Starting phenix.real_space_refine on Mon Aug 25 02:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0l_37981/08_2025/8x0l_37981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0l_37981/08_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_37981/08_2025/8x0l_37981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0l_37981/08_2025/8x0l_37981.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0l_37981/08_2025/8x0l_37981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0l_37981/08_2025/8x0l_37981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.22, per 1000 atoms: 0.25 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: 1.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.00 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: 5.57 Time building geometry restraints manager: 2.32 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- 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 : 8.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (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 ARG 0.013 0.001 ARG K1014 TYR 0.029 0.001 TYR B 629 PHE 0.034 0.001 PHE G 828 TRP 0.015 0.001 TRP B 662 HIS 0.008 0.001 HIS F 559 Details of bonding type rmsd covalent geometry : bond 0.00371 (25185) covalent geometry : angle 0.71118 (34278) SS BOND : bond 0.00376 ( 51) SS BOND : angle 1.70468 ( 102) hydrogen bonds : bond 0.24437 ( 774) hydrogen bonds : angle 7.46455 ( 1986) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 1.48171 ( 18) link_NAG-ASN : bond 0.00984 ( 9) link_NAG-ASN : angle 5.93462 ( 27) *********************** 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 : 0.925 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: 0.1627 time to fit residues: 179.9241 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 : 0.971 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 8.9990 overall best weight: 2.5794 ------------------------------------------------------------------------------- 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** C1170 HIS E 172 GLN E 186 HIS F 337 GLN F 340 ASN F 686 GLN G 957 GLN J 337 GLN J 340 ASN K1045 HIS K1050 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091961 restraints weight = 40275.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094742 restraints weight = 18673.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096550 restraints weight = 10685.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097715 restraints weight = 7098.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098477 restraints weight = 5302.923| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25251 Z= 0.204 Angle : 0.672 18.112 34425 Z= 0.336 Chirality : 0.047 0.618 3843 Planarity : 0.005 0.067 4416 Dihedral : 5.662 57.893 3760 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.88 % Allowed : 28.19 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3141 helix: 2.53 (0.28), residues: 324 sheet: -0.11 (0.16), residues: 1005 loop : -1.04 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1188 TYR 0.020 0.002 TYR F 690 PHE 0.033 0.002 PHE K1235 TRP 0.014 0.001 TRP I 251 HIS 0.006 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00481 (25185) covalent geometry : angle 0.65296 (34278) SS BOND : bond 0.00380 ( 51) SS BOND : angle 1.25429 ( 102) hydrogen bonds : bond 0.05147 ( 774) hydrogen bonds : angle 5.51943 ( 1986) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 1.37525 ( 18) link_NAG-ASN : bond 0.01053 ( 9) link_NAG-ASN : angle 5.24411 ( 27) *********************** 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 823 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 692 time to evaluate : 0.935 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: 0.7625 (mmmt) cc_final: 0.7166 (mmmt) REVERT: B 345 THR cc_start: 0.8465 (m) cc_final: 0.8007 (p) REVERT: B 430 MET cc_start: 0.7575 (tmm) cc_final: 0.6761 (tmm) REVERT: B 492 THR cc_start: 0.8119 (m) cc_final: 0.7649 (p) REVERT: B 545 ASN cc_start: 0.8597 (t160) cc_final: 0.8300 (t0) REVERT: B 586 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8093 (mtpt) REVERT: C 834 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8031 (mt) REVERT: C 890 ASP cc_start: 0.8450 (t0) cc_final: 0.7915 (t70) REVERT: C 910 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7719 (t80) REVERT: C 913 SER cc_start: 0.8193 (p) cc_final: 0.7774 (p) REVERT: C 949 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7686 (ttm-80) REVERT: C 964 ASN cc_start: 0.7995 (m-40) cc_final: 0.7501 (t0) REVERT: C 1185 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6588 (m) REVERT: C 1186 SER cc_start: 0.8605 (t) cc_final: 0.8398 (t) REVERT: C 1203 VAL cc_start: 0.8336 (m) cc_final: 0.8112 (m) REVERT: C 1216 ASP cc_start: 0.7996 (t0) cc_final: 0.7739 (t0) REVERT: C 1218 SER cc_start: 0.8445 (t) cc_final: 0.7876 (p) REVERT: E 113 MET cc_start: 0.4261 (mmm) cc_final: 0.3839 (mmm) REVERT: F 396 ASP cc_start: 0.7957 (t0) cc_final: 0.7466 (t0) REVERT: F 409 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: F 704 VAL cc_start: 0.8328 (t) cc_final: 0.8112 (p) REVERT: G 903 MET cc_start: 0.7682 (ttt) cc_final: 0.7296 (mtp) REVERT: G 948 VAL cc_start: 0.8572 (p) cc_final: 0.8252 (t) REVERT: G 986 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8059 (p) REVERT: G 1192 SER cc_start: 0.8529 (p) cc_final: 0.8281 (m) REVERT: I 266 GLU cc_start: 0.8131 (tt0) cc_final: 0.7856 (tt0) REVERT: J 341 VAL cc_start: 0.8829 (t) cc_final: 0.8599 (p) REVERT: J 483 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7416 (mm-30) REVERT: J 490 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7636 (mm-40) REVERT: J 501 ASP cc_start: 0.7750 (p0) cc_final: 0.7526 (p0) REVERT: J 547 ASP cc_start: 0.8011 (m-30) cc_final: 0.7741 (m-30) REVERT: J 556 GLU cc_start: 0.7840 (pp20) cc_final: 0.7235 (pp20) REVERT: J 707 SER cc_start: 0.7866 (t) cc_final: 0.7639 (p) REVERT: J 717 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7810 (t) REVERT: K 890 ASP cc_start: 0.8213 (t0) cc_final: 0.7929 (t70) REVERT: K 951 MET cc_start: 0.7711 (mtt) cc_final: 0.7382 (mtt) REVERT: K 1069 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7968 (mtpp) outliers start: 131 outliers final: 77 residues processed: 771 average time/residue: 0.1600 time to fit residues: 196.5841 Evaluate side-chains 760 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 676 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 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 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 949 ARG 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 1145 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 498 GLU 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 718 CYS Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 897 THR 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 1040 SER Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1200 ASP Chi-restraints excluded: chain G residue 1244 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 449 GLN 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 717 SER Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 721 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 870 VAL Chi-restraints excluded: chain K residue 882 GLU 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 1024 GLU Chi-restraints excluded: chain K residue 1112 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 251 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN F 686 GLN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 517 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088176 restraints weight = 40400.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091007 restraints weight = 18449.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092850 restraints weight = 10439.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.094029 restraints weight = 6885.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094844 restraints weight = 5084.555| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 25251 Z= 0.295 Angle : 0.721 18.620 34425 Z= 0.361 Chirality : 0.049 0.630 3843 Planarity : 0.006 0.061 4416 Dihedral : 5.418 51.846 3733 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.55 % Allowed : 26.82 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 3141 helix: 2.46 (0.28), residues: 324 sheet: -0.16 (0.16), residues: 1017 loop : -1.21 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 221 TYR 0.024 0.002 TYR F 532 PHE 0.027 0.002 PHE K1235 TRP 0.017 0.002 TRP I 251 HIS 0.021 0.002 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00691 (25185) covalent geometry : angle 0.69892 (34278) SS BOND : bond 0.00665 ( 51) SS BOND : angle 1.73863 ( 102) hydrogen bonds : bond 0.05431 ( 774) hydrogen bonds : angle 5.29062 ( 1986) link_BETA1-4 : bond 0.00606 ( 6) link_BETA1-4 : angle 1.41885 ( 18) link_NAG-ASN : bond 0.00954 ( 9) link_NAG-ASN : angle 5.41942 ( 27) *********************** 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 872 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 696 time to evaluate : 0.744 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: 0.8144 (mppt) cc_final: 0.7924 (mppt) REVERT: A 139 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7391 (mmmt) REVERT: A 167 ASP cc_start: 0.7608 (t0) cc_final: 0.7362 (t0) REVERT: B 345 THR cc_start: 0.8458 (m) cc_final: 0.8025 (p) REVERT: B 387 ILE cc_start: 0.8222 (tt) cc_final: 0.7992 (mt) REVERT: B 389 ILE cc_start: 0.8341 (mm) cc_final: 0.8060 (mt) REVERT: B 430 MET cc_start: 0.7580 (tmm) cc_final: 0.6696 (tmm) REVERT: B 492 THR cc_start: 0.8251 (m) cc_final: 0.7847 (p) REVERT: B 545 ASN cc_start: 0.8573 (t0) cc_final: 0.8283 (t0) REVERT: B 586 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8064 (mtpt) REVERT: C 890 ASP cc_start: 0.8376 (t0) cc_final: 0.7749 (t70) REVERT: C 910 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7695 (t80) REVERT: C 913 SER cc_start: 0.8453 (p) cc_final: 0.8060 (p) REVERT: C 949 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: C 964 ASN cc_start: 0.8062 (t0) cc_final: 0.7558 (t0) REVERT: C 1117 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7880 (p) REVERT: C 1218 SER cc_start: 0.8565 (t) cc_final: 0.8063 (p) REVERT: C 1227 LYS cc_start: 0.7775 (ptpp) cc_final: 0.7434 (mtmm) REVERT: F 384 SER cc_start: 0.8292 (m) cc_final: 0.7854 (p) REVERT: F 396 ASP cc_start: 0.8069 (t0) cc_final: 0.7590 (t0) REVERT: F 409 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: F 586 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7946 (mtpt) REVERT: F 591 PHE cc_start: 0.8388 (m-80) cc_final: 0.7679 (m-80) REVERT: G 888 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7995 (mttm) REVERT: G 903 MET cc_start: 0.7866 (ttt) cc_final: 0.7453 (mtp) REVERT: G 948 VAL cc_start: 0.8611 (p) cc_final: 0.8323 (t) REVERT: G 986 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8113 (p) REVERT: G 1021 ARG cc_start: 0.9015 (tpp-160) cc_final: 0.8688 (tpt170) REVERT: I 128 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7602 (ttpt) REVERT: I 152 ASN cc_start: 0.8420 (m-40) cc_final: 0.8102 (m-40) REVERT: I 208 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7626 (p) REVERT: I 240 GLU cc_start: 0.2718 (OUTLIER) cc_final: 0.1627 (tp30) REVERT: I 266 GLU cc_start: 0.8154 (tt0) cc_final: 0.7875 (tt0) REVERT: J 387 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7926 (mt) REVERT: J 396 ASP cc_start: 0.8162 (t0) cc_final: 0.7960 (t0) REVERT: J 498 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: J 548 MET cc_start: 0.7407 (ptm) cc_final: 0.7202 (ptm) REVERT: J 556 GLU cc_start: 0.7816 (pp20) cc_final: 0.7252 (pp20) REVERT: J 641 GLU cc_start: 0.7682 (pt0) cc_final: 0.7414 (pt0) REVERT: J 658 MET cc_start: 0.8132 (tmm) cc_final: 0.7323 (ttp) REVERT: J 725 ARG cc_start: 0.8008 (ttt90) cc_final: 0.7601 (ttt90) REVERT: K 890 ASP cc_start: 0.8216 (t0) cc_final: 0.7947 (t0) REVERT: K 1056 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7607 (mttp) REVERT: K 1136 LYS cc_start: 0.7821 (mttp) cc_final: 0.7379 (mtpp) REVERT: K 1196 GLU cc_start: 0.7300 (mp0) cc_final: 0.7004 (mp0) outliers start: 176 outliers final: 119 residues processed: 804 average time/residue: 0.1556 time to fit residues: 197.5734 Evaluate side-chains 810 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 681 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 219 SER Chi-restraints excluded: chain A residue 230 VAL 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 383 PHE 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 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 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 870 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 910 PHE 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 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 1115 THR Chi-restraints excluded: chain C residue 1116 CYS 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 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 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 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 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 746 ILE Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 852 SER 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 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 1068 THR Chi-restraints excluded: chain G residue 1156 GLU 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 1186 SER Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1200 ASP Chi-restraints excluded: chain G residue 1237 ILE Chi-restraints excluded: chain G residue 1245 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 231 VAL 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 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 444 LEU Chi-restraints excluded: chain J residue 484 ILE 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 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 720 MET Chi-restraints excluded: chain J residue 721 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 844 LEU Chi-restraints excluded: chain K residue 850 GLU 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 958 THR Chi-restraints excluded: chain K residue 986 THR Chi-restraints excluded: chain K residue 1107 GLU 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 1217 MET Chi-restraints excluded: chain K residue 1218 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 133 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 64 optimal weight: 0.0000 chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** K 940 HIS ** K1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092029 restraints weight = 40252.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094765 restraints weight = 18871.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096562 restraints weight = 10807.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097759 restraints weight = 7214.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098469 restraints weight = 5386.841| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1849 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= 0.122 Angle : 0.623 17.187 34425 Z= 0.306 Chirality : 0.045 0.567 3843 Planarity : 0.005 0.053 4416 Dihedral : 4.899 48.339 3732 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.03 % Allowed : 28.34 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3141 helix: 2.76 (0.28), residues: 324 sheet: -0.06 (0.17), residues: 909 loop : -1.08 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 221 TYR 0.021 0.001 TYR F 532 PHE 0.030 0.001 PHE K1235 TRP 0.007 0.001 TRP J 662 HIS 0.005 0.001 HIS I 186 Details of bonding type rmsd covalent geometry : bond 0.00288 (25185) covalent geometry : angle 0.60235 (34278) SS BOND : bond 0.00487 ( 51) SS BOND : angle 1.52421 ( 102) hydrogen bonds : bond 0.04055 ( 774) hydrogen bonds : angle 5.03649 ( 1986) link_BETA1-4 : bond 0.00517 ( 6) link_BETA1-4 : angle 1.26493 ( 18) link_NAG-ASN : bond 0.00933 ( 9) link_NAG-ASN : angle 4.94239 ( 27) *********************** 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 832 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 697 time to evaluate : 0.951 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: 0.8136 (mppt) cc_final: 0.7917 (mppt) REVERT: A 139 LYS cc_start: 0.7744 (mmmt) cc_final: 0.7311 (mmmt) REVERT: B 343 LYS cc_start: 0.8286 (mptt) cc_final: 0.7700 (ttpt) REVERT: B 345 THR cc_start: 0.8460 (m) cc_final: 0.7947 (p) REVERT: B 378 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7356 (tpp) REVERT: B 396 ASP cc_start: 0.8133 (t0) cc_final: 0.7855 (t0) REVERT: B 430 MET cc_start: 0.7566 (tmm) cc_final: 0.6822 (tmm) REVERT: B 492 THR cc_start: 0.8228 (m) cc_final: 0.7780 (p) REVERT: B 545 ASN cc_start: 0.8462 (t0) cc_final: 0.8244 (t0) REVERT: B 586 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8181 (mtpt) REVERT: B 699 THR cc_start: 0.7912 (t) cc_final: 0.7684 (p) REVERT: C 890 ASP cc_start: 0.8366 (t0) cc_final: 0.7756 (t70) REVERT: C 910 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7700 (t80) REVERT: C 964 ASN cc_start: 0.8004 (t0) cc_final: 0.7731 (t0) REVERT: C 1117 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7721 (p) REVERT: C 1138 ASP cc_start: 0.7944 (p0) cc_final: 0.7734 (p0) REVERT: C 1218 SER cc_start: 0.8441 (t) cc_final: 0.8050 (p) REVERT: C 1227 LYS cc_start: 0.7667 (ptpp) cc_final: 0.7356 (mtmm) REVERT: E 155 LEU cc_start: 0.9275 (mm) cc_final: 0.9029 (mm) REVERT: F 396 ASP cc_start: 0.7978 (t0) cc_final: 0.7415 (t0) REVERT: F 409 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: F 417 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7724 (mtpp) REVERT: F 459 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8245 (ptp-170) REVERT: F 558 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6282 (t) REVERT: F 586 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7924 (mtpt) REVERT: G 903 MET cc_start: 0.7689 (ttt) cc_final: 0.7261 (mtp) REVERT: G 948 VAL cc_start: 0.8506 (p) cc_final: 0.8254 (t) REVERT: G 970 THR cc_start: 0.8818 (t) cc_final: 0.8464 (p) REVERT: G 986 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8130 (p) REVERT: I 128 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7461 (ttpt) REVERT: I 152 ASN cc_start: 0.8446 (m-40) cc_final: 0.8126 (m-40) REVERT: I 194 ASN cc_start: 0.7033 (t0) cc_final: 0.6716 (t0) REVERT: I 208 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7615 (p) REVERT: J 387 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7762 (mt) REVERT: J 490 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7643 (mm-40) REVERT: J 498 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: J 501 ASP cc_start: 0.7775 (p0) cc_final: 0.7376 (p0) REVERT: J 547 ASP cc_start: 0.7909 (m-30) cc_final: 0.7678 (m-30) REVERT: J 548 MET cc_start: 0.7432 (ptm) cc_final: 0.7192 (ptm) REVERT: J 556 GLU cc_start: 0.7806 (pp20) cc_final: 0.7248 (pp20) REVERT: K 868 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8444 (p) REVERT: K 890 ASP cc_start: 0.8224 (t0) cc_final: 0.7920 (t70) REVERT: K 914 GLU cc_start: 0.7846 (mp0) cc_final: 0.7407 (mp0) REVERT: K 1056 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7549 (mttp) REVERT: K 1069 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7975 (ttpp) REVERT: K 1093 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (p) REVERT: K 1117 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7610 (p) REVERT: K 1136 LYS cc_start: 0.7785 (mttp) cc_final: 0.7268 (mtpp) REVERT: K 1150 ASN cc_start: 0.8343 (t0) cc_final: 0.7726 (t0) REVERT: K 1196 GLU cc_start: 0.7301 (mp0) cc_final: 0.6938 (mp0) outliers start: 135 outliers final: 91 residues processed: 777 average time/residue: 0.1615 time to fit residues: 199.1829 Evaluate side-chains 776 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 672 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 MET 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 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 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 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 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 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 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL 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 532 TYR Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 708 LEU 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 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1107 GLU 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 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 183 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 345 THR Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 450 ASP 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 719 TYR 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 870 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1024 GLU Chi-restraints excluded: chain K residue 1043 MET Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1117 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 1217 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 37 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN F 686 GLN G1026 ASN J 517 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.088855 restraints weight = 40759.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091672 restraints weight = 18606.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.093489 restraints weight = 10465.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094703 restraints weight = 6925.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095399 restraints weight = 5100.713| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25251 Z= 0.150 Angle : 0.630 17.026 34425 Z= 0.307 Chirality : 0.045 0.579 3843 Planarity : 0.005 0.050 4416 Dihedral : 4.781 47.664 3732 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.18 % Allowed : 28.19 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 3141 helix: 2.71 (0.28), residues: 324 sheet: -0.04 (0.17), residues: 909 loop : -1.05 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 604 TYR 0.029 0.001 TYR E 166 PHE 0.026 0.001 PHE K1235 TRP 0.012 0.001 TRP I 251 HIS 0.006 0.001 HIS J 395 Details of bonding type rmsd covalent geometry : bond 0.00359 (25185) covalent geometry : angle 0.61042 (34278) SS BOND : bond 0.00419 ( 51) SS BOND : angle 1.42705 ( 102) hydrogen bonds : bond 0.04133 ( 774) hydrogen bonds : angle 4.91688 ( 1986) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.20015 ( 18) link_NAG-ASN : bond 0.00892 ( 9) link_NAG-ASN : angle 4.93959 ( 27) *********************** 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 863 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 697 time to evaluate : 0.979 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: 0.8263 (mppt) cc_final: 0.8024 (mppt) REVERT: A 139 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7301 (mmmt) REVERT: B 343 LYS cc_start: 0.8282 (mptt) cc_final: 0.7732 (ttpt) REVERT: B 345 THR cc_start: 0.8505 (m) cc_final: 0.7986 (p) REVERT: B 378 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7442 (tpp) REVERT: B 396 ASP cc_start: 0.8062 (t0) cc_final: 0.7725 (t0) REVERT: B 430 MET cc_start: 0.7594 (tmm) cc_final: 0.6839 (tmm) REVERT: B 490 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7450 (mm110) REVERT: B 492 THR cc_start: 0.8256 (m) cc_final: 0.7772 (p) REVERT: B 545 ASN cc_start: 0.8384 (t0) cc_final: 0.8123 (t0) REVERT: B 699 THR cc_start: 0.7962 (t) cc_final: 0.7730 (p) REVERT: C 888 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7949 (mttp) REVERT: C 890 ASP cc_start: 0.8380 (t0) cc_final: 0.7738 (t70) REVERT: C 910 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7518 (t80) REVERT: C 949 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: C 964 ASN cc_start: 0.8024 (t0) cc_final: 0.7739 (t0) REVERT: C 1117 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7754 (p) REVERT: C 1218 SER cc_start: 0.8379 (t) cc_final: 0.7997 (p) REVERT: C 1227 LYS cc_start: 0.7672 (ptpp) cc_final: 0.7331 (mtmm) REVERT: E 155 LEU cc_start: 0.9262 (mm) cc_final: 0.8965 (mm) REVERT: E 177 MET cc_start: 0.7573 (mpp) cc_final: 0.7352 (mpp) REVERT: F 354 ASP cc_start: 0.7680 (t0) cc_final: 0.7391 (t70) REVERT: F 396 ASP cc_start: 0.8053 (t0) cc_final: 0.7424 (t0) REVERT: F 409 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: F 417 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7701 (mtpp) REVERT: F 459 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8158 (ptm160) REVERT: F 483 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: F 492 THR cc_start: 0.8465 (m) cc_final: 0.8024 (p) REVERT: F 586 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7842 (mtpt) REVERT: F 634 GLU cc_start: 0.7202 (tp30) cc_final: 0.6979 (tp30) REVERT: G 903 MET cc_start: 0.7736 (ttt) cc_final: 0.7318 (mtp) REVERT: G 948 VAL cc_start: 0.8392 (p) cc_final: 0.8164 (t) REVERT: G 970 THR cc_start: 0.8814 (t) cc_final: 0.8445 (p) REVERT: G 986 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8145 (p) REVERT: I 128 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7557 (ttpt) REVERT: I 152 ASN cc_start: 0.8463 (m-40) cc_final: 0.8126 (m-40) REVERT: I 193 TYR cc_start: 0.8354 (m-80) cc_final: 0.8053 (m-80) REVERT: I 208 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7624 (p) REVERT: J 387 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7768 (mt) REVERT: J 498 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: J 501 ASP cc_start: 0.7781 (p0) cc_final: 0.7358 (p0) REVERT: J 547 ASP cc_start: 0.8019 (m-30) cc_final: 0.7718 (m-30) REVERT: J 548 MET cc_start: 0.7524 (ptm) cc_final: 0.7262 (ptm) REVERT: J 556 GLU cc_start: 0.7842 (pp20) cc_final: 0.7308 (pp20) REVERT: J 658 MET cc_start: 0.8057 (tmm) cc_final: 0.7564 (ttp) REVERT: K 851 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (p) REVERT: K 890 ASP cc_start: 0.8227 (t0) cc_final: 0.7917 (t70) REVERT: K 914 GLU cc_start: 0.7841 (mp0) cc_final: 0.7359 (mp0) REVERT: K 1056 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7479 (mttp) REVERT: K 1069 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7982 (mtpp) REVERT: K 1093 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8343 (p) REVERT: K 1136 LYS cc_start: 0.7816 (mttp) cc_final: 0.7250 (mtpp) REVERT: K 1150 ASN cc_start: 0.8334 (t0) cc_final: 0.7677 (t0) REVERT: K 1196 GLU cc_start: 0.7329 (mp0) cc_final: 0.6930 (mp0) REVERT: K 1200 ASP cc_start: 0.7405 (m-30) cc_final: 0.7205 (m-30) REVERT: K 1210 SER cc_start: 0.8399 (t) cc_final: 0.8153 (m) outliers start: 166 outliers final: 122 residues processed: 794 average time/residue: 0.1583 time to fit residues: 199.8085 Evaluate side-chains 824 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 688 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 378 MET 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 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 688 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 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 888 LYS Chi-restraints excluded: chain C residue 910 PHE 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 1025 SER 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 1156 GLU Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU 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 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 483 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 720 MET 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 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 1175 SER 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 I residue 113 MET Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 183 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 231 VAL 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 345 THR Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 450 ASP 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 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 J residue 735 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 868 THR Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 923 VAL 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 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1158 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 1213 VAL 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 145 optimal weight: 0.7980 chunk 290 optimal weight: 0.0870 chunk 59 optimal weight: 0.0980 chunk 144 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 271 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN G1026 ASN J 406 HIS K 940 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091531 restraints weight = 40838.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094397 restraints weight = 18588.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096253 restraints weight = 10435.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097487 restraints weight = 6860.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.098292 restraints weight = 5071.067| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25251 Z= 0.096 Angle : 0.593 16.163 34425 Z= 0.290 Chirality : 0.044 0.538 3843 Planarity : 0.004 0.048 4416 Dihedral : 4.519 47.861 3732 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.40 % Allowed : 29.20 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.15), residues: 3141 helix: 2.82 (0.28), residues: 324 sheet: 0.06 (0.17), residues: 915 loop : -0.96 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 930 TYR 0.018 0.001 TYR F 532 PHE 0.030 0.001 PHE K1235 TRP 0.009 0.001 TRP E 195 HIS 0.011 0.001 HIS J 503 Details of bonding type rmsd covalent geometry : bond 0.00225 (25185) covalent geometry : angle 0.57539 (34278) SS BOND : bond 0.00278 ( 51) SS BOND : angle 1.13768 ( 102) hydrogen bonds : bond 0.03474 ( 774) hydrogen bonds : angle 4.75670 ( 1986) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 1.16067 ( 18) link_NAG-ASN : bond 0.00876 ( 9) link_NAG-ASN : angle 4.65872 ( 27) *********************** 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 836 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 691 time to evaluate : 1.032 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: 0.8141 (mppt) cc_final: 0.7908 (mppt) REVERT: A 139 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7246 (mmmt) REVERT: B 343 LYS cc_start: 0.8297 (mptt) cc_final: 0.7689 (ttpt) REVERT: B 345 THR cc_start: 0.8480 (m) cc_final: 0.7941 (p) REVERT: B 378 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7259 (tpp) REVERT: B 396 ASP cc_start: 0.8033 (t0) cc_final: 0.7656 (t0) REVERT: B 430 MET cc_start: 0.7586 (tmm) cc_final: 0.6813 (tmm) REVERT: B 490 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7539 (mm110) REVERT: B 492 THR cc_start: 0.8249 (m) cc_final: 0.7756 (p) REVERT: B 545 ASN cc_start: 0.8278 (t0) cc_final: 0.7992 (t0) REVERT: C 867 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8187 (pttm) REVERT: C 890 ASP cc_start: 0.8383 (t0) cc_final: 0.7952 (t70) REVERT: C 910 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7617 (t80) REVERT: C 1117 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7591 (p) REVERT: C 1131 LEU cc_start: 0.8264 (pp) cc_final: 0.7996 (pt) REVERT: C 1203 VAL cc_start: 0.8274 (m) cc_final: 0.8071 (m) REVERT: C 1227 LYS cc_start: 0.7595 (ptpp) cc_final: 0.7226 (mtmm) REVERT: E 155 LEU cc_start: 0.9230 (mm) cc_final: 0.8915 (mm) REVERT: E 177 MET cc_start: 0.7537 (mpp) cc_final: 0.7326 (mpp) REVERT: F 343 LYS cc_start: 0.8376 (mptt) cc_final: 0.7700 (ttpt) REVERT: F 371 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.8026 (mtt180) REVERT: F 396 ASP cc_start: 0.7979 (t0) cc_final: 0.7469 (t0) REVERT: F 409 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: F 459 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8214 (ptp-170) REVERT: F 483 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6528 (mm-30) REVERT: F 558 CYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6383 (t) REVERT: F 586 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7890 (mtpt) REVERT: F 634 GLU cc_start: 0.7211 (tp30) cc_final: 0.6980 (tp30) REVERT: F 729 LEU cc_start: 0.8448 (tp) cc_final: 0.8170 (tt) REVERT: G 870 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8075 (m) REVERT: G 903 MET cc_start: 0.7590 (ttt) cc_final: 0.7180 (mtp) REVERT: G 910 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: G 948 VAL cc_start: 0.8390 (p) cc_final: 0.8139 (t) REVERT: G 970 THR cc_start: 0.8776 (t) cc_final: 0.8397 (p) REVERT: G 986 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8141 (p) REVERT: G 1056 LYS cc_start: 0.7969 (mmtp) cc_final: 0.7668 (mttp) REVERT: I 115 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6538 (mt) REVERT: I 128 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7475 (ttpt) REVERT: I 152 ASN cc_start: 0.8461 (m-40) cc_final: 0.8121 (m-40) REVERT: I 167 ASP cc_start: 0.7535 (t0) cc_final: 0.7237 (t0) REVERT: I 208 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7600 (p) REVERT: J 387 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (mt) REVERT: J 498 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: J 501 ASP cc_start: 0.7740 (p0) cc_final: 0.7374 (p0) REVERT: J 547 ASP cc_start: 0.7913 (m-30) cc_final: 0.7555 (m-30) REVERT: J 548 MET cc_start: 0.7488 (ptm) cc_final: 0.7197 (ptm) REVERT: J 658 MET cc_start: 0.8026 (tmm) cc_final: 0.7566 (ttp) REVERT: J 714 ILE cc_start: 0.8327 (tp) cc_final: 0.8104 (tt) REVERT: K 890 ASP cc_start: 0.8244 (t0) cc_final: 0.7934 (t70) REVERT: K 1056 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7490 (mttm) REVERT: K 1069 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7904 (ttpp) REVERT: K 1093 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8343 (p) REVERT: K 1136 LYS cc_start: 0.7788 (mttp) cc_final: 0.7286 (mtpp) REVERT: K 1150 ASN cc_start: 0.8272 (t0) cc_final: 0.7600 (t0) REVERT: K 1196 GLU cc_start: 0.7327 (mp0) cc_final: 0.6895 (mp0) REVERT: K 1210 SER cc_start: 0.8457 (t) cc_final: 0.8179 (m) outliers start: 145 outliers final: 100 residues processed: 770 average time/residue: 0.1708 time to fit residues: 208.4213 Evaluate side-chains 790 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 674 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 165 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain B residue 378 MET 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 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 676 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 744 LEU 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 910 PHE Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 923 VAL 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 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 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 483 GLU Chi-restraints excluded: chain F residue 498 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 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 720 MET 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 916 THR 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 1025 SER 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 1217 MET Chi-restraints excluded: chain G residue 1240 ILE 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 183 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 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 450 ASP 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 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 857 LEU Chi-restraints excluded: chain K residue 868 THR Chi-restraints excluded: chain K residue 870 VAL Chi-restraints excluded: chain K residue 910 PHE Chi-restraints excluded: chain K residue 986 THR 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 1112 ILE 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 70 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 125 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** 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** C 964 ASN J 337 GLN J 406 HIS J 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092117 restraints weight = 40494.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094885 restraints weight = 18824.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096702 restraints weight = 10750.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097874 restraints weight = 7106.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098683 restraints weight = 5301.302| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2312 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= 0.129 Angle : 0.616 16.338 34425 Z= 0.300 Chirality : 0.045 0.567 3843 Planarity : 0.004 0.050 4416 Dihedral : 4.500 48.012 3732 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.59 % Allowed : 28.98 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3141 helix: 2.86 (0.28), residues: 324 sheet: 0.04 (0.17), residues: 957 loop : -0.95 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 930 TYR 0.020 0.001 TYR F 692 PHE 0.027 0.001 PHE K1235 TRP 0.010 0.001 TRP I 251 HIS 0.010 0.001 HIS J 503 Details of bonding type rmsd covalent geometry : bond 0.00306 (25185) covalent geometry : angle 0.59806 (34278) SS BOND : bond 0.00396 ( 51) SS BOND : angle 1.27635 ( 102) hydrogen bonds : bond 0.03745 ( 774) hydrogen bonds : angle 4.70113 ( 1986) link_BETA1-4 : bond 0.00487 ( 6) link_BETA1-4 : angle 1.10980 ( 18) link_NAG-ASN : bond 0.00828 ( 9) link_NAG-ASN : angle 4.75111 ( 27) *********************** 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 819 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 669 time to evaluate : 0.925 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: 0.8325 (mppt) cc_final: 0.8054 (mppt) REVERT: A 139 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7244 (mmmt) REVERT: B 343 LYS cc_start: 0.8191 (mptt) cc_final: 0.7741 (ttmt) REVERT: B 345 THR cc_start: 0.8516 (m) cc_final: 0.7959 (p) REVERT: B 378 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7395 (tpp) REVERT: B 396 ASP cc_start: 0.8082 (t0) cc_final: 0.7674 (t0) REVERT: B 430 MET cc_start: 0.7616 (tmm) cc_final: 0.6844 (tmm) REVERT: B 490 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7531 (mm110) REVERT: B 492 THR cc_start: 0.8248 (m) cc_final: 0.7750 (p) REVERT: B 545 ASN cc_start: 0.8319 (t0) cc_final: 0.8035 (t0) REVERT: B 729 LEU cc_start: 0.8180 (tp) cc_final: 0.7944 (tt) REVERT: C 890 ASP cc_start: 0.8399 (t0) cc_final: 0.7753 (t70) REVERT: C 910 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7719 (t80) REVERT: C 949 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7925 (ttm-80) REVERT: C 1117 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (p) REVERT: C 1131 LEU cc_start: 0.8233 (pp) cc_final: 0.7966 (pt) REVERT: C 1216 ASP cc_start: 0.7599 (t0) cc_final: 0.7296 (t0) REVERT: C 1227 LYS cc_start: 0.7591 (ptpp) cc_final: 0.7207 (mtmm) REVERT: E 155 LEU cc_start: 0.9231 (mm) cc_final: 0.8977 (mm) REVERT: E 177 MET cc_start: 0.7611 (mpp) cc_final: 0.7349 (mpp) REVERT: F 343 LYS cc_start: 0.8322 (mptt) cc_final: 0.7662 (ttpt) REVERT: F 371 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8056 (mtt180) REVERT: F 396 ASP cc_start: 0.8065 (t0) cc_final: 0.7488 (t0) REVERT: F 409 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: F 459 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8035 (ptp-170) REVERT: F 529 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7699 (ptpp) REVERT: F 558 CYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6428 (t) REVERT: F 586 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7858 (mtpt) REVERT: F 634 GLU cc_start: 0.7234 (tp30) cc_final: 0.6987 (tp30) REVERT: F 729 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (tt) REVERT: G 870 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8079 (m) REVERT: G 903 MET cc_start: 0.7679 (ttt) cc_final: 0.7267 (mtp) REVERT: G 970 THR cc_start: 0.8757 (t) cc_final: 0.8495 (m) REVERT: G 986 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8144 (p) REVERT: G 1046 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (m) REVERT: I 115 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6556 (mt) REVERT: I 128 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7554 (ttpt) REVERT: I 167 ASP cc_start: 0.7603 (t0) cc_final: 0.7249 (t0) REVERT: I 208 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7555 (p) REVERT: J 387 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7741 (mt) REVERT: J 490 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7612 (mm-40) REVERT: J 498 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: J 501 ASP cc_start: 0.7757 (p0) cc_final: 0.7289 (p0) REVERT: J 547 ASP cc_start: 0.7993 (m-30) cc_final: 0.7609 (m-30) REVERT: J 548 MET cc_start: 0.7563 (ptm) cc_final: 0.7215 (ptm) REVERT: J 641 GLU cc_start: 0.7769 (pt0) cc_final: 0.7565 (pt0) REVERT: J 658 MET cc_start: 0.8054 (tmm) cc_final: 0.7639 (ttp) REVERT: K 860 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: K 890 ASP cc_start: 0.8233 (t0) cc_final: 0.7914 (t70) REVERT: K 914 GLU cc_start: 0.7790 (mp0) cc_final: 0.7404 (mp0) REVERT: K 1056 LYS cc_start: 0.7897 (mmmm) cc_final: 0.7494 (mttm) REVERT: K 1069 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7903 (ttpp) REVERT: K 1093 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8317 (p) REVERT: K 1136 LYS cc_start: 0.7769 (mttp) cc_final: 0.7231 (mtpp) REVERT: K 1150 ASN cc_start: 0.8272 (t0) cc_final: 0.7509 (t0) REVERT: K 1196 GLU cc_start: 0.7346 (mp0) cc_final: 0.6889 (mp0) REVERT: K 1210 SER cc_start: 0.8438 (t) cc_final: 0.8139 (m) outliers start: 150 outliers final: 115 residues processed: 752 average time/residue: 0.1706 time to fit residues: 202.5837 Evaluate side-chains 796 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 664 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 378 MET 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 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 676 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 708 LEU 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 910 PHE 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 1032 THR 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 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 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 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 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 720 MET 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 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1025 SER 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 1217 MET Chi-restraints excluded: chain G residue 1240 ILE 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 387 ILE Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 450 ASP 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 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 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 735 THR Chi-restraints excluded: chain J residue 744 LEU 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 870 VAL 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 1046 VAL 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 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 7 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 228 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 467 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090718 restraints weight = 40436.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093434 restraints weight = 18922.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095195 restraints weight = 10868.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096409 restraints weight = 7230.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097061 restraints weight = 5380.404| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25251 Z= 0.152 Angle : 0.632 16.364 34425 Z= 0.309 Chirality : 0.045 0.588 3843 Planarity : 0.004 0.049 4416 Dihedral : 4.561 47.670 3732 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.59 % Allowed : 29.12 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3141 helix: 2.86 (0.28), residues: 324 sheet: 0.12 (0.18), residues: 873 loop : -0.97 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 604 TYR 0.020 0.001 TYR F 532 PHE 0.027 0.001 PHE K1235 TRP 0.011 0.001 TRP I 251 HIS 0.009 0.001 HIS J 503 Details of bonding type rmsd covalent geometry : bond 0.00361 (25185) covalent geometry : angle 0.61401 (34278) SS BOND : bond 0.00347 ( 51) SS BOND : angle 1.32641 ( 102) hydrogen bonds : bond 0.03944 ( 774) hydrogen bonds : angle 4.71092 ( 1986) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 1.16730 ( 18) link_NAG-ASN : bond 0.00803 ( 9) link_NAG-ASN : angle 4.82891 ( 27) *********************** 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 831 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 681 time to evaluate : 0.886 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: 0.8335 (mppt) cc_final: 0.8076 (mppt) REVERT: A 139 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7317 (mmmt) REVERT: A 152 ASN cc_start: 0.8728 (t0) cc_final: 0.8444 (t0) REVERT: A 183 LYS cc_start: 0.7860 (tptp) cc_final: 0.7437 (tptp) REVERT: B 343 LYS cc_start: 0.8223 (mptt) cc_final: 0.7683 (ttpt) REVERT: B 345 THR cc_start: 0.8540 (m) cc_final: 0.7992 (p) REVERT: B 396 ASP cc_start: 0.8129 (t0) cc_final: 0.7698 (t0) REVERT: B 430 MET cc_start: 0.7649 (tmm) cc_final: 0.6841 (tmm) REVERT: B 467 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7374 (mm-40) REVERT: B 490 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7538 (mm110) REVERT: B 492 THR cc_start: 0.8325 (m) cc_final: 0.7832 (p) REVERT: B 729 LEU cc_start: 0.8248 (tp) cc_final: 0.7997 (tt) REVERT: C 890 ASP cc_start: 0.8398 (t0) cc_final: 0.7726 (t70) REVERT: C 949 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7928 (ttm-80) REVERT: C 964 ASN cc_start: 0.8180 (t160) cc_final: 0.7851 (t0) REVERT: C 1035 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7264 (ttpp) REVERT: C 1117 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7706 (p) REVERT: C 1131 LEU cc_start: 0.8232 (pp) cc_final: 0.7962 (pt) REVERT: C 1216 ASP cc_start: 0.7647 (t0) cc_final: 0.7331 (t0) REVERT: C 1227 LYS cc_start: 0.7612 (ptpp) cc_final: 0.7251 (mtmm) REVERT: E 155 LEU cc_start: 0.9225 (mm) cc_final: 0.8878 (mm) REVERT: F 371 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8057 (mtt180) REVERT: F 396 ASP cc_start: 0.8103 (t0) cc_final: 0.7457 (t0) REVERT: F 409 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: F 459 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8051 (ptp-170) REVERT: F 492 THR cc_start: 0.8433 (m) cc_final: 0.7966 (p) REVERT: F 634 GLU cc_start: 0.7223 (tp30) cc_final: 0.6949 (tp30) REVERT: F 729 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8186 (tt) REVERT: G 870 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8098 (m) REVERT: G 903 MET cc_start: 0.7730 (ttt) cc_final: 0.7307 (mtp) REVERT: G 970 THR cc_start: 0.8758 (t) cc_final: 0.8519 (m) REVERT: G 986 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8138 (p) REVERT: G 1046 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8378 (m) REVERT: I 115 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6632 (mt) REVERT: I 128 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7509 (ttpt) REVERT: I 167 ASP cc_start: 0.7685 (t0) cc_final: 0.7328 (t0) REVERT: I 208 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7681 (p) REVERT: J 395 HIS cc_start: 0.7376 (t70) cc_final: 0.6775 (t70) REVERT: J 490 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7681 (mm-40) REVERT: J 498 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: J 547 ASP cc_start: 0.7979 (m-30) cc_final: 0.7637 (m-30) REVERT: J 548 MET cc_start: 0.7541 (ptm) cc_final: 0.7253 (ptm) REVERT: J 558 CYS cc_start: 0.7233 (m) cc_final: 0.6988 (m) REVERT: J 658 MET cc_start: 0.8068 (tmm) cc_final: 0.7667 (ttp) REVERT: J 717 SER cc_start: 0.8014 (m) cc_final: 0.7778 (t) REVERT: J 729 LEU cc_start: 0.8253 (tp) cc_final: 0.8051 (tt) REVERT: K 860 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: K 890 ASP cc_start: 0.8217 (t0) cc_final: 0.7886 (t70) REVERT: K 914 GLU cc_start: 0.7799 (mp0) cc_final: 0.7269 (mp0) REVERT: K 1056 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7520 (mttm) REVERT: K 1069 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7917 (ttpp) REVERT: K 1093 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8305 (p) REVERT: K 1115 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7589 (p) REVERT: K 1136 LYS cc_start: 0.7773 (mttp) cc_final: 0.7157 (mtpp) REVERT: K 1150 ASN cc_start: 0.8218 (t0) cc_final: 0.7422 (t0) REVERT: K 1196 GLU cc_start: 0.7312 (mp0) cc_final: 0.6877 (mp0) REVERT: K 1210 SER cc_start: 0.8428 (t) cc_final: 0.8115 (m) outliers start: 150 outliers final: 114 residues processed: 768 average time/residue: 0.1552 time to fit residues: 187.9791 Evaluate side-chains 802 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 674 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 500 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL 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 676 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 708 LEU 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 870 VAL 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 1032 THR 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 256 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 499 GLU Chi-restraints excluded: chain F residue 532 TYR 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 720 MET 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 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1025 SER 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 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 389 ILE Chi-restraints excluded: chain J residue 450 ASP 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 709 LEU Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 735 THR Chi-restraints excluded: chain J residue 744 LEU 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 870 VAL 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 1053 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1107 GLU Chi-restraints excluded: chain K residue 1114 LEU Chi-restraints excluded: chain K residue 1115 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1158 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 1213 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 299 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 230 optimal weight: 0.0770 chunk 218 optimal weight: 0.4980 chunk 300 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 118 optimal weight: 0.0770 chunk 43 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.0898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 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 490 GLN F 559 HIS J 503 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090250 restraints weight = 41007.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093027 restraints weight = 18918.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094842 restraints weight = 10743.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095957 restraints weight = 7071.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096795 restraints weight = 5305.913| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25251 Z= 0.117 Angle : 0.619 16.003 34425 Z= 0.302 Chirality : 0.044 0.562 3843 Planarity : 0.004 0.047 4416 Dihedral : 4.382 47.764 3729 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.14 % Allowed : 29.24 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3141 helix: 2.88 (0.28), residues: 324 sheet: 0.13 (0.18), residues: 891 loop : -0.95 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 604 TYR 0.031 0.001 TYR K 952 PHE 0.027 0.001 PHE K1235 TRP 0.024 0.001 TRP A 251 HIS 0.012 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00281 (25185) covalent geometry : angle 0.60190 (34278) SS BOND : bond 0.00311 ( 51) SS BOND : angle 1.29642 ( 102) hydrogen bonds : bond 0.03666 ( 774) hydrogen bonds : angle 4.65326 ( 1986) link_BETA1-4 : bond 0.00529 ( 6) link_BETA1-4 : angle 1.16205 ( 18) link_NAG-ASN : bond 0.00812 ( 9) link_NAG-ASN : angle 4.67811 ( 27) *********************** 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 819 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 681 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8233 (mppt) cc_final: 0.8032 (mppt) REVERT: A 139 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7328 (mmmt) REVERT: A 152 ASN cc_start: 0.8775 (t0) cc_final: 0.8493 (t0) REVERT: B 343 LYS cc_start: 0.8289 (mptt) cc_final: 0.7805 (ttmt) REVERT: B 345 THR cc_start: 0.8533 (m) cc_final: 0.8011 (p) REVERT: B 396 ASP cc_start: 0.8083 (t0) cc_final: 0.7671 (t0) REVERT: B 430 MET cc_start: 0.7632 (tmm) cc_final: 0.6841 (tmm) REVERT: B 490 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7555 (mm110) REVERT: B 492 THR cc_start: 0.8316 (m) cc_final: 0.7821 (p) REVERT: B 566 LYS cc_start: 0.8272 (pttp) cc_final: 0.7934 (ptpp) REVERT: B 701 SER cc_start: 0.8062 (t) cc_final: 0.7838 (p) REVERT: B 729 LEU cc_start: 0.8263 (tp) cc_final: 0.8005 (tt) REVERT: C 867 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8163 (pttm) REVERT: C 890 ASP cc_start: 0.8365 (t0) cc_final: 0.7701 (t70) REVERT: C 949 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: C 964 ASN cc_start: 0.8119 (t160) cc_final: 0.7795 (t0) REVERT: C 1022 THR cc_start: 0.8210 (m) cc_final: 0.7933 (t) REVERT: C 1035 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7276 (ttpp) REVERT: C 1117 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7670 (p) REVERT: C 1131 LEU cc_start: 0.8241 (pp) cc_final: 0.8015 (pt) REVERT: C 1216 ASP cc_start: 0.7623 (t0) cc_final: 0.7325 (t0) REVERT: C 1227 LYS cc_start: 0.7615 (ptpp) cc_final: 0.7270 (mtmm) REVERT: E 155 LEU cc_start: 0.9103 (mm) cc_final: 0.8894 (mm) REVERT: F 371 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.8043 (mtt180) REVERT: F 396 ASP cc_start: 0.8036 (t0) cc_final: 0.7440 (t0) REVERT: F 409 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 459 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8106 (ptp-170) REVERT: F 492 THR cc_start: 0.8438 (m) cc_final: 0.7977 (p) REVERT: F 558 CYS cc_start: 0.6757 (m) cc_final: 0.6315 (t) REVERT: F 634 GLU cc_start: 0.7212 (tp30) cc_final: 0.6933 (tp30) REVERT: F 729 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8162 (tt) REVERT: G 853 LEU cc_start: 0.7954 (tt) cc_final: 0.7726 (tt) REVERT: G 870 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (m) REVERT: G 903 MET cc_start: 0.7714 (ttt) cc_final: 0.7310 (mtp) REVERT: G 970 THR cc_start: 0.8782 (t) cc_final: 0.8532 (m) REVERT: G 986 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8154 (p) REVERT: G 1029 TYR cc_start: 0.8037 (t80) cc_final: 0.7625 (t80) REVERT: G 1046 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (m) REVERT: I 115 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6614 (mt) REVERT: I 128 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7373 (ttpt) REVERT: I 167 ASP cc_start: 0.7594 (t0) cc_final: 0.7332 (t0) REVERT: I 208 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7691 (p) REVERT: I 240 GLU cc_start: 0.2321 (OUTLIER) cc_final: 0.1143 (tp30) REVERT: J 395 HIS cc_start: 0.7306 (t70) cc_final: 0.6747 (t70) REVERT: J 490 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7711 (mm-40) REVERT: J 498 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: J 547 ASP cc_start: 0.7907 (m-30) cc_final: 0.7616 (m-30) REVERT: J 548 MET cc_start: 0.7513 (ptm) cc_final: 0.7264 (ptm) REVERT: J 658 MET cc_start: 0.8048 (tmm) cc_final: 0.7607 (ttp) REVERT: K 860 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: K 890 ASP cc_start: 0.8204 (t0) cc_final: 0.7858 (t70) REVERT: K 1056 LYS cc_start: 0.7961 (mmmm) cc_final: 0.7536 (mttm) REVERT: K 1069 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7936 (ttpp) REVERT: K 1093 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8339 (p) REVERT: K 1115 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7589 (p) REVERT: K 1136 LYS cc_start: 0.7739 (mttp) cc_final: 0.7224 (mtpp) REVERT: K 1150 ASN cc_start: 0.8161 (t0) cc_final: 0.7368 (t0) REVERT: K 1196 GLU cc_start: 0.7295 (mp0) cc_final: 0.6895 (mp0) REVERT: K 1210 SER cc_start: 0.8434 (t) cc_final: 0.8121 (m) REVERT: K 1243 LEU cc_start: 0.8007 (tp) cc_final: 0.7805 (tt) outliers start: 138 outliers final: 114 residues processed: 760 average time/residue: 0.1727 time to fit residues: 206.7610 Evaluate side-chains 810 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 680 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 208 THR 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 545 ASN 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 676 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 708 LEU 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 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 1032 THR 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 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 499 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 532 TYR 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 720 MET 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 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 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 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 450 ASP 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 575 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 709 LEU Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 735 THR Chi-restraints excluded: chain J residue 744 LEU 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 870 VAL 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 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 1213 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 22 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 225 optimal weight: 0.4980 chunk 187 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091104 restraints weight = 40634.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093963 restraints weight = 18561.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095809 restraints weight = 10516.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097056 restraints weight = 6915.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097866 restraints weight = 5101.154| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2598 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= 0.116 Angle : 0.618 15.877 34425 Z= 0.302 Chirality : 0.044 0.557 3843 Planarity : 0.004 0.047 4416 Dihedral : 4.353 48.146 3729 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.07 % Allowed : 29.39 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3141 helix: 2.87 (0.28), residues: 324 sheet: 0.18 (0.18), residues: 867 loop : -0.91 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 221 TYR 0.029 0.001 TYR K 952 PHE 0.027 0.001 PHE K1235 TRP 0.024 0.001 TRP A 251 HIS 0.004 0.001 HIS J 395 Details of bonding type rmsd covalent geometry : bond 0.00278 (25185) covalent geometry : angle 0.60071 (34278) SS BOND : bond 0.00295 ( 51) SS BOND : angle 1.26994 ( 102) hydrogen bonds : bond 0.03622 ( 774) hydrogen bonds : angle 4.59958 ( 1986) link_BETA1-4 : bond 0.00448 ( 6) link_BETA1-4 : angle 1.12605 ( 18) link_NAG-ASN : bond 0.00806 ( 9) link_NAG-ASN : angle 4.64315 ( 27) ********************** 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 816 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 680 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8271 (mppt) cc_final: 0.8043 (mppt) REVERT: A 139 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7318 (mmmt) REVERT: A 152 ASN cc_start: 0.8764 (t0) cc_final: 0.8463 (t0) REVERT: A 183 LYS cc_start: 0.7780 (tptp) cc_final: 0.7345 (tptp) REVERT: A 224 PHE cc_start: 0.7792 (m-80) cc_final: 0.7555 (m-80) REVERT: B 343 LYS cc_start: 0.8357 (mptt) cc_final: 0.7784 (ttmt) REVERT: B 345 THR cc_start: 0.8536 (m) cc_final: 0.7997 (p) REVERT: B 396 ASP cc_start: 0.8109 (t0) cc_final: 0.7665 (t0) REVERT: B 430 MET cc_start: 0.7649 (tmm) cc_final: 0.6841 (tmm) REVERT: B 490 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7542 (mm110) REVERT: B 492 THR cc_start: 0.8318 (m) cc_final: 0.7819 (p) REVERT: B 566 LYS cc_start: 0.8266 (pttp) cc_final: 0.7907 (ptpp) REVERT: B 701 SER cc_start: 0.8038 (t) cc_final: 0.7811 (p) REVERT: B 729 LEU cc_start: 0.8238 (tp) cc_final: 0.7987 (tt) REVERT: C 867 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (pttm) REVERT: C 890 ASP cc_start: 0.8377 (t0) cc_final: 0.7918 (t70) REVERT: C 949 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7933 (ttm-80) REVERT: C 964 ASN cc_start: 0.8153 (t160) cc_final: 0.7783 (t0) REVERT: C 1022 THR cc_start: 0.8122 (m) cc_final: 0.7840 (t) REVERT: C 1035 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7253 (ttpp) REVERT: C 1117 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7639 (p) REVERT: C 1131 LEU cc_start: 0.8203 (pp) cc_final: 0.7969 (pt) REVERT: C 1216 ASP cc_start: 0.7628 (t0) cc_final: 0.7309 (t0) REVERT: C 1227 LYS cc_start: 0.7599 (ptpp) cc_final: 0.7232 (mtmm) REVERT: E 155 LEU cc_start: 0.9120 (mm) cc_final: 0.8894 (mm) REVERT: E 258 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7981 (ttm170) REVERT: F 371 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.8046 (mtt180) REVERT: F 396 ASP cc_start: 0.8064 (t0) cc_final: 0.7426 (t0) REVERT: F 399 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8212 (mmtp) REVERT: F 409 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: F 459 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8072 (ptp-170) REVERT: F 492 THR cc_start: 0.8423 (m) cc_final: 0.7955 (p) REVERT: F 557 GLN cc_start: 0.7636 (mm110) cc_final: 0.7399 (mt0) REVERT: F 558 CYS cc_start: 0.6832 (m) cc_final: 0.6372 (t) REVERT: F 634 GLU cc_start: 0.7215 (tp30) cc_final: 0.6933 (tp30) REVERT: F 729 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8136 (tt) REVERT: F 740 VAL cc_start: 0.7826 (p) cc_final: 0.7604 (m) REVERT: G 853 LEU cc_start: 0.7896 (tt) cc_final: 0.7654 (tt) REVERT: G 870 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8040 (m) REVERT: G 903 MET cc_start: 0.7704 (ttt) cc_final: 0.7306 (mtp) REVERT: G 947 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: G 970 THR cc_start: 0.8762 (t) cc_final: 0.8525 (m) REVERT: G 986 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8149 (p) REVERT: G 1029 TYR cc_start: 0.8049 (t80) cc_final: 0.7658 (t80) REVERT: G 1046 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8379 (m) REVERT: G 1056 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7731 (mttp) REVERT: I 115 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6642 (mt) REVERT: I 128 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7424 (ttpt) REVERT: I 167 ASP cc_start: 0.7632 (t0) cc_final: 0.7349 (t0) REVERT: I 194 ASN cc_start: 0.7431 (t0) cc_final: 0.7096 (t0) REVERT: I 208 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7712 (p) REVERT: I 240 GLU cc_start: 0.2183 (OUTLIER) cc_final: 0.1057 (tp30) REVERT: J 395 HIS cc_start: 0.7327 (t70) cc_final: 0.6739 (t70) REVERT: J 490 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7710 (mm-40) REVERT: J 498 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: J 547 ASP cc_start: 0.7923 (m-30) cc_final: 0.7583 (m-30) REVERT: J 548 MET cc_start: 0.7537 (ptm) cc_final: 0.7268 (ptm) REVERT: J 658 MET cc_start: 0.8047 (tmm) cc_final: 0.7632 (ttp) REVERT: K 860 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: K 890 ASP cc_start: 0.8209 (t0) cc_final: 0.7881 (t70) REVERT: K 964 ASN cc_start: 0.8410 (p0) cc_final: 0.8094 (p0) REVERT: K 1022 THR cc_start: 0.8223 (m) cc_final: 0.7911 (t) REVERT: K 1056 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7532 (mttm) REVERT: K 1069 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7916 (ttpp) REVERT: K 1079 ASN cc_start: 0.8469 (t0) cc_final: 0.8247 (t0) REVERT: K 1093 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8304 (p) REVERT: K 1115 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7559 (p) REVERT: K 1136 LYS cc_start: 0.7734 (mttp) cc_final: 0.7204 (mtpp) REVERT: K 1150 ASN cc_start: 0.8135 (t0) cc_final: 0.7346 (t0) REVERT: K 1196 GLU cc_start: 0.7319 (mp0) cc_final: 0.6863 (mp0) REVERT: K 1210 SER cc_start: 0.8408 (t) cc_final: 0.8096 (m) REVERT: K 1248 CYS cc_start: 0.8299 (t) cc_final: 0.7625 (t) outliers start: 136 outliers final: 107 residues processed: 760 average time/residue: 0.1705 time to fit residues: 204.4959 Evaluate side-chains 802 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 677 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 208 THR 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 541 VAL Chi-restraints excluded: chain B residue 549 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 676 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 708 LEU 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 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 1032 THR 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 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 514 LEU Chi-restraints excluded: chain F residue 532 TYR 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 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 720 MET 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 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 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 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 450 ASP 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 575 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 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 735 THR Chi-restraints excluded: chain J residue 744 LEU 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 870 VAL 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 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 1158 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 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 60 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089889 restraints weight = 41067.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092671 restraints weight = 18969.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.094481 restraints weight = 10739.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095676 restraints weight = 7097.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096426 restraints weight = 5264.783| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 25251 Z= 0.211 Angle : 0.752 59.157 34425 Z= 0.410 Chirality : 0.047 0.562 3843 Planarity : 0.004 0.047 4416 Dihedral : 4.367 48.116 3729 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.88 % Allowed : 29.72 % Favored : 65.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3141 helix: 2.82 (0.28), residues: 324 sheet: 0.19 (0.18), residues: 873 loop : -0.91 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 930 TYR 0.025 0.002 TYR K 952 PHE 0.027 0.002 PHE K1235 TRP 0.018 0.001 TRP A 251 HIS 0.011 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00478 (25185) covalent geometry : angle 0.73830 (34278) SS BOND : bond 0.00359 ( 51) SS BOND : angle 1.31252 ( 102) hydrogen bonds : bond 0.03796 ( 774) hydrogen bonds : angle 4.60320 ( 1986) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 1.20580 ( 18) link_NAG-ASN : bond 0.00805 ( 9) link_NAG-ASN : angle 4.67121 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6001.32 seconds wall clock time: 103 minutes 48.81 seconds (6228.81 seconds total)