Starting phenix.real_space_refine on Sat Jun 21 07:16:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0l_37981/06_2025/8x0l_37981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.063 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 3 9.91 5 S 195 5.16 5 C 15438 2.51 5 N 4251 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24555 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: "L" 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: "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: "R" 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.83, per 1000 atoms: 0.64 Number of scatterers: 24555 At special positions: 0 Unit cell: (188.1, 176, 196.9, 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 3 19.99 S 195 16.00 O 4668 8.00 N 4251 7.00 C 15438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 558 " distance=2.02 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=2.03 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=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS J 424 " - pdb=" SG CYS J 438 " distance=2.04 Simple disulfide: pdb=" SG CYS J 486 " - pdb=" SG CYS J 598 " distance=2.04 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=2.03 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 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 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 L 83 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 90 " - pdb=" SG CYS L 110 " distance=2.03 Simple disulfide: pdb=" SG CYS L 104 " - pdb=" SG CYS L 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 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 R 1 " - " NAG R 2 " NAG-ASN " NAG C1701 " - " ASN C 956 " " NAG G1701 " - " ASN G 956 " " NAG K1701 " - " ASN K 956 " " NAG M 1 " - " ASN B 533 " " NAG N 1 " - " ASN B 595 " " NAG O 1 " - " ASN F 533 " " NAG P 1 " - " ASN F 595 " " NAG Q 1 " - " ASN J 533 " " NAG R 1 " - " ASN J 595 " Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.3 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 58 sheets defined 14.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.805A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.669A pdb=" N VAL B 341 " --> pdb=" O HIS B 338 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 344 " --> pdb=" O VAL B 341 " (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 730 Processing helix chain 'B' and resid 731 through 734 Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'C' and resid 1053 through 1061 removed outlier: 3.699A 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: 4.023A pdb=" N GLY C1073 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.547A 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 removed outlier: 3.730A pdb=" N ALA C1101 " --> pdb=" O PRO C1098 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C1102 " --> pdb=" O ASP C1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1098 through 1102' Processing helix chain 'C' and resid 1219 through 1253 removed outlier: 3.617A pdb=" N ARG C1253 " --> pdb=" O ILE C1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 117 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.507A pdb=" N LYS E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 214 No H-bonds generated for 'chain 'E' and resid 212 through 214' Processing helix chain 'F' and resid 336 through 344 removed outlier: 4.555A pdb=" N VAL F 341 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 344 " --> pdb=" O VAL F 341 " (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 558 Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 695 through 729 Processing helix chain 'F' and resid 730 through 734 Processing helix chain 'F' and resid 743 through 748 Processing helix chain 'G' and resid 1053 through 1061 removed outlier: 3.615A pdb=" N GLU G1061 " --> pdb=" O TYR G1057 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1069 Processing helix chain 'G' and resid 1070 through 1074 removed outlier: 4.190A pdb=" N GLY G1073 " --> pdb=" O ALA G1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS G1074 " --> pdb=" O PRO G1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1070 through 1074' Processing helix chain 'G' and resid 1098 through 1102 removed outlier: 3.600A pdb=" N ALA G1101 " --> pdb=" O PRO G1098 " (cutoff:3.500A) removed outlier: 3.866A 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 Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.825A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 157 removed outlier: 3.625A pdb=" N LYS I 157 " --> pdb=" O ALA I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.542A pdb=" N ARG I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 345 removed outlier: 4.576A pdb=" N VAL J 341 " --> pdb=" O HIS J 338 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR J 345 " --> pdb=" O TYR J 342 " (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 Processing helix chain 'J' and resid 731 through 734 Processing helix chain 'J' and resid 741 through 748 Processing helix chain 'K' and resid 1053 through 1061 Processing helix chain 'K' and resid 1065 through 1069 Processing helix chain 'K' and resid 1219 through 1253 removed outlier: 3.541A pdb=" N ARG K1253 " --> pdb=" O ILE K1249 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'L' and resid 101 through 103 No H-bonds generated for 'chain 'L' and resid 101 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.908A pdb=" N GLY A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS A 125 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TYR A 132 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 193 removed outlier: 3.574A pdb=" N GLN A 201 " --> pdb=" O THR A 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 207 through 210 current: chain 'A' and resid 230 through 240 removed outlier: 6.224A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 350 through 352 removed outlier: 3.560A pdb=" N CYS B 361 " --> pdb=" O CYS B 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 371 removed outlier: 8.968A pdb=" N ILE B 367 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N SER B 384 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA B 369 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 27.501A pdb=" N LYS B 380 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 22.587A pdb=" N ASP B 404 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 16.933A pdb=" N GLN B 382 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 14.008A pdb=" N TYR B 402 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N SER B 384 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N ILE B 400 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N GLN B 386 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR B 398 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY B 388 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 417 through 419 removed outlier: 4.467A pdb=" N GLU B 442 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 489 Processing sheet with id=AA7, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AA8, first strand: chain 'B' and resid 514 through 517 Processing sheet with id=AA9, first strand: chain 'B' and resid 541 through 544 removed outlier: 3.518A pdb=" N GLY B 542 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.516A pdb=" N VAL B 647 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 639 through 643 Processing sheet with id=AB3, first strand: chain 'C' and resid 817 through 823 removed outlier: 3.600A pdb=" N GLN C 975 " --> pdb=" O ASN C1096 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 830 through 834 removed outlier: 3.540A pdb=" N TYR C 830 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N MET C 846 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET C 951 " --> pdb=" O MET C 846 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL C 848 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG C 949 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 850 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C 856 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR C 941 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN C 858 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA C 939 " --> pdb=" O ASN C 858 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C 860 " --> pdb=" O TYR C 937 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR C 937 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 862 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER C 935 " --> pdb=" O ILE C 862 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 955 through 962 current: chain 'C' and resid 998 through 1000 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 998 through 1000 current: chain 'C' and resid 1082 through 1084 Processing sheet with id=AB5, first strand: chain 'C' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 866 through 869 current: chain 'C' and resid 916 through 925 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1018 through 1019 Processing sheet with id=AB7, first strand: chain 'C' and resid 1035 through 1036 Processing sheet with id=AB8, first strand: chain 'C' and resid 1112 through 1121 removed outlier: 5.574A pdb=" N ASP C1113 " --> pdb=" O LYS C1136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS C1136 " --> pdb=" O ASP C1113 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C1130 " --> pdb=" O ALA C1119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1158 through 1161 removed outlier: 3.534A pdb=" N GLY C1141 " --> pdb=" O VAL C1161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.646A pdb=" N GLY E 131 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS E 125 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR E 132 " --> pdb=" O PRO E 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 140 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA E 171 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 168 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 163 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 191 through 195 removed outlier: 3.548A pdb=" N GLY E 191 " --> pdb=" O TYR E 202 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N ALA E 199 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN E 201 " --> pdb=" O THR E 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 206 through 210 current: chain 'E' and resid 230 through 240 removed outlier: 6.316A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 257 " --> pdb=" O THR E 250 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 350 through 352 removed outlier: 4.016A pdb=" N CYS F 352 " --> pdb=" O CYS F 361 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS F 361 " --> pdb=" O CYS F 352 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.195A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N SER F 384 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA F 403 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS F 399 " --> pdb=" O GLY F 388 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ASP F 390 " --> pdb=" O TYR F 397 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N TYR F 397 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 402 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 417 through 419 removed outlier: 4.277A pdb=" N GLU F 442 " --> pdb=" O TYR F 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 481 through 489 Processing sheet with id=AC7, first strand: chain 'F' and resid 569 through 570 removed outlier: 3.809A pdb=" N GLY F 585 " --> pdb=" O MET F 502 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AC9, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD1, first strand: chain 'F' and resid 607 through 609 Processing sheet with id=AD2, first strand: chain 'F' and resid 639 through 643 Processing sheet with id=AD3, first strand: chain 'G' and resid 817 through 823 Processing sheet with id=AD4, first strand: chain 'G' and resid 830 through 834 removed outlier: 3.590A pdb=" N TYR G 830 " --> pdb=" O MET G 846 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 842 through 857 current: chain 'G' and resid 934 through 952 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 955 through 962 current: chain 'G' and resid 998 through 1000 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 998 through 1000 current: chain 'G' and resid 1082 through 1084 Processing sheet with id=AD5, first strand: chain 'G' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 866 through 869 current: chain 'G' and resid 916 through 925 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 1018 through 1019 Processing sheet with id=AD7, first strand: chain 'G' and resid 1035 through 1036 Processing sheet with id=AD8, first strand: chain 'G' and resid 1112 through 1121 removed outlier: 5.561A pdb=" N ASP G1113 " --> pdb=" O LYS G1136 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS G1136 " --> pdb=" O ASP G1113 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G1130 " --> pdb=" O ALA G1119 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 1141 through 1144 removed outlier: 3.544A pdb=" N ALA G1159 " --> pdb=" O CYS G1143 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 1179 through 1184 Processing sheet with id=AE2, first strand: chain 'I' and resid 149 through 150 removed outlier: 3.745A pdb=" N VAL I 136 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER I 163 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 191 through 193 removed outlier: 4.115A pdb=" N GLY I 191 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN I 201 " --> pdb=" O THR I 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 206 through 210 current: chain 'I' and resid 230 through 240 removed outlier: 6.587A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY I 236 " --> pdb=" O SER I 247 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 257 " --> pdb=" O THR I 250 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 350 through 352 removed outlier: 4.131A pdb=" N CYS J 352 " --> pdb=" O CYS J 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS J 361 " --> pdb=" O CYS J 352 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 367 through 371 removed outlier: 8.986A pdb=" N ILE J 367 " --> pdb=" O SER J 384 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER J 384 " --> pdb=" O ILE J 367 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA J 369 " --> pdb=" O GLN J 382 " (cutoff:3.500A) removed outlier: 27.629A pdb=" N LYS J 380 " --> pdb=" O ASP J 404 " (cutoff:3.500A) removed outlier: 22.750A pdb=" N ASP J 404 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 16.974A pdb=" N GLN J 382 " --> pdb=" O TYR J 402 " (cutoff:3.500A) removed outlier: 13.954A pdb=" N TYR J 402 " --> pdb=" O GLN J 382 " (cutoff:3.500A) removed outlier: 11.606A pdb=" N SER J 384 " --> pdb=" O ILE J 400 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N ILE J 400 " --> pdb=" O SER J 384 " (cutoff:3.500A) removed outlier: 11.909A pdb=" N GLN J 386 " --> pdb=" O THR J 398 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N THR J 398 " --> pdb=" O GLN J 386 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY J 388 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 417 through 419 removed outlier: 4.322A pdb=" N GLU J 442 " --> pdb=" O TYR J 462 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 482 through 489 Processing sheet with id=AE8, first strand: chain 'J' and resid 569 through 570 Processing sheet with id=AE9, first strand: chain 'J' and resid 508 through 509 removed outlier: 3.571A pdb=" N THR J 508 " --> pdb=" O VAL J 562 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS J 559 " --> pdb=" O ASN J 533 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY J 542 " --> pdb=" O TYR J 532 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 514 through 517 removed outlier: 3.583A pdb=" N MET J 548 " --> pdb=" O ILE J 523 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 607 through 610 removed outlier: 3.543A pdb=" N THR J 607 " --> pdb=" O HIS J 618 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 639 through 643 Processing sheet with id=AF4, first strand: chain 'K' and resid 817 through 823 removed outlier: 3.534A pdb=" N THR K 974 " --> pdb=" O ILE K 971 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 830 through 836 removed outlier: 5.569A pdb=" N ARG K 836 " --> pdb=" O SER K 840 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER K 840 " --> pdb=" O ARG K 836 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS K 947 " --> pdb=" O VAL K 849 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR K 851 " --> pdb=" O LYS K 945 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS K 945 " --> pdb=" O THR K 851 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU K 853 " --> pdb=" O SER K 943 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER K 943 " --> pdb=" O LEU K 853 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR K 941 " --> pdb=" O PRO K 855 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU K 857 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA K 939 " --> pdb=" O LEU K 857 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU K 859 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR K 937 " --> pdb=" O LEU K 859 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR K 861 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N SER K 935 " --> pdb=" O TYR K 861 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 955 through 962 current: chain 'K' and resid 998 through 1000 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 998 through 1000 current: chain 'K' and resid 1082 through 1084 Processing sheet with id=AF6, first strand: chain 'K' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 866 through 869 current: chain 'K' and resid 915 through 925 No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'K' and resid 1018 through 1019 Processing sheet with id=AF8, first strand: chain 'K' and resid 1035 through 1036 Processing sheet with id=AF9, first strand: chain 'K' and resid 1112 through 1121 removed outlier: 5.661A pdb=" N ASP K1113 " --> pdb=" O LYS K1136 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS K1136 " --> pdb=" O ASP K1113 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL K1130 " --> pdb=" O ALA K1119 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 1158 through 1161 Processing sheet with id=AG2, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AG3, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AG4, first strand: chain 'L' and resid 87 through 89 774 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.69 Time building geometry restraints manager: 7.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8023 1.35 - 1.47: 6170 1.47 - 1.59: 10729 1.59 - 1.72: 2 1.72 - 1.84: 261 Bond restraints: 25185 Sorted by residual: bond pdb=" CB PRO A 216 " pdb=" CG PRO A 216 " ideal model delta sigma weight residual 1.492 1.649 -0.157 5.00e-02 4.00e+02 9.88e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" CB PRO I 143 " pdb=" CG PRO I 143 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.01e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 ... (remaining 25180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 34019 3.10 - 6.20: 229 6.20 - 9.30: 24 9.30 - 12.41: 4 12.41 - 15.51: 2 Bond angle restraints: 34278 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 96.49 15.51 1.40e+00 5.10e-01 1.23e+02 angle pdb=" CA PRO I 143 " pdb=" N PRO I 143 " pdb=" CD PRO I 143 " ideal model delta sigma weight residual 112.00 101.00 11.00 1.40e+00 5.10e-01 6.17e+01 angle pdb=" C CYS C1185 " pdb=" CA CYS C1185 " pdb=" CB CYS C1185 " ideal model delta sigma weight residual 116.54 110.85 5.69 1.15e+00 7.56e-01 2.45e+01 angle pdb=" CB MET I 255 " pdb=" CG MET I 255 " pdb=" SD MET I 255 " ideal model delta sigma weight residual 112.70 125.39 -12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CA CYS J 598 " pdb=" CB CYS J 598 " pdb=" SG CYS J 598 " ideal model delta sigma weight residual 114.40 124.08 -9.68 2.30e+00 1.89e-01 1.77e+01 ... (remaining 34273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13015 17.92 - 35.84: 1805 35.84 - 53.76: 446 53.76 - 71.69: 61 71.69 - 89.61: 18 Dihedral angle restraints: 15345 sinusoidal: 6204 harmonic: 9141 Sorted by residual: dihedral pdb=" CB CYS F 352 " pdb=" SG CYS F 352 " pdb=" SG CYS F 458 " pdb=" CB CYS F 458 " ideal model delta sinusoidal sigma weight residual 93.00 171.36 -78.36 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS K 877 " pdb=" SG CYS K 877 " pdb=" SG CYS K 909 " pdb=" CB CYS K 909 " ideal model delta sinusoidal sigma weight residual -86.00 -25.15 -60.85 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS H 104 " pdb=" SG CYS H 104 " pdb=" SG CYS H 119 " pdb=" CB CYS H 119 " ideal model delta sinusoidal sigma weight residual 93.00 152.50 -59.50 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 15342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3814 0.127 - 0.255: 28 0.255 - 0.382: 0 0.382 - 0.509: 0 0.509 - 0.636: 1 Chirality restraints: 3843 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 595 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 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 2.47 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN J 595 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3840 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 215 " 0.099 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO A 216 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 142 " -0.074 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO I 143 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO I 143 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO I 143 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 900 " -0.067 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO C 901 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 901 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 901 " -0.053 5.00e-02 4.00e+02 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 413 2.66 - 3.22: 21589 3.22 - 3.78: 34793 3.78 - 4.34: 44791 4.34 - 4.90: 76951 Nonbonded interactions: 178537 Sorted by model distance: nonbonded pdb=" O ASN B 545 " pdb=" ND2 ASN B 545 " model vdw 2.094 3.120 nonbonded pdb=" OD1 ASP G 989 " pdb=" N ASN G 990 " model vdw 2.107 3.120 nonbonded pdb=" OE1 GLU J 373 " pdb=" OH TYR J 489 " model vdw 2.120 3.040 nonbonded pdb=" OE1 GLU B 373 " pdb=" OH TYR B 489 " model vdw 2.131 3.040 nonbonded pdb=" OG SER K1025 " pdb=" OD1 ASP K1027 " model vdw 2.139 3.040 ... (remaining 178532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 59.620 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 0.157 25251 Z= 0.162 Angle : 0.736 18.434 34425 Z= 0.388 Chirality : 0.046 0.636 3843 Planarity : 0.006 0.136 4416 Dihedral : 16.756 89.607 9336 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.04 % Allowed : 33.22 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3141 helix: 2.52 (0.29), residues: 321 sheet: -0.23 (0.17), residues: 969 loop : -1.04 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 662 HIS 0.008 0.001 HIS F 559 PHE 0.034 0.001 PHE G 828 TYR 0.029 0.001 TYR B 629 ARG 0.013 0.001 ARG K1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00984 ( 9) link_NAG-ASN : angle 5.93462 ( 27) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 1.48171 ( 18) hydrogen bonds : bond 0.24437 ( 774) hydrogen bonds : angle 7.46455 ( 1986) SS BOND : bond 0.00376 ( 51) SS BOND : angle 1.70468 ( 102) covalent geometry : bond 0.00371 (25185) covalent geometry : angle 0.71118 (34278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 699 time to evaluate : 3.091 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: B 430 MET cc_start: 0.7461 (tmm) cc_final: 0.6920 (tmm) REVERT: B 743 THR cc_start: 0.8516 (m) cc_final: 0.8275 (p) REVERT: C 844 LEU cc_start: 0.7817 (tp) cc_final: 0.7604 (mt) REVERT: C 890 ASP cc_start: 0.8457 (t0) cc_final: 0.7790 (t0) REVERT: C 897 THR cc_start: 0.8694 (t) cc_final: 0.8386 (p) REVERT: C 1199 LYS cc_start: 0.7696 (mmtp) cc_final: 0.7489 (mmtp) REVERT: E 113 MET cc_start: 0.4227 (mmm) cc_final: 0.4004 (mmm) REVERT: F 355 CYS cc_start: 0.6071 (t) cc_final: 0.5821 (t) REVERT: F 376 ASP cc_start: 0.7080 (t0) cc_final: 0.6563 (t0) REVERT: F 571 ASN cc_start: 0.8044 (t0) cc_final: 0.7680 (t0) REVERT: F 591 PHE cc_start: 0.8259 (m-80) cc_final: 0.7841 (m-80) REVERT: F 622 ASP cc_start: 0.7661 (m-30) cc_final: 0.7445 (m-30) REVERT: F 704 VAL cc_start: 0.8315 (t) cc_final: 0.8102 (p) REVERT: G 903 MET cc_start: 0.7464 (ttt) cc_final: 0.7162 (mtp) REVERT: K 914 GLU cc_start: 0.7746 (mp0) cc_final: 0.7492 (mp0) REVERT: K 951 MET cc_start: 0.7553 (mtt) cc_final: 0.7293 (mtt) REVERT: K 1069 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8155 (ttpp) REVERT: K 1136 LYS cc_start: 0.7553 (mttp) cc_final: 0.7181 (mtpp) outliers start: 28 outliers final: 19 residues processed: 706 average time/residue: 0.4400 time to fit residues: 487.2946 Evaluate side-chains 686 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 667 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 ASP Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1217 MET Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain K residue 1185 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN B 490 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS E 186 HIS F 337 GLN F 340 ASN F 686 GLN G 957 GLN J 337 GLN J 340 ASN K 940 HIS K1045 HIS K1209 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092573 restraints weight = 40311.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095348 restraints weight = 18673.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097162 restraints weight = 10648.186| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25251 Z= 0.144 Angle : 0.643 18.040 34425 Z= 0.321 Chirality : 0.045 0.574 3843 Planarity : 0.005 0.066 4416 Dihedral : 5.559 54.810 3760 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.17 % Allowed : 28.94 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3141 helix: 2.63 (0.28), residues: 324 sheet: -0.05 (0.16), residues: 1005 loop : -0.98 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 251 HIS 0.007 0.001 HIS E 186 PHE 0.035 0.001 PHE K1235 TYR 0.017 0.001 TYR F 690 ARG 0.006 0.001 ARG C1188 Details of bonding type rmsd link_NAG-ASN : bond 0.01049 ( 9) link_NAG-ASN : angle 5.16426 ( 27) link_BETA1-4 : bond 0.00658 ( 6) link_BETA1-4 : angle 1.26738 ( 18) hydrogen bonds : bond 0.04984 ( 774) hydrogen bonds : angle 5.62297 ( 1986) SS BOND : bond 0.00322 ( 51) SS BOND : angle 1.18306 ( 102) covalent geometry : bond 0.00337 (25185) covalent geometry : angle 0.62364 (34278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 689 time to evaluate : 3.004 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: A 139 LYS cc_start: 0.7503 (mmmt) cc_final: 0.7080 (mmmt) REVERT: B 351 TYR cc_start: 0.8287 (t80) cc_final: 0.7697 (t80) REVERT: B 396 ASP cc_start: 0.8097 (t0) cc_final: 0.7879 (t0) REVERT: B 430 MET cc_start: 0.7563 (tmm) cc_final: 0.6826 (tmm) REVERT: B 502 MET cc_start: 0.7912 (mmt) cc_final: 0.7625 (mmt) REVERT: B 545 ASN cc_start: 0.8568 (t160) cc_final: 0.8279 (t0) REVERT: B 586 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8135 (mtpt) REVERT: B 743 THR cc_start: 0.8397 (m) cc_final: 0.8175 (p) REVERT: C 834 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 890 ASP cc_start: 0.8470 (t0) cc_final: 0.7977 (t70) REVERT: C 913 SER cc_start: 0.8107 (p) cc_final: 0.7712 (p) REVERT: C 964 ASN cc_start: 0.7970 (m-40) cc_final: 0.7489 (t0) REVERT: C 1185 CYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6594 (m) REVERT: C 1216 ASP cc_start: 0.7965 (t0) cc_final: 0.7668 (t0) REVERT: C 1218 SER cc_start: 0.8396 (t) cc_final: 0.7809 (p) REVERT: E 113 MET cc_start: 0.4311 (mmm) cc_final: 0.3893 (mmm) REVERT: F 355 CYS cc_start: 0.6113 (t) cc_final: 0.5906 (t) REVERT: F 376 ASP cc_start: 0.7043 (t0) cc_final: 0.6645 (t0) REVERT: F 396 ASP cc_start: 0.7935 (t0) cc_final: 0.7547 (t0) REVERT: F 409 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: F 558 CYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6452 (t) REVERT: F 704 VAL cc_start: 0.8289 (t) cc_final: 0.8079 (p) REVERT: G 903 MET cc_start: 0.7536 (ttt) cc_final: 0.7185 (mtp) REVERT: G 948 VAL cc_start: 0.8576 (p) cc_final: 0.8240 (t) REVERT: G 1113 ASP cc_start: 0.6866 (t0) cc_final: 0.6656 (t0) REVERT: G 1192 SER cc_start: 0.8488 (p) cc_final: 0.8228 (m) REVERT: I 266 GLU cc_start: 0.8102 (tt0) cc_final: 0.7836 (tt0) REVERT: J 341 VAL cc_start: 0.8811 (t) cc_final: 0.8599 (p) REVERT: J 490 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7533 (mm-40) REVERT: J 547 ASP cc_start: 0.7947 (m-30) cc_final: 0.7654 (m-30) REVERT: J 556 GLU cc_start: 0.7874 (pp20) cc_final: 0.7248 (pp20) REVERT: J 717 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7650 (t) REVERT: K 890 ASP cc_start: 0.8196 (t0) cc_final: 0.7917 (t70) REVERT: K 951 MET cc_start: 0.7710 (mtt) cc_final: 0.7444 (mtt) REVERT: K 1069 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7973 (ttpp) REVERT: K 1216 ASP cc_start: 0.7803 (t0) cc_final: 0.7459 (t70) outliers start: 112 outliers final: 67 residues processed: 753 average time/residue: 0.4096 time to fit residues: 495.8371 Evaluate side-chains 756 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 684 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 672 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 882 GLU Chi-restraints excluded: chain K residue 910 PHE Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1210 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 175 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 287 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS F 490 GLN F 686 GLN J 517 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092069 restraints weight = 40061.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094847 restraints weight = 18569.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096648 restraints weight = 10622.263| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25251 Z= 0.157 Angle : 0.621 17.645 34425 Z= 0.308 Chirality : 0.045 0.571 3843 Planarity : 0.005 0.057 4416 Dihedral : 5.065 58.841 3733 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.36 % Allowed : 27.56 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3141 helix: 2.64 (0.28), residues: 324 sheet: -0.04 (0.17), residues: 1008 loop : -0.99 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.017 0.001 HIS E 186 PHE 0.028 0.002 PHE K1235 TYR 0.020 0.001 TYR F 532 ARG 0.005 0.000 ARG I 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00959 ( 9) link_NAG-ASN : angle 5.03705 ( 27) link_BETA1-4 : bond 0.00469 ( 6) link_BETA1-4 : angle 1.25514 ( 18) hydrogen bonds : bond 0.04477 ( 774) hydrogen bonds : angle 5.21283 ( 1986) SS BOND : bond 0.00386 ( 51) SS BOND : angle 1.40464 ( 102) covalent geometry : bond 0.00373 (25185) covalent geometry : angle 0.60081 (34278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 695 time to evaluate : 3.989 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: A 139 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7185 (mmmt) REVERT: B 345 THR cc_start: 0.8473 (m) cc_final: 0.7983 (p) REVERT: B 396 ASP cc_start: 0.8092 (t0) cc_final: 0.7820 (t0) REVERT: B 430 MET cc_start: 0.7590 (tmm) cc_final: 0.6654 (tmm) REVERT: B 450 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: B 492 THR cc_start: 0.8125 (m) cc_final: 0.7727 (p) REVERT: B 586 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8066 (mtpt) REVERT: C 834 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8019 (mt) REVERT: C 890 ASP cc_start: 0.8425 (t0) cc_final: 0.7882 (t70) REVERT: C 913 SER cc_start: 0.8315 (p) cc_final: 0.7885 (p) REVERT: C 949 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7692 (ttm-80) REVERT: C 964 ASN cc_start: 0.7963 (m-40) cc_final: 0.7486 (t0) REVERT: C 1185 CYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6582 (m) REVERT: C 1186 SER cc_start: 0.8603 (t) cc_final: 0.8383 (t) REVERT: C 1216 ASP cc_start: 0.7921 (t0) cc_final: 0.7651 (t0) REVERT: C 1218 SER cc_start: 0.8468 (t) cc_final: 0.7814 (p) REVERT: E 113 MET cc_start: 0.4253 (mmm) cc_final: 0.3804 (mmm) REVERT: F 376 ASP cc_start: 0.7029 (t0) cc_final: 0.6637 (t0) REVERT: F 396 ASP cc_start: 0.8000 (t0) cc_final: 0.7550 (t0) REVERT: F 409 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: F 459 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8295 (ptp-170) REVERT: F 558 CYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6360 (t) REVERT: F 571 ASN cc_start: 0.8237 (t0) cc_final: 0.7778 (t0) REVERT: F 591 PHE cc_start: 0.8330 (m-80) cc_final: 0.7749 (m-80) REVERT: F 704 VAL cc_start: 0.8332 (t) cc_final: 0.8123 (p) REVERT: G 903 MET cc_start: 0.7684 (ttt) cc_final: 0.7272 (mtp) REVERT: G 948 VAL cc_start: 0.8591 (p) cc_final: 0.8289 (t) REVERT: G 986 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (p) REVERT: G 1192 SER cc_start: 0.8598 (p) cc_final: 0.8266 (m) REVERT: G 1244 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8124 (p) REVERT: I 164 SER cc_start: 0.8339 (t) cc_final: 0.7918 (p) REVERT: I 208 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7443 (p) REVERT: I 266 GLU cc_start: 0.8141 (tt0) cc_final: 0.7863 (tt0) REVERT: J 341 VAL cc_start: 0.8822 (t) cc_final: 0.8594 (p) REVERT: J 387 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7807 (mt) REVERT: J 396 ASP cc_start: 0.8147 (t0) cc_final: 0.7936 (t0) REVERT: J 490 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7648 (mm-40) REVERT: J 498 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: J 556 GLU cc_start: 0.7859 (pp20) cc_final: 0.7285 (pp20) REVERT: J 707 SER cc_start: 0.7858 (t) cc_final: 0.7570 (p) REVERT: J 729 LEU cc_start: 0.8454 (tp) cc_final: 0.8136 (tt) REVERT: K 890 ASP cc_start: 0.8224 (t0) cc_final: 0.7951 (t70) REVERT: K 1056 LYS cc_start: 0.7981 (mmtp) cc_final: 0.7426 (mttp) REVERT: K 1069 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7965 (ttpp) REVERT: K 1105 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7810 (tp) REVERT: K 1115 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7756 (p) REVERT: K 1136 LYS cc_start: 0.7781 (mttp) cc_final: 0.7217 (mtpp) REVERT: K 1196 GLU cc_start: 0.7366 (mp0) cc_final: 0.7027 (mp0) REVERT: K 1210 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8213 (t) outliers start: 144 outliers final: 96 residues processed: 779 average time/residue: 0.3708 time to fit residues: 457.2214 Evaluate side-chains 783 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 672 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1217 MET Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 877 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1175 SER Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 449 GLN Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 882 GLU Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1105 ILE Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1210 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 212 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 59 optimal weight: 0.0980 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 159 optimal weight: 0.0770 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 GLN J 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.090303 restraints weight = 41084.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093118 restraints weight = 18861.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094938 restraints weight = 10695.976| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25251 Z= 0.121 Angle : 0.608 17.259 34425 Z= 0.299 Chirality : 0.045 0.561 3843 Planarity : 0.004 0.052 4416 Dihedral : 4.748 47.517 3731 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.77 % Allowed : 27.64 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3141 helix: 2.68 (0.28), residues: 324 sheet: -0.01 (0.17), residues: 975 loop : -0.96 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 251 HIS 0.005 0.001 HIS B 395 PHE 0.029 0.001 PHE K1235 TYR 0.019 0.001 TYR F 532 ARG 0.005 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 9) link_NAG-ASN : angle 4.90632 ( 27) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 1.19443 ( 18) hydrogen bonds : bond 0.03962 ( 774) hydrogen bonds : angle 5.06635 ( 1986) SS BOND : bond 0.00371 ( 51) SS BOND : angle 1.32898 ( 102) covalent geometry : bond 0.00287 (25185) covalent geometry : angle 0.58856 (34278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 694 time to evaluate : 2.849 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: A 139 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7123 (mmmt) REVERT: B 343 LYS cc_start: 0.8172 (mptt) cc_final: 0.7584 (ttmt) REVERT: B 387 ILE cc_start: 0.8115 (tt) cc_final: 0.7835 (mt) REVERT: B 396 ASP cc_start: 0.8103 (t0) cc_final: 0.7691 (t0) REVERT: B 430 MET cc_start: 0.7593 (tmm) cc_final: 0.6775 (tmm) REVERT: B 450 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: B 492 THR cc_start: 0.8118 (m) cc_final: 0.7675 (p) REVERT: B 510 ASP cc_start: 0.8075 (t0) cc_final: 0.7851 (t0) REVERT: B 586 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8144 (mtpt) REVERT: B 686 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7395 (mt0) REVERT: B 699 THR cc_start: 0.7669 (t) cc_final: 0.7414 (p) REVERT: C 867 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8042 (pttm) REVERT: C 890 ASP cc_start: 0.8447 (t0) cc_final: 0.7888 (t70) REVERT: C 949 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7588 (ttm-80) REVERT: C 964 ASN cc_start: 0.8018 (t0) cc_final: 0.7499 (t0) REVERT: C 1117 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7506 (p) REVERT: C 1138 ASP cc_start: 0.7980 (p0) cc_final: 0.7775 (p0) REVERT: C 1185 CYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6771 (m) REVERT: C 1216 ASP cc_start: 0.7871 (t0) cc_final: 0.7514 (t0) REVERT: C 1218 SER cc_start: 0.8458 (t) cc_final: 0.7757 (p) REVERT: E 178 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.5286 (ptt-90) REVERT: F 361 CYS cc_start: 0.5711 (p) cc_final: 0.5468 (p) REVERT: F 396 ASP cc_start: 0.8066 (t0) cc_final: 0.7521 (t0) REVERT: F 409 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: F 558 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6537 (t) REVERT: F 704 VAL cc_start: 0.8187 (t) cc_final: 0.7984 (p) REVERT: G 903 MET cc_start: 0.7611 (ttt) cc_final: 0.7189 (mtp) REVERT: G 914 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7331 (mm-30) REVERT: G 948 VAL cc_start: 0.8414 (p) cc_final: 0.8115 (t) REVERT: G 970 THR cc_start: 0.8675 (t) cc_final: 0.8396 (p) REVERT: G 986 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8028 (p) REVERT: G 1029 TYR cc_start: 0.7895 (t80) cc_final: 0.7683 (t80) REVERT: G 1050 GLN cc_start: 0.7911 (tt0) cc_final: 0.7708 (tt0) REVERT: G 1243 LEU cc_start: 0.8431 (tp) cc_final: 0.8208 (tt) REVERT: I 208 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7409 (p) REVERT: J 341 VAL cc_start: 0.8738 (t) cc_final: 0.8522 (p) REVERT: J 387 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7713 (mt) REVERT: J 490 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7588 (mm-40) REVERT: J 498 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: J 501 ASP cc_start: 0.7808 (p0) cc_final: 0.7582 (p0) REVERT: J 522 LYS cc_start: 0.8037 (tttp) cc_final: 0.7762 (tttp) REVERT: J 547 ASP cc_start: 0.7974 (m-30) cc_final: 0.7729 (m-30) REVERT: J 556 GLU cc_start: 0.7945 (pp20) cc_final: 0.7390 (pp20) REVERT: J 561 SER cc_start: 0.8165 (p) cc_final: 0.7838 (m) REVERT: J 707 SER cc_start: 0.7758 (t) cc_final: 0.7462 (p) REVERT: K 890 ASP cc_start: 0.8283 (t0) cc_final: 0.7994 (t70) REVERT: K 924 ASP cc_start: 0.7725 (t70) cc_final: 0.7393 (t0) REVERT: K 1056 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7223 (mttp) REVERT: K 1069 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7915 (ttpp) REVERT: K 1115 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7609 (p) REVERT: K 1136 LYS cc_start: 0.7812 (mttp) cc_final: 0.7268 (mtpp) REVERT: K 1196 GLU cc_start: 0.7414 (mp0) cc_final: 0.6958 (mp0) outliers start: 155 outliers final: 106 residues processed: 787 average time/residue: 0.3732 time to fit residues: 467.4311 Evaluate side-chains 795 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 676 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1217 MET Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 877 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 447 SER Chi-restraints excluded: chain J residue 449 GLN Chi-restraints excluded: chain J residue 450 ASP Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 559 HIS Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL 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 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 877 CYS Chi-restraints excluded: chain K residue 910 PHE Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1053 SER Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 4.9990 chunk 229 optimal weight: 0.1980 chunk 231 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN E 172 GLN F 490 GLN F 686 GLN G 957 GLN G1026 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090702 restraints weight = 40260.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093565 restraints weight = 18361.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095426 restraints weight = 10374.698| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 25251 Z= 0.272 Angle : 0.705 18.102 34425 Z= 0.351 Chirality : 0.048 0.644 3843 Planarity : 0.005 0.052 4416 Dihedral : 5.077 47.438 3731 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 7.15 % Allowed : 26.41 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3141 helix: 2.55 (0.28), residues: 324 sheet: -0.02 (0.17), residues: 942 loop : -1.11 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 251 HIS 0.007 0.001 HIS C 931 PHE 0.029 0.002 PHE K1235 TYR 0.027 0.002 TYR F 532 ARG 0.007 0.001 ARG I 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00884 ( 9) link_NAG-ASN : angle 5.28391 ( 27) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 1.33342 ( 18) hydrogen bonds : bond 0.05094 ( 774) hydrogen bonds : angle 5.07488 ( 1986) SS BOND : bond 0.00515 ( 51) SS BOND : angle 1.55283 ( 102) covalent geometry : bond 0.00636 (25185) covalent geometry : angle 0.68448 (34278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 719 time to evaluate : 2.832 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: A 128 LYS cc_start: 0.8297 (mppt) cc_final: 0.8053 (mppt) REVERT: A 139 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7411 (mmmt) REVERT: A 167 ASP cc_start: 0.7606 (t0) cc_final: 0.7351 (t0) REVERT: B 343 LYS cc_start: 0.8282 (mptt) cc_final: 0.7735 (ttmt) REVERT: B 345 THR cc_start: 0.8478 (m) cc_final: 0.8126 (p) REVERT: B 386 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 396 ASP cc_start: 0.8113 (t0) cc_final: 0.7860 (t0) REVERT: B 430 MET cc_start: 0.7556 (tmm) cc_final: 0.6828 (tmm) REVERT: B 492 THR cc_start: 0.8279 (m) cc_final: 0.7839 (p) REVERT: B 545 ASN cc_start: 0.8386 (t160) cc_final: 0.8165 (t0) REVERT: B 586 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8281 (mtpt) REVERT: C 890 ASP cc_start: 0.8333 (t0) cc_final: 0.7717 (t70) REVERT: C 949 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: C 964 ASN cc_start: 0.7979 (t0) cc_final: 0.7713 (t0) REVERT: C 1117 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 1216 ASP cc_start: 0.7923 (t0) cc_final: 0.7671 (t70) REVERT: C 1218 SER cc_start: 0.8589 (t) cc_final: 0.8062 (p) REVERT: C 1227 LYS cc_start: 0.7799 (ptpp) cc_final: 0.7438 (mtmm) REVERT: E 167 ASP cc_start: 0.6913 (t0) cc_final: 0.6521 (t0) REVERT: F 384 SER cc_start: 0.8275 (m) cc_final: 0.7844 (p) REVERT: F 396 ASP cc_start: 0.8107 (t0) cc_final: 0.7545 (t0) REVERT: F 409 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: F 492 THR cc_start: 0.8523 (m) cc_final: 0.8092 (p) REVERT: G 858 ASN cc_start: 0.8102 (p0) cc_final: 0.7837 (p0) REVERT: G 869 VAL cc_start: 0.8643 (t) cc_final: 0.8365 (m) REVERT: G 888 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8021 (mttm) REVERT: G 903 MET cc_start: 0.7848 (ttt) cc_final: 0.7478 (mtp) REVERT: G 948 VAL cc_start: 0.8566 (p) cc_final: 0.8296 (t) REVERT: G 970 THR cc_start: 0.8830 (t) cc_final: 0.8427 (p) REVERT: G 986 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8144 (p) REVERT: G 1031 ASN cc_start: 0.8529 (t0) cc_final: 0.8134 (t0) REVERT: G 1218 SER cc_start: 0.8621 (t) cc_final: 0.8412 (p) REVERT: I 115 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6610 (mt) REVERT: I 188 LYS cc_start: 0.7440 (ptpt) cc_final: 0.7161 (mtmt) REVERT: I 208 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7634 (p) REVERT: I 230 VAL cc_start: 0.7073 (p) cc_final: 0.6824 (t) REVERT: I 240 GLU cc_start: 0.2522 (OUTLIER) cc_final: 0.1407 (tp30) REVERT: J 387 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (mt) REVERT: J 395 HIS cc_start: 0.7349 (t70) cc_final: 0.6831 (t70) REVERT: J 498 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7190 (pm20) REVERT: J 501 ASP cc_start: 0.7716 (p0) cc_final: 0.7396 (p0) REVERT: J 511 ARG cc_start: 0.8534 (tpt170) cc_final: 0.8334 (mmt180) REVERT: J 522 LYS cc_start: 0.8218 (tttp) cc_final: 0.7955 (tttp) REVERT: J 546 SER cc_start: 0.8175 (p) cc_final: 0.7954 (p) REVERT: J 547 ASP cc_start: 0.8140 (m-30) cc_final: 0.7850 (m-30) REVERT: J 556 GLU cc_start: 0.7851 (pp20) cc_final: 0.7301 (pp20) REVERT: J 604 ARG cc_start: 0.7335 (mtt-85) cc_final: 0.7097 (mtt-85) REVERT: J 622 ASP cc_start: 0.7121 (m-30) cc_final: 0.6736 (m-30) REVERT: J 658 MET cc_start: 0.8134 (tmm) cc_final: 0.7385 (ttp) REVERT: J 717 SER cc_start: 0.8180 (m) cc_final: 0.7914 (t) REVERT: J 729 LEU cc_start: 0.8561 (tp) cc_final: 0.8305 (tt) REVERT: K 851 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8438 (p) REVERT: K 890 ASP cc_start: 0.8194 (t0) cc_final: 0.7895 (t70) REVERT: K 920 GLU cc_start: 0.7580 (pm20) cc_final: 0.7114 (pm20) REVERT: K 1056 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7577 (mttp) REVERT: K 1093 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (p) REVERT: K 1115 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7806 (p) REVERT: K 1120 THR cc_start: 0.8521 (t) cc_final: 0.8315 (p) REVERT: K 1136 LYS cc_start: 0.7816 (mttp) cc_final: 0.7320 (mtpp) REVERT: K 1150 ASN cc_start: 0.8174 (t0) cc_final: 0.7900 (t0) REVERT: K 1196 GLU cc_start: 0.7304 (mp0) cc_final: 0.6987 (mp0) outliers start: 192 outliers final: 132 residues processed: 828 average time/residue: 0.3527 time to fit residues: 458.6457 Evaluate side-chains 839 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 693 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1049 THR Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1217 MET Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 888 LYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 912 ASP Chi-restraints excluded: chain G residue 916 THR Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 928 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 971 ILE Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1186 SER Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1200 ASP Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1245 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL 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 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 910 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1060 LYS Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1153 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1210 SER Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 28 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1026 ASN J 517 GLN J 569 GLN K 847 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089897 restraints weight = 40443.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092605 restraints weight = 18929.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094374 restraints weight = 10849.131| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25251 Z= 0.173 Angle : 0.654 17.182 34425 Z= 0.320 Chirality : 0.046 0.605 3843 Planarity : 0.005 0.052 4416 Dihedral : 4.824 46.853 3729 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.70 % Allowed : 28.72 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3141 helix: 2.74 (0.28), residues: 324 sheet: -0.04 (0.17), residues: 909 loop : -1.09 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 251 HIS 0.005 0.001 HIS C 931 PHE 0.028 0.002 PHE K1235 TYR 0.030 0.002 TYR E 166 ARG 0.006 0.000 ARG I 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00882 ( 9) link_NAG-ASN : angle 5.03410 ( 27) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.27028 ( 18) hydrogen bonds : bond 0.04356 ( 774) hydrogen bonds : angle 4.99606 ( 1986) SS BOND : bond 0.00430 ( 51) SS BOND : angle 1.60432 ( 102) covalent geometry : bond 0.00410 (25185) covalent geometry : angle 0.63312 (34278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 697 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8442 (mppt) cc_final: 0.8066 (mppt) REVERT: A 139 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7296 (mmmt) REVERT: B 343 LYS cc_start: 0.8254 (mptt) cc_final: 0.7719 (ttmt) REVERT: B 345 THR cc_start: 0.8522 (m) cc_final: 0.8021 (p) REVERT: B 396 ASP cc_start: 0.8116 (t0) cc_final: 0.7777 (t0) REVERT: B 430 MET cc_start: 0.7591 (tmm) cc_final: 0.6850 (tmm) REVERT: B 492 THR cc_start: 0.8265 (m) cc_final: 0.7772 (p) REVERT: B 545 ASN cc_start: 0.8401 (t160) cc_final: 0.8163 (t0) REVERT: B 566 LYS cc_start: 0.8349 (pttp) cc_final: 0.7926 (ptpp) REVERT: B 699 THR cc_start: 0.8032 (t) cc_final: 0.7706 (p) REVERT: C 890 ASP cc_start: 0.8382 (t0) cc_final: 0.7727 (t70) REVERT: C 949 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: C 964 ASN cc_start: 0.8032 (t0) cc_final: 0.7743 (t0) REVERT: C 1035 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7279 (ttpp) REVERT: C 1117 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7700 (p) REVERT: C 1216 ASP cc_start: 0.7812 (t0) cc_final: 0.7565 (t0) REVERT: C 1218 SER cc_start: 0.8568 (t) cc_final: 0.8045 (p) REVERT: C 1242 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7517 (t) REVERT: F 396 ASP cc_start: 0.8128 (t0) cc_final: 0.7475 (t0) REVERT: F 409 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: F 459 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8005 (ptp-170) REVERT: F 492 THR cc_start: 0.8462 (m) cc_final: 0.8015 (p) REVERT: F 634 GLU cc_start: 0.7253 (tp30) cc_final: 0.7006 (tp30) REVERT: G 903 MET cc_start: 0.7772 (ttt) cc_final: 0.7370 (mtp) REVERT: G 948 VAL cc_start: 0.8386 (p) cc_final: 0.8175 (t) REVERT: G 970 THR cc_start: 0.8760 (t) cc_final: 0.8413 (p) REVERT: G 986 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8128 (p) REVERT: G 1105 ILE cc_start: 0.8636 (tp) cc_final: 0.8435 (tt) REVERT: I 115 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6607 (mt) REVERT: I 162 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8178 (tmtt) REVERT: I 188 LYS cc_start: 0.7542 (ptpt) cc_final: 0.7203 (mtmt) REVERT: I 194 ASN cc_start: 0.7205 (t0) cc_final: 0.6828 (t0) REVERT: I 208 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7616 (p) REVERT: J 395 HIS cc_start: 0.7392 (t70) cc_final: 0.6744 (t70) REVERT: J 498 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: J 511 ARG cc_start: 0.8596 (tpt170) cc_final: 0.8342 (mmt180) REVERT: J 522 LYS cc_start: 0.8140 (tttp) cc_final: 0.7864 (tttp) REVERT: J 546 SER cc_start: 0.8216 (p) cc_final: 0.7988 (p) REVERT: J 547 ASP cc_start: 0.8089 (m-30) cc_final: 0.7760 (m-30) REVERT: J 604 ARG cc_start: 0.7218 (mtt-85) cc_final: 0.6951 (mtt-85) REVERT: J 622 ASP cc_start: 0.7163 (m-30) cc_final: 0.6691 (m-30) REVERT: J 658 MET cc_start: 0.8063 (tmm) cc_final: 0.7575 (ttp) REVERT: J 729 LEU cc_start: 0.8501 (tp) cc_final: 0.8263 (tt) REVERT: K 890 ASP cc_start: 0.8235 (t0) cc_final: 0.7927 (t0) REVERT: K 910 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: K 1056 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7604 (mttp) REVERT: K 1069 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7981 (mtpp) REVERT: K 1093 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8381 (p) REVERT: K 1115 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7667 (p) REVERT: K 1120 THR cc_start: 0.8477 (t) cc_final: 0.8259 (p) REVERT: K 1136 LYS cc_start: 0.7832 (mttp) cc_final: 0.7242 (mtpp) REVERT: K 1150 ASN cc_start: 0.8195 (t0) cc_final: 0.7745 (t0) REVERT: K 1196 GLU cc_start: 0.7354 (mp0) cc_final: 0.6926 (mp0) outliers start: 153 outliers final: 118 residues processed: 786 average time/residue: 0.3770 time to fit residues: 468.9307 Evaluate side-chains 820 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 690 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 SER Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 531 LYS Chi-restraints excluded: chain J residue 607 THR Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 910 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 58 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 177 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 252 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN F 559 HIS G1026 ASN J 406 HIS ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 GLN K 940 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090270 restraints weight = 40740.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093094 restraints weight = 18592.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094943 restraints weight = 10519.718| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25251 Z= 0.105 Angle : 0.615 16.073 34425 Z= 0.300 Chirality : 0.044 0.550 3843 Planarity : 0.004 0.052 4416 Dihedral : 4.544 47.216 3729 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.07 % Allowed : 29.20 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3141 helix: 2.83 (0.28), residues: 324 sheet: 0.06 (0.17), residues: 891 loop : -1.01 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 642 HIS 0.012 0.001 HIS E 176 PHE 0.029 0.001 PHE K1235 TYR 0.019 0.001 TYR F 532 ARG 0.005 0.000 ARG I 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00888 ( 9) link_NAG-ASN : angle 4.72177 ( 27) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 1.17320 ( 18) hydrogen bonds : bond 0.03685 ( 774) hydrogen bonds : angle 4.86239 ( 1986) SS BOND : bond 0.00341 ( 51) SS BOND : angle 1.33382 ( 102) covalent geometry : bond 0.00247 (25185) covalent geometry : angle 0.59684 (34278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 705 time to evaluate : 2.516 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: A 128 LYS cc_start: 0.8380 (mppt) cc_final: 0.7978 (mppt) REVERT: A 139 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7225 (mmmt) REVERT: A 183 LYS cc_start: 0.7829 (tptp) cc_final: 0.7385 (tptp) REVERT: B 343 LYS cc_start: 0.8224 (mptt) cc_final: 0.7688 (ttpt) REVERT: B 345 THR cc_start: 0.8536 (m) cc_final: 0.7951 (p) REVERT: B 346 ARG cc_start: 0.8695 (ptt90) cc_final: 0.8436 (ptt90) REVERT: B 396 ASP cc_start: 0.8121 (t0) cc_final: 0.7713 (t0) REVERT: B 430 MET cc_start: 0.7609 (tmm) cc_final: 0.6832 (tmm) REVERT: B 492 THR cc_start: 0.8285 (m) cc_final: 0.7792 (p) REVERT: B 545 ASN cc_start: 0.8367 (t0) cc_final: 0.8143 (t0) REVERT: B 699 THR cc_start: 0.7811 (t) cc_final: 0.7526 (p) REVERT: C 890 ASP cc_start: 0.8389 (t0) cc_final: 0.7961 (t70) REVERT: C 949 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: C 964 ASN cc_start: 0.8017 (t0) cc_final: 0.7784 (t0) REVERT: C 1035 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7225 (ttpp) REVERT: C 1117 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7604 (p) REVERT: C 1131 LEU cc_start: 0.8187 (pp) cc_final: 0.7919 (pt) REVERT: C 1216 ASP cc_start: 0.7791 (t0) cc_final: 0.7412 (t0) REVERT: C 1218 SER cc_start: 0.8502 (t) cc_final: 0.7971 (p) REVERT: C 1222 LEU cc_start: 0.7753 (mm) cc_final: 0.7517 (mt) REVERT: C 1242 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.7317 (t) REVERT: E 258 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8025 (ttm170) REVERT: F 371 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8064 (mtt180) REVERT: F 396 ASP cc_start: 0.8088 (t0) cc_final: 0.7407 (t0) REVERT: F 409 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: F 459 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8023 (ptp-170) REVERT: F 487 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7741 (t) REVERT: F 492 THR cc_start: 0.8375 (m) cc_final: 0.7901 (p) REVERT: F 558 CYS cc_start: 0.6975 (m) cc_final: 0.6511 (t) REVERT: F 634 GLU cc_start: 0.7273 (tp30) cc_final: 0.7039 (tp30) REVERT: F 704 VAL cc_start: 0.8210 (t) cc_final: 0.8009 (p) REVERT: F 729 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8215 (tt) REVERT: G 819 SER cc_start: 0.8396 (m) cc_final: 0.8068 (p) REVERT: G 870 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8078 (m) REVERT: G 903 MET cc_start: 0.7666 (ttt) cc_final: 0.7275 (mtp) REVERT: G 970 THR cc_start: 0.8703 (t) cc_final: 0.8365 (p) REVERT: G 986 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8113 (p) REVERT: G 1021 ARG cc_start: 0.8939 (tpp-160) cc_final: 0.8582 (tpt170) REVERT: G 1056 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7626 (mttp) REVERT: I 115 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6623 (mt) REVERT: I 167 ASP cc_start: 0.7584 (t0) cc_final: 0.7266 (t0) REVERT: J 395 HIS cc_start: 0.7356 (t70) cc_final: 0.6685 (t70) REVERT: J 490 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7671 (mm-40) REVERT: J 498 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: J 511 ARG cc_start: 0.8497 (tpt170) cc_final: 0.8279 (mmt180) REVERT: J 522 LYS cc_start: 0.8047 (tttp) cc_final: 0.7788 (tttp) REVERT: J 547 ASP cc_start: 0.8023 (m-30) cc_final: 0.7731 (m-30) REVERT: J 561 SER cc_start: 0.8134 (p) cc_final: 0.7813 (m) REVERT: J 622 ASP cc_start: 0.7263 (m-30) cc_final: 0.6710 (m-30) REVERT: J 729 LEU cc_start: 0.8369 (tp) cc_final: 0.8153 (tt) REVERT: K 860 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: K 890 ASP cc_start: 0.8249 (t0) cc_final: 0.7931 (t0) REVERT: K 920 GLU cc_start: 0.7624 (pm20) cc_final: 0.7147 (pm20) REVERT: K 1056 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7409 (mttp) REVERT: K 1061 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6612 (mp0) REVERT: K 1069 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7894 (ttpp) REVERT: K 1079 ASN cc_start: 0.8444 (t0) cc_final: 0.8232 (t0) REVERT: K 1093 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8255 (p) REVERT: K 1115 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7515 (p) REVERT: K 1136 LYS cc_start: 0.7792 (mttp) cc_final: 0.7181 (mtpp) REVERT: K 1150 ASN cc_start: 0.8196 (t0) cc_final: 0.7668 (t0) REVERT: K 1196 GLU cc_start: 0.7380 (mp0) cc_final: 0.6880 (mp0) outliers start: 136 outliers final: 101 residues processed: 782 average time/residue: 0.3605 time to fit residues: 440.6282 Evaluate side-chains 808 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 692 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 508 THR Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain G residue 857 LEU 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 912 ASP Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 531 LYS Chi-restraints excluded: chain J residue 559 HIS Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 860 GLU Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 205 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 278 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 257 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 HIS ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.090961 restraints weight = 40539.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093683 restraints weight = 18947.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095477 restraints weight = 10829.601| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25251 Z= 0.145 Angle : 0.632 16.317 34425 Z= 0.307 Chirality : 0.045 0.571 3843 Planarity : 0.005 0.052 4416 Dihedral : 4.547 47.772 3729 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.33 % Allowed : 28.72 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3141 helix: 2.80 (0.28), residues: 324 sheet: 0.05 (0.17), residues: 891 loop : -1.02 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 251 HIS 0.006 0.001 HIS E 176 PHE 0.027 0.001 PHE K1235 TYR 0.022 0.001 TYR E 166 ARG 0.007 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 9) link_NAG-ASN : angle 4.80201 ( 27) link_BETA1-4 : bond 0.00477 ( 6) link_BETA1-4 : angle 1.16886 ( 18) hydrogen bonds : bond 0.03944 ( 774) hydrogen bonds : angle 4.81225 ( 1986) SS BOND : bond 0.00357 ( 51) SS BOND : angle 1.37755 ( 102) covalent geometry : bond 0.00346 (25185) covalent geometry : angle 0.61366 (34278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 689 time to evaluate : 2.670 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: A 128 LYS cc_start: 0.8321 (mppt) cc_final: 0.7997 (mppt) REVERT: A 139 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7337 (mmmt) REVERT: A 183 LYS cc_start: 0.7891 (tptp) cc_final: 0.7467 (tptp) REVERT: B 343 LYS cc_start: 0.8285 (mptt) cc_final: 0.7741 (ttpt) REVERT: B 345 THR cc_start: 0.8527 (m) cc_final: 0.8019 (p) REVERT: B 396 ASP cc_start: 0.8141 (t0) cc_final: 0.7782 (t0) REVERT: B 430 MET cc_start: 0.7598 (tmm) cc_final: 0.6835 (tmm) REVERT: B 490 GLN cc_start: 0.7889 (mm110) cc_final: 0.7521 (mm-40) REVERT: B 492 THR cc_start: 0.8336 (m) cc_final: 0.7839 (p) REVERT: B 545 ASN cc_start: 0.8305 (t0) cc_final: 0.8084 (t0) REVERT: B 699 THR cc_start: 0.7905 (t) cc_final: 0.7649 (p) REVERT: B 729 LEU cc_start: 0.8317 (tp) cc_final: 0.7997 (tt) REVERT: C 867 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8184 (pttm) REVERT: C 890 ASP cc_start: 0.8356 (t0) cc_final: 0.7924 (t70) REVERT: C 949 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7981 (ttm-80) REVERT: C 1035 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7277 (ttpp) REVERT: C 1117 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 1131 LEU cc_start: 0.8272 (pp) cc_final: 0.8027 (pt) REVERT: C 1216 ASP cc_start: 0.7800 (t0) cc_final: 0.7462 (t0) REVERT: C 1218 SER cc_start: 0.8523 (t) cc_final: 0.8024 (p) REVERT: C 1222 LEU cc_start: 0.7785 (mm) cc_final: 0.7528 (mt) REVERT: E 177 MET cc_start: 0.7655 (mpp) cc_final: 0.7260 (mpp) REVERT: E 258 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8087 (ttm170) REVERT: F 396 ASP cc_start: 0.8090 (t0) cc_final: 0.7455 (t0) REVERT: F 399 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8433 (mmtt) REVERT: F 409 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: F 459 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8107 (ptp-170) REVERT: F 492 THR cc_start: 0.8435 (m) cc_final: 0.7984 (p) REVERT: F 634 GLU cc_start: 0.7223 (tp30) cc_final: 0.6984 (tp30) REVERT: F 704 VAL cc_start: 0.8295 (t) cc_final: 0.8094 (p) REVERT: F 729 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8248 (tt) REVERT: G 819 SER cc_start: 0.8398 (m) cc_final: 0.8102 (p) REVERT: G 870 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8128 (m) REVERT: G 903 MET cc_start: 0.7773 (ttt) cc_final: 0.7381 (mtp) REVERT: G 970 THR cc_start: 0.8744 (t) cc_final: 0.8440 (m) REVERT: G 986 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8144 (p) REVERT: G 1046 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8379 (m) REVERT: G 1056 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7697 (mttp) REVERT: I 115 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6643 (mt) REVERT: I 167 ASP cc_start: 0.7619 (t0) cc_final: 0.7293 (t0) REVERT: I 208 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7746 (p) REVERT: J 395 HIS cc_start: 0.7324 (t70) cc_final: 0.6704 (t70) REVERT: J 396 ASP cc_start: 0.8206 (t0) cc_final: 0.7754 (t0) REVERT: J 490 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7681 (mm-40) REVERT: J 498 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: J 522 LYS cc_start: 0.8111 (tttp) cc_final: 0.7848 (tttp) REVERT: J 547 ASP cc_start: 0.8021 (m-30) cc_final: 0.7759 (m-30) REVERT: J 622 ASP cc_start: 0.7133 (m-30) cc_final: 0.6782 (m-30) REVERT: J 658 MET cc_start: 0.8057 (tmm) cc_final: 0.7555 (ttp) REVERT: J 714 ILE cc_start: 0.8347 (tp) cc_final: 0.8132 (tt) REVERT: J 729 LEU cc_start: 0.8476 (tp) cc_final: 0.8232 (tt) REVERT: K 860 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: K 890 ASP cc_start: 0.8228 (t0) cc_final: 0.7912 (t0) REVERT: K 914 GLU cc_start: 0.7828 (mp0) cc_final: 0.7564 (mp0) REVERT: K 1056 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7591 (mttp) REVERT: K 1069 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7961 (ttpp) REVERT: K 1093 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8346 (p) REVERT: K 1115 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7622 (p) REVERT: K 1136 LYS cc_start: 0.7769 (mttp) cc_final: 0.7188 (mtpp) REVERT: K 1150 ASN cc_start: 0.8150 (t0) cc_final: 0.7549 (t0) REVERT: K 1196 GLU cc_start: 0.7345 (mp0) cc_final: 0.6925 (mp0) outliers start: 143 outliers final: 111 residues processed: 773 average time/residue: 0.3579 time to fit residues: 434.3658 Evaluate side-chains 811 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 684 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU 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 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 531 LYS Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 860 GLU Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1153 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 83 optimal weight: 0.0980 chunk 134 optimal weight: 0.7980 chunk 175 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091288 restraints weight = 40670.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094031 restraints weight = 18994.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095814 restraints weight = 10864.391| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25251 Z= 0.118 Angle : 0.618 15.966 34425 Z= 0.300 Chirality : 0.044 0.553 3843 Planarity : 0.004 0.057 4416 Dihedral : 4.451 47.713 3729 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.88 % Allowed : 29.01 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3141 helix: 2.83 (0.28), residues: 324 sheet: 0.13 (0.17), residues: 885 loop : -0.99 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 251 HIS 0.006 0.001 HIS E 176 PHE 0.028 0.001 PHE K1235 TYR 0.019 0.001 TYR F 532 ARG 0.008 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 9) link_NAG-ASN : angle 4.69105 ( 27) link_BETA1-4 : bond 0.00480 ( 6) link_BETA1-4 : angle 1.17325 ( 18) hydrogen bonds : bond 0.03671 ( 774) hydrogen bonds : angle 4.72160 ( 1986) SS BOND : bond 0.00333 ( 51) SS BOND : angle 1.33248 ( 102) covalent geometry : bond 0.00282 (25185) covalent geometry : angle 0.60061 (34278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 683 time to evaluate : 2.536 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: A 128 LYS cc_start: 0.8336 (mppt) cc_final: 0.8002 (mppt) REVERT: A 139 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7322 (mmmt) REVERT: A 152 ASN cc_start: 0.8744 (t0) cc_final: 0.8439 (t0) REVERT: A 183 LYS cc_start: 0.7876 (tptp) cc_final: 0.7462 (tptp) REVERT: B 343 LYS cc_start: 0.8274 (mptt) cc_final: 0.7731 (ttpt) REVERT: B 345 THR cc_start: 0.8531 (m) cc_final: 0.7995 (p) REVERT: B 396 ASP cc_start: 0.8158 (t0) cc_final: 0.7755 (t0) REVERT: B 430 MET cc_start: 0.7625 (tmm) cc_final: 0.6840 (tmm) REVERT: B 490 GLN cc_start: 0.7856 (mm110) cc_final: 0.7512 (mm-40) REVERT: B 492 THR cc_start: 0.8335 (m) cc_final: 0.7830 (p) REVERT: B 545 ASN cc_start: 0.8270 (t0) cc_final: 0.8057 (t0) REVERT: B 699 THR cc_start: 0.7903 (t) cc_final: 0.7612 (p) REVERT: B 729 LEU cc_start: 0.8296 (tp) cc_final: 0.8035 (tt) REVERT: C 867 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8198 (pttm) REVERT: C 890 ASP cc_start: 0.8365 (t0) cc_final: 0.7919 (t70) REVERT: C 949 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7945 (ttm-80) REVERT: C 1117 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7698 (p) REVERT: C 1131 LEU cc_start: 0.8244 (pp) cc_final: 0.8002 (pt) REVERT: C 1216 ASP cc_start: 0.7791 (t0) cc_final: 0.7456 (t0) REVERT: C 1218 SER cc_start: 0.8520 (t) cc_final: 0.8050 (p) REVERT: E 177 MET cc_start: 0.7767 (mpp) cc_final: 0.7322 (mpp) REVERT: E 234 VAL cc_start: 0.8347 (p) cc_final: 0.8046 (m) REVERT: E 258 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8032 (ttm170) REVERT: F 371 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8080 (mtt180) REVERT: F 396 ASP cc_start: 0.8090 (t0) cc_final: 0.7459 (t0) REVERT: F 399 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8433 (mmtt) REVERT: F 409 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: F 459 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8117 (ptp-170) REVERT: F 492 THR cc_start: 0.8410 (m) cc_final: 0.7943 (p) REVERT: F 499 GLU cc_start: 0.7561 (pt0) cc_final: 0.7356 (pt0) REVERT: F 586 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7837 (mtmm) REVERT: F 634 GLU cc_start: 0.7238 (tp30) cc_final: 0.6961 (tp30) REVERT: F 729 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8202 (tt) REVERT: G 819 SER cc_start: 0.8408 (m) cc_final: 0.8099 (p) REVERT: G 858 ASN cc_start: 0.7996 (p0) cc_final: 0.7766 (p0) REVERT: G 870 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8117 (m) REVERT: G 903 MET cc_start: 0.7739 (ttt) cc_final: 0.7355 (mtp) REVERT: G 970 THR cc_start: 0.8730 (t) cc_final: 0.8442 (m) REVERT: G 986 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8139 (p) REVERT: G 1046 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8369 (m) REVERT: G 1056 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7667 (mttp) REVERT: I 115 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6662 (mt) REVERT: I 167 ASP cc_start: 0.7632 (t0) cc_final: 0.7334 (t0) REVERT: I 194 ASN cc_start: 0.7350 (t0) cc_final: 0.7044 (t0) REVERT: I 208 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7722 (p) REVERT: J 395 HIS cc_start: 0.7318 (t70) cc_final: 0.6674 (t70) REVERT: J 396 ASP cc_start: 0.8212 (t0) cc_final: 0.7702 (t0) REVERT: J 490 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7674 (mm-40) REVERT: J 498 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: J 522 LYS cc_start: 0.8084 (tttp) cc_final: 0.7816 (tttp) REVERT: J 547 ASP cc_start: 0.7962 (m-30) cc_final: 0.7675 (m-30) REVERT: J 622 ASP cc_start: 0.7181 (m-30) cc_final: 0.6968 (m-30) REVERT: J 658 MET cc_start: 0.8045 (tmm) cc_final: 0.7577 (ttp) REVERT: J 714 ILE cc_start: 0.8332 (tp) cc_final: 0.8106 (tt) REVERT: J 717 SER cc_start: 0.7972 (m) cc_final: 0.7768 (t) REVERT: J 729 LEU cc_start: 0.8414 (tp) cc_final: 0.8201 (tt) REVERT: K 860 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: K 890 ASP cc_start: 0.8229 (t0) cc_final: 0.7907 (t0) REVERT: K 920 GLU cc_start: 0.7553 (pm20) cc_final: 0.7175 (pm20) REVERT: K 1056 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7557 (mttp) REVERT: K 1069 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7932 (ttpp) REVERT: K 1079 ASN cc_start: 0.8450 (t0) cc_final: 0.8233 (t0) REVERT: K 1093 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (p) REVERT: K 1115 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7561 (p) REVERT: K 1136 LYS cc_start: 0.7765 (mttp) cc_final: 0.7165 (mtpp) REVERT: K 1150 ASN cc_start: 0.8094 (t0) cc_final: 0.7465 (t0) REVERT: K 1196 GLU cc_start: 0.7339 (mp0) cc_final: 0.6917 (mp0) outliers start: 131 outliers final: 108 residues processed: 760 average time/residue: 0.3712 time to fit residues: 442.3782 Evaluate side-chains 803 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 679 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain G residue 857 LEU 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 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL 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 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 860 GLU Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN B 490 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 517 GLN ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090670 restraints weight = 40648.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093428 restraints weight = 18857.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095217 restraints weight = 10784.217| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25251 Z= 0.134 Angle : 0.635 15.990 34425 Z= 0.307 Chirality : 0.045 0.563 3843 Planarity : 0.005 0.059 4416 Dihedral : 4.450 47.899 3729 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.95 % Allowed : 28.90 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3141 helix: 2.30 (0.28), residues: 348 sheet: 0.14 (0.17), residues: 885 loop : -1.05 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 251 HIS 0.005 0.001 HIS E 176 PHE 0.027 0.001 PHE K1235 TYR 0.018 0.001 TYR F 532 ARG 0.009 0.000 ARG C 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 9) link_NAG-ASN : angle 4.71596 ( 27) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 1.15348 ( 18) hydrogen bonds : bond 0.03797 ( 774) hydrogen bonds : angle 4.68367 ( 1986) SS BOND : bond 0.00336 ( 51) SS BOND : angle 1.36686 ( 102) covalent geometry : bond 0.00320 (25185) covalent geometry : angle 0.61726 (34278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 684 time to evaluate : 2.719 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: A 128 LYS cc_start: 0.8361 (mppt) cc_final: 0.8041 (mppt) REVERT: A 139 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7349 (mmmt) REVERT: A 152 ASN cc_start: 0.8755 (t0) cc_final: 0.8451 (t0) REVERT: A 183 LYS cc_start: 0.7884 (tptp) cc_final: 0.7468 (tptp) REVERT: B 343 LYS cc_start: 0.8279 (mptt) cc_final: 0.7788 (ttmt) REVERT: B 345 THR cc_start: 0.8498 (m) cc_final: 0.7968 (p) REVERT: B 430 MET cc_start: 0.7618 (tmm) cc_final: 0.6835 (tmm) REVERT: B 490 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7537 (mm-40) REVERT: B 492 THR cc_start: 0.8369 (m) cc_final: 0.7869 (p) REVERT: B 545 ASN cc_start: 0.8278 (t0) cc_final: 0.8063 (t0) REVERT: B 699 THR cc_start: 0.7888 (t) cc_final: 0.7621 (p) REVERT: B 729 LEU cc_start: 0.8328 (tp) cc_final: 0.7963 (tt) REVERT: C 867 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8177 (pttm) REVERT: C 890 ASP cc_start: 0.8363 (t0) cc_final: 0.7902 (t70) REVERT: C 949 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: C 1117 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7685 (p) REVERT: C 1131 LEU cc_start: 0.8250 (pp) cc_final: 0.8004 (pt) REVERT: C 1222 LEU cc_start: 0.7788 (mm) cc_final: 0.7579 (mt) REVERT: E 177 MET cc_start: 0.7801 (mpp) cc_final: 0.7322 (mpp) REVERT: E 234 VAL cc_start: 0.8350 (p) cc_final: 0.8060 (m) REVERT: E 258 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8047 (ttm170) REVERT: F 371 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8081 (mtt180) REVERT: F 396 ASP cc_start: 0.8121 (t0) cc_final: 0.7496 (t0) REVERT: F 399 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8357 (mmtt) REVERT: F 409 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: F 459 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8152 (ptp-170) REVERT: F 492 THR cc_start: 0.8429 (m) cc_final: 0.7961 (p) REVERT: F 557 GLN cc_start: 0.7722 (mm110) cc_final: 0.7461 (mt0) REVERT: F 586 LYS cc_start: 0.8236 (mtpt) cc_final: 0.8033 (mtmm) REVERT: F 634 GLU cc_start: 0.7230 (tp30) cc_final: 0.6950 (tp30) REVERT: F 729 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8247 (tt) REVERT: F 740 VAL cc_start: 0.7887 (p) cc_final: 0.7658 (m) REVERT: G 819 SER cc_start: 0.8407 (m) cc_final: 0.8091 (p) REVERT: G 870 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8099 (m) REVERT: G 903 MET cc_start: 0.7764 (ttt) cc_final: 0.7358 (mtp) REVERT: G 970 THR cc_start: 0.8735 (t) cc_final: 0.8465 (m) REVERT: G 986 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8152 (p) REVERT: G 1046 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (m) REVERT: G 1056 LYS cc_start: 0.7956 (mmtp) cc_final: 0.7676 (mttp) REVERT: G 1227 LYS cc_start: 0.7667 (mttm) cc_final: 0.7416 (mttm) REVERT: I 115 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6694 (mt) REVERT: I 167 ASP cc_start: 0.7671 (t0) cc_final: 0.7357 (t0) REVERT: I 194 ASN cc_start: 0.7396 (t0) cc_final: 0.7073 (t0) REVERT: I 208 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7704 (p) REVERT: J 395 HIS cc_start: 0.7323 (t70) cc_final: 0.6682 (t70) REVERT: J 396 ASP cc_start: 0.8220 (t0) cc_final: 0.7731 (t0) REVERT: J 490 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7696 (mm-40) REVERT: J 498 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: J 502 MET cc_start: 0.7921 (mtp) cc_final: 0.7620 (mtt) REVERT: J 522 LYS cc_start: 0.8082 (tttp) cc_final: 0.7814 (tttp) REVERT: J 547 ASP cc_start: 0.7986 (m-30) cc_final: 0.7736 (m-30) REVERT: J 658 MET cc_start: 0.8056 (tmm) cc_final: 0.7570 (ttp) REVERT: J 714 ILE cc_start: 0.8356 (tp) cc_final: 0.8133 (tt) REVERT: J 729 LEU cc_start: 0.8438 (tp) cc_final: 0.8211 (tt) REVERT: K 860 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: K 890 ASP cc_start: 0.8219 (t0) cc_final: 0.7895 (t0) REVERT: K 920 GLU cc_start: 0.7573 (pm20) cc_final: 0.7160 (pm20) REVERT: K 1056 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7665 (mttp) REVERT: K 1069 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7950 (ttpp) REVERT: K 1079 ASN cc_start: 0.8456 (t0) cc_final: 0.8229 (t0) REVERT: K 1093 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8325 (p) REVERT: K 1115 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7583 (p) REVERT: K 1136 LYS cc_start: 0.7778 (mttp) cc_final: 0.7176 (mtpp) REVERT: K 1150 ASN cc_start: 0.8047 (t0) cc_final: 0.7467 (t0) REVERT: K 1196 GLU cc_start: 0.7331 (mp0) cc_final: 0.6927 (mp0) outliers start: 133 outliers final: 106 residues processed: 764 average time/residue: 0.3609 time to fit residues: 435.8337 Evaluate side-chains 803 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 681 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1217 MET Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain G residue 857 LEU 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 923 VAL Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 858 ASN Chi-restraints excluded: chain K residue 860 GLU Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 241 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 216 optimal weight: 0.0570 chunk 135 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN J 517 GLN ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.093126 restraints weight = 40221.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096014 restraints weight = 18419.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097896 restraints weight = 10415.236| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25251 Z= 0.130 Angle : 0.635 15.962 34425 Z= 0.307 Chirality : 0.045 0.561 3843 Planarity : 0.004 0.058 4416 Dihedral : 4.436 47.992 3729 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.07 % Allowed : 29.20 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3141 helix: 2.31 (0.28), residues: 348 sheet: 0.15 (0.17), residues: 885 loop : -1.04 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 251 HIS 0.006 0.001 HIS E 176 PHE 0.026 0.001 PHE K1235 TYR 0.018 0.001 TYR F 532 ARG 0.009 0.000 ARG J 604 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 9) link_NAG-ASN : angle 4.68244 ( 27) link_BETA1-4 : bond 0.00463 ( 6) link_BETA1-4 : angle 1.15209 ( 18) hydrogen bonds : bond 0.03739 ( 774) hydrogen bonds : angle 4.66145 ( 1986) SS BOND : bond 0.00324 ( 51) SS BOND : angle 1.41565 ( 102) covalent geometry : bond 0.00310 (25185) covalent geometry : angle 0.61773 (34278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13448.58 seconds wall clock time: 236 minutes 40.26 seconds (14200.26 seconds total)