and resid 607 through 609 Processing sheet with id=AG4, first strand: chain 'J' and resid 639 through 643 Processing sheet with id=AG5, first strand: chain 'K' and resid 817 through 823 Processing sheet with id=AG6, first strand: chain 'K' and resid 830 through 834 removed outlier: 5.430A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 955 through 962 removed outlier: 6.777A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AG9, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AH1, first strand: chain 'K' and resid 902 through 903 Processing sheet with id=AH2, first strand: chain 'K' and resid 1018 through 1019 Processing sheet with id=AH3, first strand: chain 'K' and resid 1035 through 1036 Processing sheet with id=AH4, first strand: chain 'K' and resid 1112 through 1121 removed outlier: 6.877A pdb=" N LEU K1114 " --> pdb=" O LYS K1136 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS K1136 " --> pdb=" O LEU K1114 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N CYS K1116 " --> pdb=" O THR K1134 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR K1134 " --> pdb=" O CYS K1116 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL K1118 " --> pdb=" O THR K1132 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR K1132 " --> pdb=" O VAL K1118 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 1158 through 1161 Processing sheet with id=AH6, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AH7, first strand: chain 'H' and resid 87 through 89 990 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7917 1.34 - 1.47: 6157 1.47 - 1.60: 10571 1.60 - 1.72: 1 1.72 - 1.85: 255 Bond restraints: 24901 Sorted by residual: bond pdb=" CB PRO A 216 " pdb=" CG PRO A 216 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" CB ASN J 545 " pdb=" CG ASN J 545 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.85e+00 bond pdb=" CE LYS G1227 " pdb=" NZ LYS G1227 " ideal model delta sigma weight residual 1.489 1.427 0.062 3.00e-02 1.11e+03 4.24e+00 ... (remaining 24896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 33652 3.15 - 6.29: 216 6.29 - 9.44: 21 9.44 - 12.59: 3 12.59 - 15.74: 3 Bond angle restraints: 33895 Sorted by residual: angle pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" CD PRO A 216 " ideal model delta sigma weight residual 112.00 96.26 15.74 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA CYS J 598 " pdb=" CB CYS J 598 " pdb=" SG CYS J 598 " ideal model delta sigma weight residual 114.40 127.40 -13.00 2.30e+00 1.89e-01 3.20e+01 angle pdb=" C GLU G1061 " pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " ideal model delta sigma weight residual 111.35 120.99 -9.64 1.72e+00 3.38e-01 3.14e+01 angle pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " pdb=" CG GLU G1061 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" N GLU G1061 " pdb=" CA GLU G1061 " pdb=" CB GLU G1061 " ideal model delta sigma weight residual 111.65 104.51 7.14 1.40e+00 5.10e-01 2.60e+01 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12948 17.98 - 35.96: 1670 35.96 - 53.95: 447 53.95 - 71.93: 69 71.93 - 89.91: 31 Dihedral angle restraints: 15165 sinusoidal: 6128 harmonic: 9037 Sorted by residual: dihedral pdb=" CB CYS H 83 " pdb=" SG CYS H 83 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 175.89 -82.89 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " pdb=" SG CYS F 598 " pdb=" CB CYS F 598 " ideal model delta sinusoidal sigma weight residual -86.00 -166.90 80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS F 355 " pdb=" SG CYS F 355 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual 93.00 172.43 -79.43 1 1.00e+01 1.00e-02 7.84e+01 ... (remaining 15162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3762 0.125 - 0.250: 40 0.250 - 0.376: 1 0.376 - 0.501: 0 0.501 - 0.626: 1 Chirality restraints: 3804 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN F 595 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 595 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" C PRO A 216 " pdb=" CB PRO A 216 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 3801 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 215 " 0.088 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO A 216 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 595 " -0.003 2.00e-02 2.50e+03 3.53e-02 1.56e+01 pdb=" CG ASN B 595 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 595 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 595 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 545 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C ASN J 545 " -0.052 2.00e-02 2.50e+03 pdb=" O ASN J 545 " 0.020 2.00e-02 2.50e+03 pdb=" N SER J 546 " 0.017 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 722 2.70 - 3.25: 22776 3.25 - 3.80: 36401 3.80 - 4.35: 43184 4.35 - 4.90: 75667 Nonbonded interactions: 178750 Sorted by model distance: nonbonded pdb=" OH TYR B 402 " pdb=" OD1 ASP B 450 " model vdw 2.146 3.040 nonbonded pdb=" O PRO E 189 " pdb=" OH TYR E 193 " model vdw 2.161 3.040 nonbonded pdb=" O PRO A 189 " pdb=" OH TYR A 193 " model vdw 2.169 3.040 nonbonded pdb=" O THR E 211 " pdb=" OG1 THR E 244 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 112 " pdb=" OE2 GLU D 114 " model vdw 2.189 3.040 ... (remaining 178745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- 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 : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.68 % Allowed : 32.73 % Favored : 66.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3106 helix: 2.85 (0.28), residues: 327 sheet: 0.44 (0.17), residues: 972 loop : -1.04 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 949 TYR 0.031 0.002 TYR K 861 PHE 0.034 0.002 PHE B 339 TRP 0.023 0.001 TRP I 251 HIS 0.005 0.001 HIS F 623 Details of bonding type rmsd covalent geometry : bond 0.00358 (24901) covalent geometry : angle 0.70328 (33895) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.40664 ( 96) hydrogen bonds : bond 0.11436 ( 943) hydrogen bonds : angle 5.29821 ( 2466) link_BETA1-4 : bond 0.00727 ( 6) link_BETA1-4 : angle 1.72960 ( 18) link_NAG-ASN : bond 0.00952 ( 9) link_NAG-ASN : angle 5.49814 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 694 time to evaluate : 0.701 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: 0.1767 time to fit residues: 189.7191 Evaluate side-chains 704 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 692 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 251 TRP Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1190 THR Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain K residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 9.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 557 GLN E 125 HIS ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 845 GLN G 847 GLN G 954 ASN G1148 HIS G1201 HIS J 461 GLN 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 = 0.3702 r_free = 0.3702 target = 0.133903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115665 restraints weight = 40934.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118889 restraints weight = 17649.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120962 restraints weight = 9521.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122197 restraints weight = 6058.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123108 restraints weight = 4523.980| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24964 Z= 0.105 Angle : 0.585 17.095 34036 Z= 0.293 Chirality : 0.044 0.514 3804 Planarity : 0.004 0.054 4362 Dihedral : 4.802 51.580 3706 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.43 % Allowed : 28.70 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 3106 helix: 2.97 (0.28), residues: 324 sheet: 0.50 (0.17), residues: 972 loop : -0.99 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 836 TYR 0.021 0.001 TYR B 532 PHE 0.011 0.001 PHE F 474 TRP 0.011 0.001 TRP D 102 HIS 0.004 0.001 HIS F 395 Details of bonding type rmsd covalent geometry : bond 0.00236 (24901) covalent geometry : angle 0.56747 (33895) SS BOND : bond 0.00306 ( 48) SS BOND : angle 0.99142 ( 96) hydrogen bonds : bond 0.03474 ( 943) hydrogen bonds : angle 4.60000 ( 2466) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 1.11222 ( 18) link_NAG-ASN : bond 0.01071 ( 9) link_NAG-ASN : angle 4.80443 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 703 time to evaluate : 0.859 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: 0.7196 (mmmt) cc_final: 0.6709 (mmmt) REVERT: B 396 ASP cc_start: 0.7251 (t0) cc_final: 0.6950 (t0) REVERT: B 462 TYR cc_start: 0.7882 (t80) cc_final: 0.7521 (t80) REVERT: B 566 LYS cc_start: 0.7147 (mmmm) cc_final: 0.6901 (mmmm) REVERT: B 586 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7873 (mtmt) REVERT: C 917 GLN cc_start: 0.8477 (tt0) cc_final: 0.8140 (tt0) REVERT: E 113 MET cc_start: 0.4917 (mmp) cc_final: 0.4554 (mmp) REVERT: F 659 GLU cc_start: 0.7303 (tt0) cc_final: 0.6898 (tt0) REVERT: G 914 GLU cc_start: 0.7599 (mp0) cc_final: 0.7144 (mp0) REVERT: G 1021 ARG cc_start: 0.8857 (mmt180) cc_final: 0.8571 (mmt-90) REVERT: G 1148 HIS cc_start: 0.8219 (m-70) cc_final: 0.7904 (m170) REVERT: I 113 MET cc_start: 0.7155 (mmm) cc_final: 0.6881 (mmm) REVERT: J 475 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8579 (p) REVERT: J 529 LYS cc_start: 0.8190 (tppt) cc_final: 0.7718 (tppt) REVERT: J 545 ASN cc_start: 0.8645 (t0) cc_final: 0.8403 (t0) REVERT: J 586 LYS cc_start: 0.6774 (mptt) cc_final: 0.6300 (mmtp) REVERT: K 997 ASP cc_start: 0.7614 (p0) cc_final: 0.7348 (p0) REVERT: K 1019 GLN cc_start: 0.7514 (mt0) cc_final: 0.7051 (mm-40) REVERT: K 1029 TYR cc_start: 0.8371 (t80) cc_final: 0.7447 (t80) REVERT: K 1226 GLN cc_start: 0.8004 (tp40) cc_final: 0.7779 (tt0) REVERT: K 1227 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (pttt) outliers start: 91 outliers final: 51 residues processed: 746 average time/residue: 0.1677 time to fit residues: 194.1992 Evaluate side-chains 743 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 690 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 665 ASN Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1137 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 689 GLN Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1079 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1227 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 283 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 201 GLN B 517 GLN B 540 ASN B 551 ASN B 623 HIS E 125 HIS F 461 GLN ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 845 GLN G 847 GLN G 917 GLN G 954 ASN G1067 ASN G1201 HIS ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS J 664 ASN J 686 GLN K1045 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107646 restraints weight = 41083.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110972 restraints weight = 17631.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113079 restraints weight = 9551.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114410 restraints weight = 6207.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115338 restraints weight = 4612.726| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24964 Z= 0.248 Angle : 0.677 18.384 34036 Z= 0.347 Chirality : 0.047 0.547 3804 Planarity : 0.005 0.065 4362 Dihedral : 4.858 51.354 3691 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3106 helix: 2.69 (0.27), residues: 324 sheet: 0.41 (0.17), residues: 963 loop : -1.11 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 243 TYR 0.028 0.002 TYR J 690 PHE 0.022 0.002 PHE C1235 TRP 0.015 0.002 TRP A 251 HIS 0.014 0.001 HIS J 559 Details of bonding type rmsd covalent geometry : bond 0.00550 (24901) covalent geometry : angle 0.65709 (33895) SS BOND : bond 0.00672 ( 48) SS BOND : angle 1.49757 ( 96) hydrogen bonds : bond 0.04825 ( 943) hydrogen bonds : angle 4.66540 ( 2466) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 1.38276 ( 18) link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 5.18912 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 754 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7052 (mmmt) REVERT: A 160 PHE cc_start: 0.7762 (m-80) cc_final: 0.7560 (m-10) REVERT: B 394 ASN cc_start: 0.7965 (p0) cc_final: 0.7684 (p0) REVERT: B 396 ASP cc_start: 0.7674 (t0) cc_final: 0.7284 (t0) REVERT: B 462 TYR cc_start: 0.8035 (t80) cc_final: 0.7624 (t80) REVERT: B 484 ILE cc_start: 0.8209 (mm) cc_final: 0.7920 (mt) REVERT: B 498 GLU cc_start: 0.7020 (pm20) cc_final: 0.6779 (pm20) REVERT: B 677 GLU cc_start: 0.7618 (pm20) cc_final: 0.7227 (pm20) REVERT: B 711 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 818 HIS cc_start: 0.6122 (t-90) cc_final: 0.5891 (t-90) REVERT: C 819 SER cc_start: 0.8179 (m) cc_final: 0.7751 (p) REVERT: C 857 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 919 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8219 (p) REVERT: C 998 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6397 (mt-10) REVERT: C 1024 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6996 (mm-30) REVERT: C 1095 MET cc_start: 0.7075 (ppp) cc_final: 0.6561 (ppp) REVERT: E 113 MET cc_start: 0.5076 (mmp) cc_final: 0.4685 (mmp) REVERT: E 252 ASN cc_start: 0.7902 (t0) cc_final: 0.7636 (t0) REVERT: F 340 ASN cc_start: 0.6502 (m110) cc_final: 0.6016 (p0) REVERT: F 370 VAL cc_start: 0.8655 (t) cc_final: 0.8423 (m) REVERT: F 394 ASN cc_start: 0.7787 (t0) cc_final: 0.7278 (t0) REVERT: F 511 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8289 (mmm160) REVERT: F 659 GLU cc_start: 0.7357 (tt0) cc_final: 0.7132 (tt0) REVERT: F 694 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8058 (mp) REVERT: G 822 MET cc_start: 0.7699 (ttm) cc_final: 0.7490 (ttm) REVERT: G 945 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7768 (mtpp) REVERT: G 954 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7457 (t0) REVERT: G 966 ASP cc_start: 0.7584 (p0) cc_final: 0.7278 (t70) REVERT: G 1019 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7315 (mm-40) REVERT: G 1059 LEU cc_start: 0.8501 (tp) cc_final: 0.8140 (mt) REVERT: G 1061 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6827 (tm-30) REVERT: G 1139 LYS cc_start: 0.8534 (pttt) cc_final: 0.8325 (ptmt) REVERT: G 1144 SER cc_start: 0.8666 (t) cc_final: 0.8353 (m) REVERT: I 113 MET cc_start: 0.7219 (mmm) cc_final: 0.6883 (mmm) REVERT: I 142 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7499 (tmtt) REVERT: I 177 MET cc_start: 0.3513 (OUTLIER) cc_final: 0.3115 (mpp) REVERT: J 373 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7381 (mm-30) REVERT: J 409 GLU cc_start: 0.7180 (mp0) cc_final: 0.6877 (mp0) REVERT: J 467 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7137 (mm-40) REVERT: J 473 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8094 (mmtp) REVERT: J 496 THR cc_start: 0.7897 (p) cc_final: 0.7638 (p) REVERT: J 498 GLU cc_start: 0.6945 (pm20) cc_final: 0.6651 (pm20) REVERT: J 529 LYS cc_start: 0.8202 (tppt) cc_final: 0.7413 (tppt) REVERT: J 544 THR cc_start: 0.7826 (p) cc_final: 0.7510 (t) REVERT: J 545 ASN cc_start: 0.8604 (t0) cc_final: 0.8380 (t0) REVERT: J 567 LYS cc_start: 0.7546 (mmtp) cc_final: 0.7288 (mmtt) REVERT: J 600 VAL cc_start: 0.8578 (p) cc_final: 0.8320 (t) REVERT: J 634 GLU cc_start: 0.7321 (tp30) cc_final: 0.7053 (tp30) REVERT: J 668 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.8003 (t) REVERT: K 876 LYS cc_start: 0.7848 (tttp) cc_final: 0.7522 (tttm) REVERT: K 951 MET cc_start: 0.7774 (mtm) cc_final: 0.7537 (mtp) REVERT: K 970 THR cc_start: 0.8511 (t) cc_final: 0.8277 (m) REVERT: K 1001 ASN cc_start: 0.7968 (m-40) cc_final: 0.7597 (m-40) REVERT: K 1019 GLN cc_start: 0.8209 (mt0) cc_final: 0.7900 (mt0) REVERT: K 1130 VAL cc_start: 0.8124 (p) cc_final: 0.7813 (t) REVERT: K 1223 SER cc_start: 0.8083 (t) cc_final: 0.7876 (t) outliers start: 124 outliers final: 80 residues processed: 813 average time/residue: 0.1712 time to fit residues: 214.8309 Evaluate side-chains 830 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 743 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 919 SER 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 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 E residue 257 THR Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain 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 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 1043 MET Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1137 THR 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 1199 LYS Chi-restraints excluded: chain G residue 1217 MET 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 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 249 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 528 LYS Chi-restraints excluded: chain J residue 560 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1059 LEU Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1168 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1186 SER Chi-restraints excluded: chain K residue 1213 VAL Chi-restraints excluded: chain K residue 1227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 218 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 chunk 82 optimal weight: 0.0070 chunk 228 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN B 340 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 623 HIS F 559 HIS ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN G 847 GLN G 954 ASN G1001 ASN G1075 GLN G1155 GLN ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 559 HIS J 689 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108448 restraints weight = 40644.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111773 restraints weight = 17362.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113897 restraints weight = 9379.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115216 restraints weight = 6050.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116118 restraints weight = 4475.740| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1795 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= 0.151 Angle : 0.613 17.357 34036 Z= 0.307 Chirality : 0.045 0.558 3804 Planarity : 0.005 0.062 4362 Dihedral : 4.592 54.390 3691 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.45 % Allowed : 28.47 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.15), residues: 3106 helix: 2.81 (0.28), residues: 324 sheet: 0.43 (0.16), residues: 969 loop : -1.09 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1014 TYR 0.028 0.002 TYR B 397 PHE 0.023 0.002 PHE F 570 TRP 0.011 0.001 TRP B 642 HIS 0.017 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00347 (24901) covalent geometry : angle 0.59313 (33895) SS BOND : bond 0.00350 ( 48) SS BOND : angle 1.31738 ( 96) hydrogen bonds : bond 0.04003 ( 943) hydrogen bonds : angle 4.57769 ( 2466) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.18891 ( 18) link_NAG-ASN : bond 0.00888 ( 9) link_NAG-ASN : angle 4.97638 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 757 time to evaluate : 0.913 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: 0.7601 (mmmt) cc_final: 0.7133 (mmmt) REVERT: B 394 ASN cc_start: 0.7933 (p0) cc_final: 0.7678 (p0) REVERT: B 395 HIS cc_start: 0.7475 (t-90) cc_final: 0.7063 (t-90) REVERT: B 396 ASP cc_start: 0.7688 (t0) cc_final: 0.7084 (t0) REVERT: B 462 TYR cc_start: 0.8008 (t80) cc_final: 0.7527 (t80) REVERT: B 484 ILE cc_start: 0.8204 (mm) cc_final: 0.7937 (mt) REVERT: B 498 GLU cc_start: 0.7012 (pm20) cc_final: 0.6678 (pm20) REVERT: C 819 SER cc_start: 0.8217 (m) cc_final: 0.7809 (p) REVERT: C 954 ASN cc_start: 0.7703 (p0) cc_final: 0.7369 (p0) REVERT: C 1018 ILE cc_start: 0.8011 (pt) cc_final: 0.7781 (pt) REVERT: C 1021 ARG cc_start: 0.8952 (tpp-160) cc_final: 0.8589 (tpt170) REVERT: C 1024 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6886 (mm-30) REVERT: C 1059 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7982 (mp) REVERT: C 1095 MET cc_start: 0.7084 (ppp) cc_final: 0.6518 (ppp) REVERT: C 1117 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8218 (p) REVERT: E 113 MET cc_start: 0.5130 (mmp) cc_final: 0.4754 (mmp) REVERT: F 394 ASN cc_start: 0.7686 (t0) cc_final: 0.7165 (t0) REVERT: F 511 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8237 (mmm160) REVERT: F 638 TYR cc_start: 0.8514 (p90) cc_final: 0.8195 (p90) REVERT: F 658 MET cc_start: 0.7059 (tmm) cc_final: 0.6757 (tmm) REVERT: F 694 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7949 (mp) REVERT: G 914 GLU cc_start: 0.7633 (mp0) cc_final: 0.7017 (mp0) REVERT: G 945 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7687 (mtpp) REVERT: G 1019 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7209 (mm-40) REVERT: G 1059 LEU cc_start: 0.8436 (tp) cc_final: 0.8081 (mt) REVERT: G 1061 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6772 (tm-30) REVERT: G 1113 ASP cc_start: 0.7862 (t0) cc_final: 0.7622 (t0) REVERT: G 1139 LYS cc_start: 0.8527 (pttt) cc_final: 0.8302 (ptmt) REVERT: G 1144 SER cc_start: 0.8615 (t) cc_final: 0.8273 (m) REVERT: I 142 LYS cc_start: 0.7947 (tmmt) cc_final: 0.7681 (tmtt) REVERT: I 177 MET cc_start: 0.3627 (OUTLIER) cc_final: 0.3407 (mpp) REVERT: J 373 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7390 (mm-30) REVERT: J 467 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7163 (mm-40) REVERT: J 496 THR cc_start: 0.7894 (p) cc_final: 0.7613 (p) REVERT: J 498 GLU cc_start: 0.6896 (pm20) cc_final: 0.6577 (pm20) REVERT: J 529 LYS cc_start: 0.8187 (tppt) cc_final: 0.7201 (tppt) REVERT: J 544 THR cc_start: 0.7802 (p) cc_final: 0.7198 (t) REVERT: J 567 LYS cc_start: 0.7528 (mmtp) cc_final: 0.7312 (mmtt) REVERT: J 634 GLU cc_start: 0.7322 (tp30) cc_final: 0.7103 (tp30) REVERT: J 686 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: K 876 LYS cc_start: 0.7836 (tttp) cc_final: 0.7485 (tttm) REVERT: K 970 THR cc_start: 0.8508 (t) cc_final: 0.8168 (p) REVERT: K 1019 GLN cc_start: 0.8082 (mt0) cc_final: 0.7858 (mt0) REVERT: K 1022 THR cc_start: 0.8538 (t) cc_final: 0.8059 (p) REVERT: K 1130 VAL cc_start: 0.8061 (p) cc_final: 0.7770 (t) outliers start: 118 outliers final: 72 residues processed: 808 average time/residue: 0.1708 time to fit residues: 212.1961 Evaluate side-chains 825 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 748 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 709 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 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 1223 SER Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1199 LYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 249 VAL 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 655 VAL Chi-restraints excluded: chain J residue 686 GLN 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 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 254 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 301 optimal weight: 40.0000 chunk 296 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 GLN F 565 HIS F 569 GLN G 847 GLN G 954 ASN G1075 GLN G1155 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 623 HIS ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104932 restraints weight = 40470.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108206 restraints weight = 17190.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110309 restraints weight = 9276.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111672 restraints weight = 5979.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112427 restraints weight = 4408.244| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24964 Z= 0.259 Angle : 0.690 18.337 34036 Z= 0.350 Chirality : 0.048 0.541 3804 Planarity : 0.005 0.066 4362 Dihedral : 4.910 55.544 3691 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.24 % Allowed : 28.05 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3106 helix: 2.68 (0.28), residues: 324 sheet: 0.37 (0.17), residues: 963 loop : -1.20 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 178 TYR 0.032 0.002 TYR B 397 PHE 0.023 0.002 PHE C1235 TRP 0.012 0.002 TRP D 102 HIS 0.049 0.002 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00587 (24901) covalent geometry : angle 0.66715 (33895) SS BOND : bond 0.00400 ( 48) SS BOND : angle 1.59985 ( 96) hydrogen bonds : bond 0.04878 ( 943) hydrogen bonds : angle 4.72937 ( 2466) link_BETA1-4 : bond 0.00412 ( 6) link_BETA1-4 : angle 1.30966 ( 18) link_NAG-ASN : bond 0.00943 ( 9) link_NAG-ASN : angle 5.53834 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 772 time to evaluate : 0.953 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: 0.7641 (mmmt) cc_final: 0.7126 (mmmt) REVERT: A 142 LYS cc_start: 0.7910 (tptp) cc_final: 0.7690 (tptp) REVERT: B 343 LYS cc_start: 0.8713 (mptt) cc_final: 0.8462 (mptt) REVERT: B 394 ASN cc_start: 0.7931 (p0) cc_final: 0.7649 (p0) REVERT: B 395 HIS cc_start: 0.7439 (t70) cc_final: 0.6804 (t70) REVERT: B 396 ASP cc_start: 0.7799 (t0) cc_final: 0.7263 (t0) REVERT: B 462 TYR cc_start: 0.8070 (t80) cc_final: 0.7575 (t80) REVERT: B 484 ILE cc_start: 0.8249 (mm) cc_final: 0.8007 (mt) REVERT: B 498 GLU cc_start: 0.7045 (pm20) cc_final: 0.6677 (pm20) REVERT: B 711 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 712 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 857 LEU cc_start: 0.8474 (mt) cc_final: 0.8255 (mt) REVERT: C 954 ASN cc_start: 0.7767 (p0) cc_final: 0.7416 (p0) REVERT: C 983 SER cc_start: 0.8826 (t) cc_final: 0.8277 (p) REVERT: C 997 ASP cc_start: 0.7853 (p0) cc_final: 0.6943 (p0) REVERT: C 998 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6243 (mp0) REVERT: C 1014 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8309 (mmt180) REVERT: C 1018 ILE cc_start: 0.8050 (pt) cc_final: 0.7815 (pt) REVERT: C 1021 ARG cc_start: 0.8998 (tpp-160) cc_final: 0.8427 (tpt170) REVERT: C 1024 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6842 (mm-30) REVERT: C 1053 SER cc_start: 0.8123 (t) cc_final: 0.7844 (p) REVERT: C 1059 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8047 (mp) REVERT: C 1095 MET cc_start: 0.6997 (ppp) cc_final: 0.6360 (ppp) REVERT: C 1117 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8317 (p) REVERT: C 1166 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8110 (mmtp) REVERT: C 1227 LYS cc_start: 0.8305 (mttt) cc_final: 0.7922 (mttt) REVERT: E 113 MET cc_start: 0.5235 (mmp) cc_final: 0.4892 (mmp) REVERT: F 370 VAL cc_start: 0.8644 (t) cc_final: 0.8411 (m) REVERT: F 394 ASN cc_start: 0.7690 (t0) cc_final: 0.7239 (t0) REVERT: F 399 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8162 (mtpp) REVERT: F 504 MET cc_start: 0.7107 (tpt) cc_final: 0.6875 (tpt) REVERT: F 516 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7986 (tp40) REVERT: F 586 LYS cc_start: 0.7398 (pttt) cc_final: 0.7108 (pptt) REVERT: F 638 TYR cc_start: 0.8542 (p90) cc_final: 0.8282 (p90) REVERT: F 694 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8106 (mp) REVERT: F 699 THR cc_start: 0.8135 (t) cc_final: 0.7932 (p) REVERT: F 720 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7216 (ppp) REVERT: G 914 GLU cc_start: 0.7629 (mp0) cc_final: 0.6998 (mp0) REVERT: G 945 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7714 (mtpp) REVERT: G 1019 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7278 (mm-40) REVERT: G 1059 LEU cc_start: 0.8501 (tp) cc_final: 0.8173 (mt) REVERT: G 1061 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6829 (tm-30) REVERT: G 1113 ASP cc_start: 0.7763 (t0) cc_final: 0.7512 (t0) REVERT: G 1139 LYS cc_start: 0.8621 (pttt) cc_final: 0.8387 (ptmt) REVERT: G 1144 SER cc_start: 0.8683 (t) cc_final: 0.8402 (m) REVERT: G 1150 ASN cc_start: 0.8329 (p0) cc_final: 0.7847 (p0) REVERT: G 1249 ILE cc_start: 0.8923 (tt) cc_final: 0.8693 (tp) REVERT: I 113 MET cc_start: 0.7300 (mmm) cc_final: 0.6878 (mmm) REVERT: I 142 LYS cc_start: 0.8227 (tmmt) cc_final: 0.8000 (tmtt) REVERT: I 177 MET cc_start: 0.3964 (OUTLIER) cc_final: 0.3608 (mpp) REVERT: J 373 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7410 (mm-30) REVERT: J 409 GLU cc_start: 0.7114 (mp0) cc_final: 0.6704 (mp0) REVERT: J 467 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7169 (mm-40) REVERT: J 496 THR cc_start: 0.7987 (p) cc_final: 0.7679 (p) REVERT: J 498 GLU cc_start: 0.6870 (pm20) cc_final: 0.6497 (pm20) REVERT: J 522 LYS cc_start: 0.8170 (tttp) cc_final: 0.7532 (tttp) REVERT: J 529 LYS cc_start: 0.8236 (tppt) cc_final: 0.7232 (tppt) REVERT: J 533 ASN cc_start: 0.8529 (t0) cc_final: 0.7740 (t0) REVERT: J 544 THR cc_start: 0.7865 (p) cc_final: 0.7106 (p) REVERT: J 586 LYS cc_start: 0.6989 (mptt) cc_final: 0.6501 (mmtp) REVERT: K 876 LYS cc_start: 0.7971 (tttp) cc_final: 0.7602 (tttm) REVERT: K 960 ASP cc_start: 0.7627 (p0) cc_final: 0.7416 (p0) REVERT: K 970 THR cc_start: 0.8469 (t) cc_final: 0.8189 (p) REVERT: K 1014 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7282 (mmt90) REVERT: K 1019 GLN cc_start: 0.8241 (mt0) cc_final: 0.7990 (mt0) REVERT: K 1022 THR cc_start: 0.8516 (t) cc_final: 0.8025 (p) REVERT: K 1079 ASN cc_start: 0.8549 (t0) cc_final: 0.8348 (t0) REVERT: K 1115 THR cc_start: 0.8653 (t) cc_final: 0.8343 (p) REVERT: K 1130 VAL cc_start: 0.8083 (p) cc_final: 0.7803 (t) REVERT: K 1196 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6752 (mm-30) outliers start: 139 outliers final: 99 residues processed: 832 average time/residue: 0.1746 time to fit residues: 222.9810 Evaluate side-chains 856 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 747 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 383 PHE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 512 THR 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 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 712 ILE 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 1014 ARG Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 516 GLN Chi-restraints excluded: chain F residue 523 ILE Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 833 HIS Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 886 LYS 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 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 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 689 GLN Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 1014 ARG 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 1107 GLU Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 257 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 623 HIS ** C1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN F 382 GLN ** G 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 623 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 = 0.3549 r_free = 0.3549 target = 0.123323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105818 restraints weight = 40043.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108979 restraints weight = 16741.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111002 restraints weight = 8908.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112319 restraints weight = 5692.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113071 restraints weight = 4152.118| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24964 Z= 0.198 Angle : 0.666 18.530 34036 Z= 0.335 Chirality : 0.046 0.547 3804 Planarity : 0.005 0.047 4362 Dihedral : 4.857 58.916 3691 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.02 % Allowed : 29.15 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3106 helix: 2.75 (0.28), residues: 324 sheet: 0.36 (0.17), residues: 966 loop : -1.23 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 836 TYR 0.030 0.002 TYR B 397 PHE 0.026 0.002 PHE C1235 TRP 0.010 0.001 TRP B 642 HIS 0.019 0.001 HIS J 623 Details of bonding type rmsd covalent geometry : bond 0.00454 (24901) covalent geometry : angle 0.64515 (33895) SS BOND : bond 0.00606 ( 48) SS BOND : angle 1.45480 ( 96) hydrogen bonds : bond 0.04475 ( 943) hydrogen bonds : angle 4.70790 ( 2466) link_BETA1-4 : bond 0.00362 ( 6) link_BETA1-4 : angle 1.25874 ( 18) link_NAG-ASN : bond 0.00921 ( 9) link_NAG-ASN : angle 5.25993 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 759 time to evaluate : 0.887 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: 0.7669 (mmmt) cc_final: 0.7115 (mmmt) REVERT: B 394 ASN cc_start: 0.7983 (p0) cc_final: 0.7685 (p0) REVERT: B 395 HIS cc_start: 0.7546 (t70) cc_final: 0.6967 (t70) REVERT: B 396 ASP cc_start: 0.7793 (t0) cc_final: 0.7257 (t0) REVERT: B 462 TYR cc_start: 0.8067 (t80) cc_final: 0.7572 (t80) REVERT: B 484 ILE cc_start: 0.8201 (mm) cc_final: 0.7961 (mt) REVERT: B 496 THR cc_start: 0.8005 (m) cc_final: 0.7765 (p) REVERT: B 635 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7189 (t0) REVERT: C 920 GLU cc_start: 0.7510 (pm20) cc_final: 0.7271 (pm20) REVERT: C 954 ASN cc_start: 0.7818 (p0) cc_final: 0.7446 (p0) REVERT: C 983 SER cc_start: 0.8832 (t) cc_final: 0.8273 (p) REVERT: C 997 ASP cc_start: 0.7839 (p0) cc_final: 0.6906 (p0) REVERT: C 998 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6179 (mp0) REVERT: C 1014 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8266 (mmt180) REVERT: C 1018 ILE cc_start: 0.8056 (pt) cc_final: 0.7818 (pt) REVERT: C 1021 ARG cc_start: 0.8970 (tpp-160) cc_final: 0.8419 (tpt170) REVERT: C 1024 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 1035 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7689 (ttmm) REVERT: C 1059 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8058 (mp) REVERT: C 1060 LYS cc_start: 0.8223 (ttmm) cc_final: 0.8007 (tppp) REVERT: C 1095 MET cc_start: 0.7000 (ppp) cc_final: 0.6329 (ppp) REVERT: C 1117 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8280 (p) REVERT: C 1166 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8166 (mmtp) REVERT: C 1227 LYS cc_start: 0.8294 (mttt) cc_final: 0.7918 (mttt) REVERT: E 113 MET cc_start: 0.5146 (mmp) cc_final: 0.4818 (mmp) REVERT: F 370 VAL cc_start: 0.8641 (t) cc_final: 0.8410 (m) REVERT: F 394 ASN cc_start: 0.7719 (t0) cc_final: 0.7241 (t0) REVERT: F 396 ASP cc_start: 0.7122 (t0) cc_final: 0.6846 (t0) REVERT: F 399 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8179 (mtpp) REVERT: F 548 MET cc_start: 0.7186 (mpp) cc_final: 0.6834 (mpp) REVERT: F 570 PHE cc_start: 0.7874 (t80) cc_final: 0.7671 (t80) REVERT: F 586 LYS cc_start: 0.7389 (pttt) cc_final: 0.7097 (pptt) REVERT: F 638 TYR cc_start: 0.8539 (p90) cc_final: 0.8263 (p90) REVERT: F 694 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7984 (mp) REVERT: F 699 THR cc_start: 0.8072 (t) cc_final: 0.7835 (p) REVERT: G 912 ASP cc_start: 0.7770 (m-30) cc_final: 0.7426 (t0) REVERT: G 914 GLU cc_start: 0.7622 (mp0) cc_final: 0.7012 (mp0) REVERT: G 945 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7682 (mtpp) REVERT: G 989 ASP cc_start: 0.7171 (m-30) cc_final: 0.6887 (m-30) REVERT: G 1019 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7335 (mm-40) REVERT: G 1059 LEU cc_start: 0.8479 (tp) cc_final: 0.8159 (mt) REVERT: G 1061 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6839 (tm-30) REVERT: G 1113 ASP cc_start: 0.7666 (t0) cc_final: 0.7411 (t0) REVERT: G 1144 SER cc_start: 0.8632 (t) cc_final: 0.8328 (m) REVERT: G 1150 ASN cc_start: 0.8334 (p0) cc_final: 0.7799 (p0) REVERT: I 126 GLU cc_start: 0.6263 (tp30) cc_final: 0.5753 (tp30) REVERT: I 162 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8005 (tttt) REVERT: I 177 MET cc_start: 0.4232 (OUTLIER) cc_final: 0.4011 (mpp) REVERT: I 221 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7427 (mtt180) REVERT: I 252 ASN cc_start: 0.7694 (t0) cc_final: 0.7367 (t0) REVERT: J 435 LEU cc_start: 0.8047 (tp) cc_final: 0.7647 (tt) REVERT: J 467 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7186 (mm-40) REVERT: J 496 THR cc_start: 0.7955 (p) cc_final: 0.7666 (p) REVERT: J 498 GLU cc_start: 0.6833 (pm20) cc_final: 0.6492 (pm20) REVERT: J 522 LYS cc_start: 0.8220 (tttp) cc_final: 0.7526 (tttp) REVERT: J 529 LYS cc_start: 0.8283 (tppt) cc_final: 0.7305 (tppt) REVERT: J 544 THR cc_start: 0.7873 (p) cc_final: 0.7235 (p) REVERT: J 586 LYS cc_start: 0.6991 (mptt) cc_final: 0.6389 (mmtp) REVERT: J 692 TYR cc_start: 0.8369 (t80) cc_final: 0.8129 (t80) REVERT: K 875 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8097 (p) REVERT: K 876 LYS cc_start: 0.7981 (tttp) cc_final: 0.7624 (tttm) REVERT: K 938 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8204 (mtmm) REVERT: K 960 ASP cc_start: 0.7618 (p0) cc_final: 0.7405 (p0) REVERT: K 970 THR cc_start: 0.8444 (t) cc_final: 0.8192 (p) REVERT: K 1014 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7890 (mmt90) REVERT: K 1019 GLN cc_start: 0.8223 (mt0) cc_final: 0.8015 (mt0) REVERT: K 1022 THR cc_start: 0.8529 (t) cc_final: 0.8019 (p) REVERT: K 1115 THR cc_start: 0.8641 (t) cc_final: 0.8345 (p) REVERT: K 1130 VAL cc_start: 0.8067 (p) cc_final: 0.7809 (t) outliers start: 133 outliers final: 92 residues processed: 820 average time/residue: 0.1723 time to fit residues: 217.4442 Evaluate side-chains 850 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 749 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 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 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 1199 LYS Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE 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 674 LEU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 694 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 833 HIS Chi-restraints excluded: chain G residue 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 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 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 177 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 834 ILE Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 875 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 1043 MET Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1185 CYS 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 120 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 296 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C1019 GLN F 517 GLN F 545 ASN ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 ASN J 559 HIS J 686 GLN J 689 GLN K1079 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106383 restraints weight = 40434.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109687 restraints weight = 17076.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111783 restraints weight = 9198.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113108 restraints weight = 5906.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114017 restraints weight = 4345.113| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24964 Z= 0.135 Angle : 0.643 17.992 34036 Z= 0.322 Chirality : 0.045 0.542 3804 Planarity : 0.005 0.049 4362 Dihedral : 4.691 54.784 3691 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.86 % Allowed : 29.83 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3106 helix: 2.84 (0.28), residues: 324 sheet: 0.37 (0.17), residues: 969 loop : -1.11 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 836 TYR 0.031 0.002 TYR B 397 PHE 0.026 0.001 PHE C1235 TRP 0.009 0.001 TRP B 642 HIS 0.010 0.001 HIS J 623 Details of bonding type rmsd covalent geometry : bond 0.00314 (24901) covalent geometry : angle 0.62307 (33895) SS BOND : bond 0.00384 ( 48) SS BOND : angle 1.41408 ( 96) hydrogen bonds : bond 0.03967 ( 943) hydrogen bonds : angle 4.60957 ( 2466) link_BETA1-4 : bond 0.00375 ( 6) link_BETA1-4 : angle 1.20783 ( 18) link_NAG-ASN : bond 0.00924 ( 9) link_NAG-ASN : angle 5.11382 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 762 time to evaluate : 0.945 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: 0.7696 (mmmt) cc_final: 0.7122 (mmmt) REVERT: A 258 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7682 (ttp-110) REVERT: B 394 ASN cc_start: 0.7980 (p0) cc_final: 0.7680 (p0) REVERT: B 395 HIS cc_start: 0.7529 (t70) cc_final: 0.7003 (t70) REVERT: B 396 ASP cc_start: 0.7772 (t0) cc_final: 0.7208 (t0) REVERT: B 462 TYR cc_start: 0.8034 (t80) cc_final: 0.7516 (t80) REVERT: B 484 ILE cc_start: 0.8259 (mm) cc_final: 0.8008 (mt) REVERT: B 517 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7751 (mm-40) REVERT: C 920 GLU cc_start: 0.7553 (pm20) cc_final: 0.7296 (pm20) REVERT: C 954 ASN cc_start: 0.7782 (p0) cc_final: 0.7415 (p0) REVERT: C 983 SER cc_start: 0.8784 (t) cc_final: 0.8233 (p) REVERT: C 997 ASP cc_start: 0.7831 (p0) cc_final: 0.6879 (p0) REVERT: C 998 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6152 (mp0) REVERT: C 1014 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8218 (mmt180) REVERT: C 1018 ILE cc_start: 0.8075 (pt) cc_final: 0.7867 (pt) REVERT: C 1021 ARG cc_start: 0.8963 (tpp-160) cc_final: 0.8445 (tpt170) REVERT: C 1024 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6926 (mm-30) REVERT: C 1059 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8001 (mp) REVERT: C 1069 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8179 (ttpp) REVERT: C 1095 MET cc_start: 0.7005 (ppp) cc_final: 0.6323 (ppp) REVERT: C 1117 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 1166 LYS cc_start: 0.8527 (mmtp) cc_final: 0.8166 (mmtp) REVERT: C 1227 LYS cc_start: 0.8284 (mttt) cc_final: 0.7881 (mttt) REVERT: E 113 MET cc_start: 0.5170 (mmp) cc_final: 0.4842 (mmp) REVERT: E 178 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.5194 (ppt170) REVERT: F 370 VAL cc_start: 0.8641 (t) cc_final: 0.8405 (m) REVERT: F 394 ASN cc_start: 0.7729 (t0) cc_final: 0.7336 (t0) REVERT: F 396 ASP cc_start: 0.7070 (t0) cc_final: 0.6751 (t0) REVERT: F 399 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8178 (mtpp) REVERT: F 548 MET cc_start: 0.7177 (mpp) cc_final: 0.6711 (mpp) REVERT: F 584 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5133 (ttmm) REVERT: F 586 LYS cc_start: 0.7385 (pttt) cc_final: 0.7077 (pptt) REVERT: F 638 TYR cc_start: 0.8540 (p90) cc_final: 0.8262 (p90) REVERT: F 694 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7872 (mp) REVERT: F 699 THR cc_start: 0.7962 (t) cc_final: 0.7739 (p) REVERT: G 912 ASP cc_start: 0.7779 (m-30) cc_final: 0.7415 (t0) REVERT: G 914 GLU cc_start: 0.7605 (mp0) cc_final: 0.6961 (mp0) REVERT: G 945 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7674 (mtpp) REVERT: G 989 ASP cc_start: 0.7192 (m-30) cc_final: 0.6934 (m-30) REVERT: G 1019 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7328 (mm-40) REVERT: G 1059 LEU cc_start: 0.8441 (tp) cc_final: 0.8112 (mt) REVERT: G 1061 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6896 (tm-30) REVERT: G 1113 ASP cc_start: 0.7633 (t0) cc_final: 0.7360 (t0) REVERT: G 1144 SER cc_start: 0.8572 (t) cc_final: 0.8234 (m) REVERT: G 1227 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8010 (mtmm) REVERT: I 113 MET cc_start: 0.7256 (mmm) cc_final: 0.6858 (mmm) REVERT: I 124 LYS cc_start: 0.7815 (tppt) cc_final: 0.7476 (tppt) REVERT: I 126 GLU cc_start: 0.6295 (tp30) cc_final: 0.5744 (tp30) REVERT: I 221 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7463 (mtt180) REVERT: J 402 TYR cc_start: 0.8216 (p90) cc_final: 0.7829 (p90) REVERT: J 435 LEU cc_start: 0.8056 (tp) cc_final: 0.7570 (tt) REVERT: J 467 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7181 (mm-40) REVERT: J 486 CYS cc_start: 0.5391 (p) cc_final: 0.4955 (p) REVERT: J 496 THR cc_start: 0.7873 (p) cc_final: 0.7554 (p) REVERT: J 498 GLU cc_start: 0.6851 (pm20) cc_final: 0.6494 (pm20) REVERT: J 522 LYS cc_start: 0.8217 (tttp) cc_final: 0.7506 (tttp) REVERT: J 529 LYS cc_start: 0.8278 (tppt) cc_final: 0.7298 (tppt) REVERT: J 544 THR cc_start: 0.7784 (p) cc_final: 0.7125 (p) REVERT: J 545 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8494 (t0) REVERT: J 586 LYS cc_start: 0.6935 (mptt) cc_final: 0.6309 (mttm) REVERT: J 692 TYR cc_start: 0.8278 (t80) cc_final: 0.7996 (t80) REVERT: J 735 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7124 (p) REVERT: K 875 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (p) REVERT: K 876 LYS cc_start: 0.7927 (tttp) cc_final: 0.7575 (tttm) REVERT: K 928 VAL cc_start: 0.8982 (p) cc_final: 0.8718 (t) REVERT: K 938 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8175 (mtmm) REVERT: K 970 THR cc_start: 0.8435 (t) cc_final: 0.8172 (p) REVERT: K 986 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8378 (p) REVERT: K 1022 THR cc_start: 0.8555 (t) cc_final: 0.8060 (p) REVERT: K 1115 THR cc_start: 0.8619 (t) cc_final: 0.8333 (p) REVERT: K 1130 VAL cc_start: 0.8032 (p) cc_final: 0.7793 (t) outliers start: 129 outliers final: 95 residues processed: 816 average time/residue: 0.1793 time to fit residues: 222.7506 Evaluate side-chains 857 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 750 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 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 511 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET 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 1014 ARG Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1069 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 135 LEU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 186 HIS 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 E residue 257 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 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 G residue 817 GLU Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 833 HIS Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 854 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1118 VAL Chi-restraints excluded: chain G residue 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 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 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 605 GLU Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 655 VAL Chi-restraints excluded: chain J residue 689 GLN 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 875 VAL Chi-restraints excluded: chain K residue 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1112 ILE Chi-restraints excluded: chain K residue 1116 CYS Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 0.0040 chunk 274 optimal weight: 0.0870 chunk 265 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 545 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS G 954 ASN ** G 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 GLN J 545 ASN J 559 HIS J 686 GLN J 689 GLN K1079 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107823 restraints weight = 40461.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111092 restraints weight = 17176.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113202 restraints weight = 9270.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114556 restraints weight = 5987.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115271 restraints weight = 4437.608| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24964 Z= 0.114 Angle : 0.639 17.680 34036 Z= 0.318 Chirality : 0.044 0.534 3804 Planarity : 0.004 0.050 4362 Dihedral : 4.530 52.615 3691 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.41 % Allowed : 30.35 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3106 helix: 2.89 (0.28), residues: 324 sheet: 0.43 (0.16), residues: 978 loop : -1.09 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1082 TYR 0.029 0.001 TYR K 861 PHE 0.014 0.001 PHE C 910 TRP 0.012 0.001 TRP I 251 HIS 0.011 0.001 HIS F 559 Details of bonding type rmsd covalent geometry : bond 0.00260 (24901) covalent geometry : angle 0.61981 (33895) SS BOND : bond 0.00348 ( 48) SS BOND : angle 1.40184 ( 96) hydrogen bonds : bond 0.03596 ( 943) hydrogen bonds : angle 4.50528 ( 2466) link_BETA1-4 : bond 0.00469 ( 6) link_BETA1-4 : angle 1.16758 ( 18) link_NAG-ASN : bond 0.00926 ( 9) link_NAG-ASN : angle 4.94573 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 765 time to evaluate : 0.929 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: 0.7681 (mmmt) cc_final: 0.7123 (mmmt) REVERT: A 258 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7627 (ttp-110) REVERT: B 343 LYS cc_start: 0.8796 (mptt) cc_final: 0.8511 (mptt) REVERT: B 394 ASN cc_start: 0.8115 (p0) cc_final: 0.7835 (p0) REVERT: B 395 HIS cc_start: 0.7476 (t70) cc_final: 0.6953 (t70) REVERT: B 396 ASP cc_start: 0.7732 (t0) cc_final: 0.7111 (t0) REVERT: B 435 LEU cc_start: 0.8034 (tt) cc_final: 0.7823 (tp) REVERT: B 462 TYR cc_start: 0.8014 (t80) cc_final: 0.7553 (t80) REVERT: B 714 ILE cc_start: 0.8478 (tp) cc_final: 0.8262 (tt) REVERT: C 920 GLU cc_start: 0.7570 (pm20) cc_final: 0.7289 (pm20) REVERT: C 954 ASN cc_start: 0.7622 (p0) cc_final: 0.7272 (p0) REVERT: C 983 SER cc_start: 0.8791 (t) cc_final: 0.8245 (p) REVERT: C 997 ASP cc_start: 0.7794 (p0) cc_final: 0.6813 (p0) REVERT: C 998 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6110 (mp0) REVERT: C 1018 ILE cc_start: 0.8094 (pt) cc_final: 0.7891 (pt) REVERT: C 1021 ARG cc_start: 0.8967 (tpp-160) cc_final: 0.8340 (tpt170) REVERT: C 1024 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6901 (mm-30) REVERT: C 1059 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 1069 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8086 (ttpp) REVERT: C 1095 MET cc_start: 0.7002 (ppp) cc_final: 0.6319 (ppp) REVERT: C 1117 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (p) REVERT: C 1166 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8163 (mmtp) REVERT: C 1227 LYS cc_start: 0.8271 (mttt) cc_final: 0.7836 (mttt) REVERT: E 113 MET cc_start: 0.5206 (mmp) cc_final: 0.4880 (mmp) REVERT: E 178 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.5303 (ppt170) REVERT: F 394 ASN cc_start: 0.7790 (t0) cc_final: 0.7318 (t0) REVERT: F 396 ASP cc_start: 0.7059 (t0) cc_final: 0.6708 (t0) REVERT: F 399 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8150 (mtpp) REVERT: F 548 MET cc_start: 0.7169 (mpp) cc_final: 0.6739 (mpp) REVERT: F 584 LYS cc_start: 0.5413 (OUTLIER) cc_final: 0.5065 (ttmm) REVERT: F 586 LYS cc_start: 0.7353 (pttt) cc_final: 0.7045 (pptt) REVERT: F 638 TYR cc_start: 0.8510 (p90) cc_final: 0.8203 (p90) REVERT: G 912 ASP cc_start: 0.7756 (m-30) cc_final: 0.7374 (t0) REVERT: G 914 GLU cc_start: 0.7597 (mp0) cc_final: 0.6939 (mp0) REVERT: G 930 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7860 (ttp-110) REVERT: G 945 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7606 (mtpp) REVERT: G 989 ASP cc_start: 0.7195 (m-30) cc_final: 0.6967 (m-30) REVERT: G 1019 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7327 (mm-40) REVERT: G 1059 LEU cc_start: 0.8400 (tp) cc_final: 0.8091 (mt) REVERT: G 1061 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6832 (tm-30) REVERT: G 1082 ARG cc_start: 0.8418 (ptt90) cc_final: 0.8118 (ptt-90) REVERT: G 1113 ASP cc_start: 0.7626 (t0) cc_final: 0.7354 (t0) REVERT: G 1144 SER cc_start: 0.8497 (t) cc_final: 0.8148 (m) REVERT: G 1148 HIS cc_start: 0.8265 (m-70) cc_final: 0.7891 (m-70) REVERT: G 1213 VAL cc_start: 0.8574 (p) cc_final: 0.8368 (t) REVERT: I 113 MET cc_start: 0.7293 (mmm) cc_final: 0.6902 (mmm) REVERT: I 126 GLU cc_start: 0.6189 (tp30) cc_final: 0.5638 (tp30) REVERT: I 142 LYS cc_start: 0.8007 (tttt) cc_final: 0.7686 (ttpt) REVERT: I 221 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7405 (mtt180) REVERT: J 402 TYR cc_start: 0.8094 (p90) cc_final: 0.7880 (p90) REVERT: J 435 LEU cc_start: 0.8013 (tp) cc_final: 0.7561 (tt) REVERT: J 467 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7201 (mm-40) REVERT: J 486 CYS cc_start: 0.5416 (p) cc_final: 0.5008 (p) REVERT: J 522 LYS cc_start: 0.8218 (tttp) cc_final: 0.7492 (tttp) REVERT: J 529 LYS cc_start: 0.8240 (tppt) cc_final: 0.7411 (tppt) REVERT: J 544 THR cc_start: 0.7818 (p) cc_final: 0.7224 (p) REVERT: J 577 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7717 (ptp-170) REVERT: J 586 LYS cc_start: 0.6926 (mptt) cc_final: 0.6350 (mttm) REVERT: J 692 TYR cc_start: 0.8161 (t80) cc_final: 0.7887 (t80) REVERT: J 735 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7076 (p) REVERT: K 876 LYS cc_start: 0.7884 (tttp) cc_final: 0.7526 (tttm) REVERT: K 928 VAL cc_start: 0.8949 (p) cc_final: 0.8660 (t) REVERT: K 938 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8157 (mtmm) REVERT: K 970 THR cc_start: 0.8443 (t) cc_final: 0.8141 (p) REVERT: K 986 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 1014 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7826 (mmt90) REVERT: K 1022 THR cc_start: 0.8581 (t) cc_final: 0.8106 (p) REVERT: K 1029 TYR cc_start: 0.8264 (t80) cc_final: 0.8024 (t80) REVERT: K 1115 THR cc_start: 0.8627 (t) cc_final: 0.8325 (p) REVERT: K 1130 VAL cc_start: 0.8022 (p) cc_final: 0.7766 (t) outliers start: 117 outliers final: 89 residues processed: 815 average time/residue: 0.1766 time to fit residues: 219.7282 Evaluate side-chains 863 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 765 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1069 LYS Chi-restraints excluded: chain C residue 1107 GLU 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 1223 SER Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 499 GLU 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 589 ILE 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 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 833 HIS 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 1160 LYS Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1199 LYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 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 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 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 689 GLN Chi-restraints excluded: chain J residue 694 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 929 CYS Chi-restraints excluded: chain K residue 975 GLN Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1075 GLN Chi-restraints excluded: chain K residue 1079 ASN 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 9 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN F 517 GLN G 954 ASN J 545 ASN J 559 HIS J 686 GLN J 689 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107759 restraints weight = 40333.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110898 restraints weight = 16931.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112903 restraints weight = 9050.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114113 restraints weight = 5810.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115019 restraints weight = 4306.738| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24964 Z= 0.128 Angle : 0.645 17.814 34036 Z= 0.320 Chirality : 0.045 0.534 3804 Planarity : 0.004 0.048 4362 Dihedral : 4.498 53.731 3691 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.37 % Allowed : 30.73 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3106 helix: 2.83 (0.28), residues: 324 sheet: 0.46 (0.16), residues: 978 loop : -1.05 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 836 TYR 0.028 0.002 TYR B 397 PHE 0.026 0.001 PHE C1235 TRP 0.018 0.001 TRP I 251 HIS 0.008 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00301 (24901) covalent geometry : angle 0.62517 (33895) SS BOND : bond 0.00365 ( 48) SS BOND : angle 1.49928 ( 96) hydrogen bonds : bond 0.03677 ( 943) hydrogen bonds : angle 4.48097 ( 2466) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 1.18297 ( 18) link_NAG-ASN : bond 0.00893 ( 9) link_NAG-ASN : angle 4.96882 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 769 time to evaluate : 0.960 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: 0.7645 (mmmt) cc_final: 0.7100 (mmmt) REVERT: A 258 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7607 (ttp-110) REVERT: B 343 LYS cc_start: 0.8794 (mptt) cc_final: 0.8535 (mptt) REVERT: B 394 ASN cc_start: 0.8108 (p0) cc_final: 0.7836 (p0) REVERT: B 395 HIS cc_start: 0.7457 (t70) cc_final: 0.6902 (t70) REVERT: B 396 ASP cc_start: 0.7745 (t0) cc_final: 0.7138 (t0) REVERT: B 435 LEU cc_start: 0.8051 (tt) cc_final: 0.7815 (tp) REVERT: B 462 TYR cc_start: 0.8033 (t80) cc_final: 0.7510 (t80) REVERT: B 714 ILE cc_start: 0.8521 (tp) cc_final: 0.8308 (tt) REVERT: C 845 GLN cc_start: 0.7718 (mt0) cc_final: 0.7451 (mt0) REVERT: C 917 GLN cc_start: 0.8521 (tt0) cc_final: 0.8277 (tt0) REVERT: C 920 GLU cc_start: 0.7560 (pm20) cc_final: 0.7320 (pm20) REVERT: C 954 ASN cc_start: 0.7716 (p0) cc_final: 0.7340 (p0) REVERT: C 983 SER cc_start: 0.8802 (t) cc_final: 0.8259 (p) REVERT: C 997 ASP cc_start: 0.7783 (p0) cc_final: 0.6792 (p0) REVERT: C 998 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6129 (mp0) REVERT: C 1021 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8430 (tpt170) REVERT: C 1024 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6902 (mm-30) REVERT: C 1059 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 1069 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (ttpp) REVERT: C 1095 MET cc_start: 0.6992 (ppp) cc_final: 0.6305 (ppp) REVERT: C 1117 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (p) REVERT: C 1160 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7325 (mmtp) REVERT: C 1166 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8171 (mmtp) REVERT: C 1227 LYS cc_start: 0.8259 (mttt) cc_final: 0.7828 (mttt) REVERT: E 113 MET cc_start: 0.5122 (mmp) cc_final: 0.4800 (mmp) REVERT: E 178 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.5128 (ppt170) REVERT: F 370 VAL cc_start: 0.8628 (t) cc_final: 0.8402 (m) REVERT: F 394 ASN cc_start: 0.7758 (t0) cc_final: 0.7349 (t0) REVERT: F 396 ASP cc_start: 0.7023 (t0) cc_final: 0.6695 (t0) REVERT: F 399 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8188 (mtpp) REVERT: F 548 MET cc_start: 0.7149 (mpp) cc_final: 0.6661 (mpp) REVERT: F 584 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5037 (ttmm) REVERT: F 586 LYS cc_start: 0.7371 (pttt) cc_final: 0.7059 (pptt) REVERT: F 638 TYR cc_start: 0.8508 (p90) cc_final: 0.8200 (p90) REVERT: G 912 ASP cc_start: 0.7751 (m-30) cc_final: 0.7383 (t0) REVERT: G 914 GLU cc_start: 0.7580 (mp0) cc_final: 0.6960 (mp0) REVERT: G 930 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: G 945 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7618 (mtpp) REVERT: G 989 ASP cc_start: 0.7198 (m-30) cc_final: 0.6957 (m-30) REVERT: G 1019 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7328 (mm-40) REVERT: G 1023 VAL cc_start: 0.8745 (t) cc_final: 0.8503 (p) REVERT: G 1059 LEU cc_start: 0.8417 (tp) cc_final: 0.8125 (mt) REVERT: G 1061 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6872 (tm-30) REVERT: G 1082 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8141 (ptt-90) REVERT: G 1113 ASP cc_start: 0.7623 (t0) cc_final: 0.7344 (t0) REVERT: G 1144 SER cc_start: 0.8492 (t) cc_final: 0.8167 (m) REVERT: I 126 GLU cc_start: 0.6184 (tp30) cc_final: 0.5646 (tp30) REVERT: I 142 LYS cc_start: 0.8123 (tttt) cc_final: 0.7849 (ttpt) REVERT: I 190 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: I 221 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7408 (mtt180) REVERT: J 387 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7351 (mt) REVERT: J 402 TYR cc_start: 0.8149 (p90) cc_final: 0.7794 (p90) REVERT: J 435 LEU cc_start: 0.7992 (tp) cc_final: 0.7556 (tt) REVERT: J 467 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7199 (mm-40) REVERT: J 486 CYS cc_start: 0.5414 (p) cc_final: 0.4990 (p) REVERT: J 511 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8222 (tpt-90) REVERT: J 529 LYS cc_start: 0.8326 (tppt) cc_final: 0.7534 (tppt) REVERT: J 544 THR cc_start: 0.7864 (p) cc_final: 0.7448 (p) REVERT: J 577 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7744 (ptp-170) REVERT: J 586 LYS cc_start: 0.6972 (mptt) cc_final: 0.6388 (mttm) REVERT: J 692 TYR cc_start: 0.8193 (t80) cc_final: 0.7932 (t80) REVERT: J 735 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7122 (p) REVERT: K 822 MET cc_start: 0.7987 (ptp) cc_final: 0.7780 (ptt) REVERT: K 876 LYS cc_start: 0.7930 (tttp) cc_final: 0.7544 (tttm) REVERT: K 928 VAL cc_start: 0.8956 (p) cc_final: 0.8658 (t) REVERT: K 938 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8168 (mtmm) REVERT: K 970 THR cc_start: 0.8442 (t) cc_final: 0.8135 (p) REVERT: K 986 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8382 (p) REVERT: K 1014 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7773 (mmt90) REVERT: K 1022 THR cc_start: 0.8566 (t) cc_final: 0.8086 (p) REVERT: K 1029 TYR cc_start: 0.8311 (t80) cc_final: 0.8079 (t80) REVERT: K 1050 GLN cc_start: 0.8352 (tt0) cc_final: 0.8144 (tt0) REVERT: K 1115 THR cc_start: 0.8641 (t) cc_final: 0.8335 (p) REVERT: K 1130 VAL cc_start: 0.8058 (p) cc_final: 0.7788 (t) outliers start: 116 outliers final: 88 residues processed: 821 average time/residue: 0.1829 time to fit residues: 230.3308 Evaluate side-chains 854 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 755 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1069 LYS 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 1223 SER Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 517 GLN Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 534 CYS Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 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 706 MET Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 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 1160 LYS Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1199 LYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 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 365 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS 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 689 GLN Chi-restraints excluded: chain J residue 694 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 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 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 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 196 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 G 954 ASN G1002 GLN J 545 ASN J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107073 restraints weight = 40430.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110328 restraints weight = 17194.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112415 restraints weight = 9305.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113731 restraints weight = 6024.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114662 restraints weight = 4463.628| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.454 24964 Z= 0.219 Angle : 0.835 59.200 34036 Z= 0.441 Chirality : 0.046 0.573 3804 Planarity : 0.005 0.118 4362 Dihedral : 4.495 53.715 3691 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.22 % Allowed : 31.15 % Favored : 64.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3106 helix: 2.83 (0.28), residues: 324 sheet: 0.46 (0.16), residues: 978 loop : -1.06 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 836 TYR 0.027 0.002 TYR K 861 PHE 0.031 0.001 PHE C1072 TRP 0.016 0.001 TRP I 251 HIS 0.006 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00520 (24901) covalent geometry : angle 0.78690 (33895) SS BOND : bond 0.02968 ( 48) SS BOND : angle 4.64083 ( 96) hydrogen bonds : bond 0.03731 ( 943) hydrogen bonds : angle 4.48638 ( 2466) link_BETA1-4 : bond 0.00345 ( 6) link_BETA1-4 : angle 1.17317 ( 18) link_NAG-ASN : bond 0.00891 ( 9) link_NAG-ASN : angle 4.96656 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 754 time to evaluate : 0.971 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: 0.7655 (mmmt) cc_final: 0.7182 (mmmt) REVERT: A 258 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7613 (ttp-110) REVERT: B 343 LYS cc_start: 0.8787 (mptt) cc_final: 0.8532 (mptt) REVERT: B 394 ASN cc_start: 0.8100 (p0) cc_final: 0.7821 (p0) REVERT: B 395 HIS cc_start: 0.7466 (t70) cc_final: 0.6912 (t70) REVERT: B 396 ASP cc_start: 0.7757 (t0) cc_final: 0.7137 (t0) REVERT: B 435 LEU cc_start: 0.8048 (tt) cc_final: 0.7816 (tp) REVERT: B 462 TYR cc_start: 0.8037 (t80) cc_final: 0.7505 (t80) REVERT: B 714 ILE cc_start: 0.8494 (tp) cc_final: 0.8284 (tt) REVERT: C 845 GLN cc_start: 0.7728 (mt0) cc_final: 0.7455 (mt0) REVERT: C 917 GLN cc_start: 0.8519 (tt0) cc_final: 0.8276 (tt0) REVERT: C 920 GLU cc_start: 0.7562 (pm20) cc_final: 0.7311 (pm20) REVERT: C 954 ASN cc_start: 0.7724 (p0) cc_final: 0.7349 (p0) REVERT: C 983 SER cc_start: 0.8789 (t) cc_final: 0.8256 (p) REVERT: C 997 ASP cc_start: 0.7787 (p0) cc_final: 0.6794 (p0) REVERT: C 998 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6133 (mp0) REVERT: C 1021 ARG cc_start: 0.8970 (tpp-160) cc_final: 0.8419 (mmt180) REVERT: C 1024 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6906 (mm-30) REVERT: C 1059 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (mp) REVERT: C 1069 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8112 (ttpp) REVERT: C 1095 MET cc_start: 0.6977 (ppp) cc_final: 0.6295 (ppp) REVERT: C 1117 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8146 (p) REVERT: C 1160 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7277 (mmtp) REVERT: C 1166 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8173 (mmtp) REVERT: C 1227 LYS cc_start: 0.8262 (mttt) cc_final: 0.7833 (mttt) REVERT: E 113 MET cc_start: 0.5197 (mmp) cc_final: 0.4870 (mmp) REVERT: E 178 ARG cc_start: 0.5552 (OUTLIER) cc_final: 0.5123 (ppt170) REVERT: F 394 ASN cc_start: 0.7788 (t0) cc_final: 0.7349 (t0) REVERT: F 396 ASP cc_start: 0.7038 (t0) cc_final: 0.6696 (t0) REVERT: F 399 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8194 (mtpp) REVERT: F 459 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (ttm170) REVERT: F 529 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7963 (mmtp) REVERT: F 548 MET cc_start: 0.7112 (mpp) cc_final: 0.6606 (mpp) REVERT: F 584 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.5047 (ttmm) REVERT: F 586 LYS cc_start: 0.7375 (pttt) cc_final: 0.7062 (pptt) REVERT: F 638 TYR cc_start: 0.8510 (p90) cc_final: 0.8202 (p90) REVERT: G 912 ASP cc_start: 0.7773 (m-30) cc_final: 0.7385 (t0) REVERT: G 914 GLU cc_start: 0.7584 (mp0) cc_final: 0.6950 (mp0) REVERT: G 930 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: G 945 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7623 (mtpp) REVERT: G 989 ASP cc_start: 0.7206 (m-30) cc_final: 0.6963 (m-30) REVERT: G 1019 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7330 (mm-40) REVERT: G 1023 VAL cc_start: 0.8749 (t) cc_final: 0.8502 (p) REVERT: G 1059 LEU cc_start: 0.8419 (tp) cc_final: 0.8127 (mt) REVERT: G 1061 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6873 (tm-30) REVERT: G 1082 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8133 (ptt-90) REVERT: G 1113 ASP cc_start: 0.7630 (t0) cc_final: 0.7354 (t0) REVERT: G 1144 SER cc_start: 0.8496 (t) cc_final: 0.8174 (m) REVERT: I 126 GLU cc_start: 0.6209 (tp30) cc_final: 0.5659 (tp30) REVERT: I 142 LYS cc_start: 0.8117 (tttt) cc_final: 0.7842 (ttpt) REVERT: I 190 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: I 221 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7428 (mtt180) REVERT: J 387 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7347 (mt) REVERT: J 402 TYR cc_start: 0.8141 (p90) cc_final: 0.7779 (p90) REVERT: J 435 LEU cc_start: 0.7994 (tp) cc_final: 0.7559 (tt) REVERT: J 467 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7199 (mm-40) REVERT: J 511 ARG cc_start: 0.8514 (mmt90) cc_final: 0.8248 (tpt-90) REVERT: J 529 LYS cc_start: 0.8317 (tppt) cc_final: 0.7509 (tppt) REVERT: J 544 THR cc_start: 0.7844 (p) cc_final: 0.7421 (p) REVERT: J 577 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7736 (ptp-170) REVERT: J 586 LYS cc_start: 0.6963 (mptt) cc_final: 0.6372 (mttm) REVERT: J 692 TYR cc_start: 0.8198 (t80) cc_final: 0.7930 (t80) REVERT: J 735 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7119 (p) REVERT: K 822 MET cc_start: 0.7992 (ptp) cc_final: 0.7774 (ptt) REVERT: K 876 LYS cc_start: 0.7899 (tttp) cc_final: 0.7520 (tttm) REVERT: K 938 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8167 (mtmm) REVERT: K 970 THR cc_start: 0.8442 (t) cc_final: 0.8138 (p) REVERT: K 986 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8385 (p) REVERT: K 1014 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7772 (mmt90) REVERT: K 1022 THR cc_start: 0.8565 (t) cc_final: 0.8085 (p) REVERT: K 1029 TYR cc_start: 0.8306 (t80) cc_final: 0.8080 (t80) REVERT: K 1115 THR cc_start: 0.8635 (t) cc_final: 0.8329 (p) REVERT: K 1130 VAL cc_start: 0.8052 (p) cc_final: 0.7782 (t) outliers start: 112 outliers final: 91 residues processed: 806 average time/residue: 0.1755 time to fit residues: 216.3721 Evaluate side-chains 854 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 751 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1069 LYS 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 1223 SER Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR 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 499 GLU 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 589 ILE Chi-restraints excluded: chain F residue 597 THR 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 706 MET Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain G residue 846 MET Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 958 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 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 G residue 1199 LYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 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 426 VAL Chi-restraints excluded: chain J residue 528 LYS Chi-restraints excluded: chain J residue 534 CYS 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 689 GLN Chi-restraints excluded: chain J residue 694 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 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 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 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 139 optimal weight: 8.9990 chunk 112 optimal weight: 0.0170 chunk 261 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 233 optimal weight: 0.4980 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 954 ASN G1002 GLN J 545 ASN J 559 HIS J 686 GLN ** J 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105834 restraints weight = 40745.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109104 restraints weight = 17351.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111206 restraints weight = 9378.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112578 restraints weight = 6056.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113381 restraints weight = 4479.173| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.454 24964 Z= 0.219 Angle : 0.875 59.200 34036 Z= 0.459 Chirality : 0.046 0.573 3804 Planarity : 0.005 0.118 4362 Dihedral : 4.495 53.715 3691 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.00 % Allowed : 31.15 % Favored : 64.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3106 helix: 2.83 (0.28), residues: 324 sheet: 0.46 (0.16), residues: 978 loop : -1.06 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 836 TYR 0.027 0.002 TYR K 861 PHE 0.031 0.001 PHE C1072 TRP 0.016 0.001 TRP I 251 HIS 0.006 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00520 (24901) covalent geometry : angle 0.78690 (33895) SS BOND : bond 0.02956 ( 48) SS BOND : angle 6.76353 ( 96) hydrogen bonds : bond 0.03731 ( 943) hydrogen bonds : angle 4.48638 ( 2466) link_BETA1-4 : bond 0.00345 ( 6) link_BETA1-4 : angle 1.17317 ( 18) link_NAG-ASN : bond 0.00891 ( 9) link_NAG-ASN : angle 4.96656 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.52 seconds wall clock time: 94 minutes 17.29 seconds (5657.29 seconds total)