Starting phenix.real_space_refine on Sun Jul 5 00:57:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_37981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_37981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_37981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_37981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0l_37981/07_2026/8x0l_37981.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 6.25, 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: 2.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 58 sheets defined 14.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 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: 7.60 Time building geometry restraints manager: 3.02 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.140 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 are 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/Z covalent geometry : bond 0.00371 / 0.16 (25185) covalent geometry : angle 0.71118 / 0.38 (34278) SS BOND : bond 0.00376 / 0.24 ( 51) SS BOND : angle 1.70468 / 1.18 ( 102) hydrogen bonds : bond 0.24437 / 16.37 ( 774) hydrogen bonds : angle 7.46455 / 5.29 ( 1986) link_BETA1-4 : bond 0.00597 / 0.44 ( 6) link_BETA1-4 : angle 1.48171 / 0.87 ( 18) link_NAG-ASN : bond 0.00984 / 0.55 ( 9) link_NAG-ASN : angle 5.93462 / 5.06 ( 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 : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.1576 time to fit residues: 175.1323 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 : 0.838 ------------------------------------------------------------------------------- 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... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090818 restraints weight = 40413.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093668 restraints weight = 18433.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095516 restraints weight = 10429.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096711 restraints weight = 6894.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097497 restraints weight = 5100.178| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25251 Z= 0.204 Angle : 0.674 18.294 34425 Z= 0.337 Chirality : 0.047 0.615 3843 Planarity : 0.005 0.067 4416 Dihedral : 5.649 58.547 3760 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.03 % Allowed : 27.82 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3141 helix: 2.51 (0.28), residues: 324 sheet: -0.12 (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 0.030 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/Z covalent geometry : bond 0.00480 / 0.20 (25185) covalent geometry : angle 0.65469 / 0.33 (34278) SS BOND : bond 0.00415 / 0.27 ( 51) SS BOND : angle 1.23667 / 0.94 ( 102) hydrogen bonds : bond 0.05318 / 3.59 ( 774) hydrogen bonds : angle 5.49894 / 3.89 ( 1986) link_BETA1-4 : bond 0.00613 / 0.43 ( 6) link_BETA1-4 : angle 1.36268 / 0.86 ( 18) link_NAG-ASN : bond 0.00994 / 0.57 ( 9) link_NAG-ASN : angle 5.26083 / 4.84 ( 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 825 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 690 time to evaluate : 0.983 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: 0.7649 (mmmt) cc_final: 0.7229 (mmmt) REVERT: B 345 THR cc_start: 0.8443 (m) cc_final: 0.8015 (p) REVERT: B 430 MET cc_start: 0.7548 (tmm) cc_final: 0.6729 (tmm) REVERT: B 492 THR cc_start: 0.8119 (m) cc_final: 0.7670 (p) REVERT: B 545 ASN cc_start: 0.8561 (t160) cc_final: 0.8276 (t0) REVERT: B 586 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8079 (mtpt) REVERT: C 834 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8084 (mt) REVERT: C 890 ASP cc_start: 0.8418 (t0) cc_final: 0.7886 (t70) REVERT: C 910 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 913 SER cc_start: 0.8218 (p) cc_final: 0.7814 (p) REVERT: C 949 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: C 964 ASN cc_start: 0.7950 (m-40) cc_final: 0.7495 (t0) REVERT: C 1185 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6505 (m) REVERT: C 1186 SER cc_start: 0.8598 (t) cc_final: 0.8389 (t) REVERT: C 1203 VAL cc_start: 0.8373 (m) cc_final: 0.8152 (m) REVERT: C 1216 ASP cc_start: 0.7994 (t0) cc_final: 0.7752 (t0) REVERT: C 1218 SER cc_start: 0.8421 (t) cc_final: 0.7830 (p) REVERT: C 1227 LYS cc_start: 0.7670 (ptpp) cc_final: 0.7327 (mtmm) REVERT: E 113 MET cc_start: 0.4214 (mmm) cc_final: 0.3781 (mmm) REVERT: F 396 ASP cc_start: 0.7892 (t0) cc_final: 0.7453 (t0) REVERT: F 409 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: F 622 ASP cc_start: 0.7695 (m-30) cc_final: 0.7485 (m-30) REVERT: F 704 VAL cc_start: 0.8405 (t) cc_final: 0.8202 (p) REVERT: G 903 MET cc_start: 0.7704 (ttt) cc_final: 0.7332 (mtp) REVERT: G 948 VAL cc_start: 0.8648 (p) cc_final: 0.8314 (t) REVERT: G 986 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8068 (p) REVERT: G 1192 SER cc_start: 0.8525 (p) cc_final: 0.8288 (m) REVERT: I 266 GLU cc_start: 0.8051 (tt0) cc_final: 0.7772 (tt0) REVERT: J 341 VAL cc_start: 0.8860 (t) cc_final: 0.8644 (p) REVERT: J 368 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7324 (mm-30) REVERT: J 490 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7643 (mm-40) REVERT: J 501 ASP cc_start: 0.7697 (p0) cc_final: 0.7479 (p0) REVERT: J 547 ASP cc_start: 0.7941 (m-30) cc_final: 0.7683 (m-30) REVERT: J 556 GLU cc_start: 0.7783 (pp20) cc_final: 0.7165 (pp20) REVERT: J 707 SER cc_start: 0.7876 (t) cc_final: 0.7666 (p) REVERT: J 717 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7825 (t) REVERT: K 890 ASP cc_start: 0.8186 (t0) cc_final: 0.7905 (t70) REVERT: K 951 MET cc_start: 0.7654 (mtt) cc_final: 0.7280 (mtt) outliers start: 135 outliers final: 80 residues processed: 773 average time/residue: 0.1512 time to fit residues: 186.4817 Evaluate side-chains 762 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 675 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 556 GLU 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 363 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE 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 910 PHE Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 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 607 THR 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 717 SER Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 850 GLU 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: 0.8980 chunk 307 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN F 686 GLN J 517 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089052 restraints weight = 40579.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.091850 restraints weight = 18621.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093670 restraints weight = 10534.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094779 restraints weight = 6950.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095633 restraints weight = 5217.011| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25251 Z= 0.188 Angle : 0.644 17.908 34425 Z= 0.320 Chirality : 0.046 0.588 3843 Planarity : 0.005 0.057 4416 Dihedral : 5.140 55.092 3733 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.51 % Allowed : 27.60 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3141 helix: 2.62 (0.28), residues: 324 sheet: -0.12 (0.16), residues: 1008 loop : -1.07 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 221 TYR 0.021 0.002 TYR F 532 PHE 0.027 0.002 PHE K1235 TRP 0.011 0.001 TRP I 251 HIS 0.017 0.001 HIS E 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (25185) covalent geometry : angle 0.62317 / 0.31 (34278) SS BOND : bond 0.00534 / 0.38 ( 51) SS BOND : angle 1.46997 / 1.02 ( 102) hydrogen bonds : bond 0.04751 / 3.19 ( 774) hydrogen bonds : angle 5.20931 / 3.68 ( 1986) link_BETA1-4 : bond 0.00431 / 0.31 ( 6) link_BETA1-4 : angle 1.30923 / 0.80 ( 18) link_NAG-ASN : bond 0.00955 / 0.53 ( 9) link_NAG-ASN : angle 5.11818 / 4.71 ( 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 834 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 686 time to evaluate : 0.920 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: 0.7955 (mppt) cc_final: 0.7701 (mppt) REVERT: A 139 LYS cc_start: 0.7712 (mmmt) cc_final: 0.7289 (mmmt) REVERT: A 258 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8137 (tmm-80) REVERT: B 343 LYS cc_start: 0.8306 (mptt) cc_final: 0.7667 (ttmt) REVERT: B 387 ILE cc_start: 0.8198 (tt) cc_final: 0.7972 (mt) REVERT: B 430 MET cc_start: 0.7578 (tmm) cc_final: 0.6680 (tmm) REVERT: B 450 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6471 (m-30) REVERT: B 492 THR cc_start: 0.8172 (m) cc_final: 0.7766 (p) REVERT: B 586 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8086 (mtpt) REVERT: B 686 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7552 (mt0) REVERT: C 834 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (mt) REVERT: C 890 ASP cc_start: 0.8408 (t0) cc_final: 0.7815 (t70) REVERT: C 910 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7758 (t80) REVERT: C 913 SER cc_start: 0.8328 (p) cc_final: 0.7930 (p) REVERT: C 949 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7735 (ttm-80) REVERT: C 964 ASN cc_start: 0.7988 (t0) cc_final: 0.7529 (t0) REVERT: C 1117 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7729 (p) REVERT: C 1138 ASP cc_start: 0.7846 (p0) cc_final: 0.7637 (p0) REVERT: C 1185 CYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6534 (m) REVERT: C 1216 ASP cc_start: 0.7896 (t0) cc_final: 0.7685 (t0) REVERT: C 1218 SER cc_start: 0.8494 (t) cc_final: 0.7855 (p) REVERT: C 1227 LYS cc_start: 0.7710 (ptpp) cc_final: 0.7356 (mtmm) REVERT: E 113 MET cc_start: 0.4215 (mmm) cc_final: 0.3727 (mmm) REVERT: E 178 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5476 (ptt-90) REVERT: F 361 CYS cc_start: 0.5518 (p) cc_final: 0.5292 (p) REVERT: F 396 ASP cc_start: 0.7987 (t0) cc_final: 0.7546 (t0) REVERT: F 409 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: F 491 GLN cc_start: 0.8005 (mt0) cc_final: 0.7781 (mt0) REVERT: F 591 PHE cc_start: 0.8354 (m-80) cc_final: 0.7741 (m-80) REVERT: F 704 VAL cc_start: 0.8371 (t) cc_final: 0.8165 (p) REVERT: G 903 MET cc_start: 0.7756 (ttt) cc_final: 0.7330 (mtp) REVERT: G 948 VAL cc_start: 0.8623 (p) cc_final: 0.8334 (t) REVERT: G 986 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8083 (p) REVERT: I 208 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7565 (p) REVERT: I 266 GLU cc_start: 0.8111 (tt0) cc_final: 0.7832 (tt0) REVERT: J 341 VAL cc_start: 0.8881 (t) cc_final: 0.8652 (p) REVERT: J 387 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7865 (mt) REVERT: J 490 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7661 (mm-40) REVERT: J 498 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: J 501 ASP cc_start: 0.7733 (p0) cc_final: 0.7507 (p0) REVERT: J 522 LYS cc_start: 0.8211 (tttp) cc_final: 0.7942 (tttp) REVERT: J 547 ASP cc_start: 0.7845 (m-30) cc_final: 0.7615 (m-30) REVERT: J 556 GLU cc_start: 0.7793 (pp20) cc_final: 0.7245 (pp20) REVERT: J 707 SER cc_start: 0.7867 (t) cc_final: 0.7584 (p) REVERT: K 890 ASP cc_start: 0.8223 (t0) cc_final: 0.7933 (t70) REVERT: K 1056 LYS cc_start: 0.8021 (mmmm) cc_final: 0.7610 (mttp) REVERT: K 1069 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7991 (mtpp) REVERT: K 1136 LYS cc_start: 0.7784 (mttp) cc_final: 0.7373 (mtpp) REVERT: K 1196 GLU cc_start: 0.7300 (mp0) cc_final: 0.7020 (mp0) REVERT: K 1210 SER cc_start: 0.8448 (t) cc_final: 0.8245 (t) outliers start: 148 outliers final: 96 residues processed: 778 average time/residue: 0.1592 time to fit residues: 195.8869 Evaluate side-chains 771 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 662 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 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 834 ILE 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 923 VAL 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 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1168 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 129 VAL Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 486 CYS 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 623 HIS Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS 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 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1175 SER Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 208 THR 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 449 GLN 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 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 720 MET Chi-restraints excluded: chain J residue 722 VAL Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain K residue 825 VAL Chi-restraints excluded: chain K residue 857 LEU Chi-restraints excluded: chain K residue 882 GLU Chi-restraints excluded: chain K residue 910 PHE 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: 1.9990 chunk 299 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 259 optimal weight: 0.3980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 GLN G1026 ASN J 517 GLN K 940 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089627 restraints weight = 40601.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092462 restraints weight = 18495.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094292 restraints weight = 10416.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095444 restraints weight = 6852.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096284 restraints weight = 5098.117| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25251 Z= 0.140 Angle : 0.627 17.245 34425 Z= 0.308 Chirality : 0.045 0.578 3843 Planarity : 0.005 0.056 4416 Dihedral : 4.883 50.936 3732 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.85 % Allowed : 27.30 % Favored : 66.85 % 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 are not related in a simple way. whole: -0.50 (0.15), residues: 3141 helix: 2.73 (0.28), residues: 324 sheet: -0.08 (0.17), residues: 975 loop : -1.06 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 604 TYR 0.021 0.001 TYR F 532 PHE 0.029 0.001 PHE K1235 TRP 0.008 0.001 TRP I 251 HIS 0.005 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (25185) covalent geometry : angle 0.60571 / 0.30 (34278) SS BOND : bond 0.00432 / 0.29 ( 51) SS BOND : angle 1.57521 / 1.04 ( 102) hydrogen bonds : bond 0.04145 / 2.80 ( 774) hydrogen bonds : angle 5.05210 / 3.56 ( 1986) link_BETA1-4 : bond 0.00462 / 0.32 ( 6) link_BETA1-4 : angle 1.21574 / 0.74 ( 18) link_NAG-ASN : bond 0.00923 / 0.52 ( 9) link_NAG-ASN : angle 4.97345 / 4.56 ( 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 837 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 680 time to evaluate : 1.110 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: 0.8007 (mppt) cc_final: 0.7766 (mppt) REVERT: A 139 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7312 (mmmt) REVERT: A 258 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (tmm-80) REVERT: B 343 LYS cc_start: 0.8301 (mptt) cc_final: 0.7683 (ttpt) REVERT: B 345 THR cc_start: 0.8523 (m) cc_final: 0.8049 (p) REVERT: B 378 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7275 (tpp) REVERT: B 396 ASP cc_start: 0.8064 (t0) cc_final: 0.7779 (t0) REVERT: B 430 MET cc_start: 0.7554 (tmm) cc_final: 0.6791 (tmm) REVERT: B 450 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: B 492 THR cc_start: 0.8183 (m) cc_final: 0.7753 (p) REVERT: B 586 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8167 (mtpt) REVERT: B 686 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7634 (mt0) REVERT: B 699 THR cc_start: 0.7921 (t) cc_final: 0.7703 (p) REVERT: C 867 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8257 (pttm) REVERT: C 890 ASP cc_start: 0.8381 (t0) cc_final: 0.7780 (t70) REVERT: C 910 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7640 (t80) REVERT: C 949 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: C 964 ASN cc_start: 0.7957 (t0) cc_final: 0.7703 (t0) REVERT: C 1035 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7224 (ttpp) REVERT: C 1117 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7720 (p) REVERT: C 1138 ASP cc_start: 0.7872 (p0) cc_final: 0.7656 (p0) REVERT: C 1185 CYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6561 (m) REVERT: C 1216 ASP cc_start: 0.7849 (t0) cc_final: 0.7629 (t0) REVERT: C 1218 SER cc_start: 0.8538 (t) cc_final: 0.7957 (p) REVERT: C 1227 LYS cc_start: 0.7687 (ptpp) cc_final: 0.7356 (mtmm) REVERT: F 396 ASP cc_start: 0.7971 (t0) cc_final: 0.7583 (t0) REVERT: F 408 ILE cc_start: 0.8275 (mt) cc_final: 0.7722 (mt) REVERT: F 409 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: F 459 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8259 (ptp-170) REVERT: F 558 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6241 (t) REVERT: F 586 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7999 (mtpt) REVERT: F 591 PHE cc_start: 0.8343 (m-80) cc_final: 0.7721 (m-80) REVERT: F 720 MET cc_start: 0.7379 (tmm) cc_final: 0.7158 (tmm) REVERT: G 903 MET cc_start: 0.7716 (ttt) cc_final: 0.7321 (mtp) REVERT: G 948 VAL cc_start: 0.8582 (p) cc_final: 0.8305 (t) REVERT: G 970 THR cc_start: 0.8812 (t) cc_final: 0.8426 (p) REVERT: G 986 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8103 (p) REVERT: I 139 LYS cc_start: 0.8152 (mttm) cc_final: 0.7820 (mttm) REVERT: I 208 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7585 (p) REVERT: J 387 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (mt) REVERT: J 490 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7605 (mm-40) REVERT: J 498 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: J 522 LYS cc_start: 0.8187 (tttp) cc_final: 0.7913 (tttp) REVERT: J 547 ASP cc_start: 0.7857 (m-30) cc_final: 0.7618 (m-30) REVERT: J 556 GLU cc_start: 0.7810 (pp20) cc_final: 0.7254 (pp20) REVERT: J 641 GLU cc_start: 0.7636 (pt0) cc_final: 0.7328 (pt0) REVERT: J 707 SER cc_start: 0.7866 (t) cc_final: 0.7578 (p) REVERT: K 822 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (ptm) REVERT: K 890 ASP cc_start: 0.8225 (t0) cc_final: 0.7926 (t70) REVERT: K 910 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: K 1056 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7591 (mttp) REVERT: K 1069 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7994 (ttpp) REVERT: K 1093 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (p) REVERT: K 1117 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7621 (p) REVERT: K 1136 LYS cc_start: 0.7789 (mttp) cc_final: 0.7284 (mtpp) REVERT: K 1196 GLU cc_start: 0.7306 (mp0) cc_final: 0.6982 (mp0) REVERT: K 1210 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8227 (t) outliers start: 157 outliers final: 110 residues processed: 778 average time/residue: 0.1539 time to fit residues: 190.5103 Evaluate side-chains 803 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 673 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 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 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 SER Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 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 722 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 877 CYS Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 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 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 147 LYS Chi-restraints excluded: chain I residue 208 THR 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 345 THR Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 447 SER Chi-restraints excluded: chain J residue 449 GLN Chi-restraints excluded: chain J residue 450 ASP Chi-restraints excluded: chain J residue 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 709 LEU 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 822 MET 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 868 THR Chi-restraints excluded: chain K residue 870 VAL 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 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 1117 THR Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1210 SER 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: 10.0000 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 277 optimal weight: 0.0070 chunk 148 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 545 ASN F 686 GLN G1026 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089233 restraints weight = 40777.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092029 restraints weight = 18624.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093866 restraints weight = 10536.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095076 restraints weight = 6907.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095877 restraints weight = 5115.203| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25251 Z= 0.150 Angle : 0.626 16.940 34425 Z= 0.306 Chirality : 0.045 0.584 3843 Planarity : 0.005 0.051 4416 Dihedral : 4.772 47.595 3732 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.44 % Allowed : 26.93 % 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 are not related in a simple way. whole: -0.48 (0.15), residues: 3141 helix: 2.71 (0.28), residues: 324 sheet: -0.04 (0.17), residues: 909 loop : -1.03 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 604 TYR 0.022 0.001 TYR F 532 PHE 0.029 0.001 PHE K1235 TRP 0.012 0.001 TRP E 195 HIS 0.005 0.001 HIS J 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (25185) covalent geometry : angle 0.60641 / 0.30 (34278) SS BOND : bond 0.00399 / 0.27 ( 51) SS BOND : angle 1.43313 / 0.94 ( 102) hydrogen bonds : bond 0.04107 / 2.78 ( 774) hydrogen bonds : angle 4.93370 / 3.47 ( 1986) link_BETA1-4 : bond 0.00491 / 0.34 ( 6) link_BETA1-4 : angle 1.19377 / 0.72 ( 18) link_NAG-ASN : bond 0.00874 / 0.49 ( 9) link_NAG-ASN : angle 4.92736 / 4.50 ( 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 847 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 674 time to evaluate : 0.649 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: 0.8230 (mppt) cc_final: 0.7929 (mppt) REVERT: A 139 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7271 (mmmt) REVERT: A 258 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (tmm-80) REVERT: B 343 LYS cc_start: 0.8251 (mptt) cc_final: 0.7656 (ttpt) REVERT: B 378 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7330 (tpp) REVERT: B 389 ILE cc_start: 0.8196 (mm) cc_final: 0.7896 (mt) REVERT: B 396 ASP cc_start: 0.8101 (t0) cc_final: 0.7723 (t0) REVERT: B 430 MET cc_start: 0.7593 (tmm) cc_final: 0.6835 (tmm) REVERT: B 492 THR cc_start: 0.8230 (m) cc_final: 0.7764 (p) REVERT: B 586 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8189 (mtpt) REVERT: B 686 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7559 (mt0) REVERT: B 699 THR cc_start: 0.7872 (t) cc_final: 0.7630 (p) REVERT: C 890 ASP cc_start: 0.8403 (t0) cc_final: 0.7770 (t70) REVERT: C 910 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7707 (t80) REVERT: C 949 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: C 964 ASN cc_start: 0.8013 (t0) cc_final: 0.7715 (t0) REVERT: C 1035 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7137 (ttpp) REVERT: C 1117 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7716 (p) REVERT: C 1185 CYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6610 (m) REVERT: C 1216 ASP cc_start: 0.7860 (t0) cc_final: 0.7570 (t0) REVERT: C 1218 SER cc_start: 0.8544 (t) cc_final: 0.8007 (p) REVERT: C 1227 LYS cc_start: 0.7660 (ptpp) cc_final: 0.7319 (mtmm) REVERT: E 167 ASP cc_start: 0.6928 (t0) cc_final: 0.6474 (t0) REVERT: E 177 MET cc_start: 0.7513 (mpp) cc_final: 0.7189 (mpp) REVERT: F 396 ASP cc_start: 0.8064 (t0) cc_final: 0.7416 (t0) REVERT: F 409 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: F 459 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8103 (ptp-170) REVERT: F 529 LYS cc_start: 0.8279 (mtpp) cc_final: 0.8041 (mtpp) REVERT: F 558 CYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6390 (t) REVERT: F 586 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7911 (mtpt) REVERT: G 888 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7900 (mttm) REVERT: G 903 MET cc_start: 0.7715 (ttt) cc_final: 0.7300 (mtp) REVERT: G 948 VAL cc_start: 0.8443 (p) cc_final: 0.8214 (t) REVERT: G 970 THR cc_start: 0.8771 (t) cc_final: 0.8417 (p) REVERT: G 986 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8111 (p) REVERT: I 115 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6529 (mt) REVERT: I 194 ASN cc_start: 0.7114 (t0) cc_final: 0.6739 (t0) REVERT: I 208 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7590 (p) REVERT: I 240 GLU cc_start: 0.1973 (OUTLIER) cc_final: 0.1033 (tp30) REVERT: J 387 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7783 (mt) REVERT: J 449 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: J 498 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: J 501 ASP cc_start: 0.7816 (p0) cc_final: 0.7403 (p0) REVERT: J 522 LYS cc_start: 0.8129 (tttp) cc_final: 0.7824 (tttp) REVERT: J 547 ASP cc_start: 0.7954 (m-30) cc_final: 0.7680 (m-30) REVERT: J 556 GLU cc_start: 0.7867 (pp20) cc_final: 0.7317 (pp20) REVERT: J 641 GLU cc_start: 0.7702 (pt0) cc_final: 0.7395 (pt0) REVERT: J 658 MET cc_start: 0.8083 (tmm) cc_final: 0.7554 (ttp) REVERT: J 707 SER cc_start: 0.7886 (t) cc_final: 0.7582 (p) REVERT: K 890 ASP cc_start: 0.8252 (t0) cc_final: 0.7943 (t70) REVERT: K 910 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: K 1056 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7532 (mttp) REVERT: K 1069 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7932 (ttpp) REVERT: K 1093 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8326 (p) REVERT: K 1136 LYS cc_start: 0.7815 (mttp) cc_final: 0.7243 (mtpp) REVERT: K 1196 GLU cc_start: 0.7357 (mp0) cc_final: 0.6931 (mp0) outliers start: 173 outliers final: 126 residues processed: 779 average time/residue: 0.1518 time to fit residues: 188.0155 Evaluate side-chains 815 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 669 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 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 586 LYS 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 637 GLN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain 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 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 SER Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1185 CYS 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 384 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 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 722 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 852 SER Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 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 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 1186 SER Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 240 GLU 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 449 GLN 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 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 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 1043 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 145 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 144 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 116 optimal weight: 0.0370 chunk 202 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 HIS A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C1019 GLN F 686 GLN G1026 ASN J 406 HIS K 940 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090638 restraints weight = 40942.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.093397 restraints weight = 18887.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095197 restraints weight = 10740.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096395 restraints weight = 7107.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097186 restraints weight = 5274.355| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25251 Z= 0.104 Angle : 0.600 16.312 34425 Z= 0.292 Chirality : 0.044 0.555 3843 Planarity : 0.004 0.049 4416 Dihedral : 4.579 47.645 3732 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.62 % Allowed : 28.42 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3141 helix: 2.79 (0.28), residues: 324 sheet: 0.03 (0.17), residues: 915 loop : -0.98 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 930 TYR 0.028 0.001 TYR E 166 PHE 0.029 0.001 PHE K1235 TRP 0.007 0.001 TRP E 195 HIS 0.004 0.001 HIS J 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (25185) covalent geometry : angle 0.58177 / 0.29 (34278) SS BOND : bond 0.00306 / 0.20 ( 51) SS BOND : angle 1.22802 / 0.78 ( 102) hydrogen bonds : bond 0.03654 / 2.48 ( 774) hydrogen bonds : angle 4.82761 / 3.39 ( 1986) link_BETA1-4 : bond 0.00481 / 0.33 ( 6) link_BETA1-4 : angle 1.14815 / 0.71 ( 18) link_NAG-ASN : bond 0.00876 / 0.49 ( 9) link_NAG-ASN : angle 4.72647 / 4.34 ( 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 840 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 689 time to evaluate : 0.933 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: 0.8263 (mppt) cc_final: 0.7946 (mppt) REVERT: A 139 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7176 (mmmt) REVERT: B 343 LYS cc_start: 0.8223 (mptt) cc_final: 0.7653 (ttpt) REVERT: B 378 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7205 (tpp) REVERT: B 389 ILE cc_start: 0.8075 (mm) cc_final: 0.7781 (mt) REVERT: B 396 ASP cc_start: 0.8041 (t0) cc_final: 0.7584 (t0) REVERT: B 430 MET cc_start: 0.7547 (tmm) cc_final: 0.6813 (tmm) REVERT: B 490 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7351 (mm110) REVERT: B 492 THR cc_start: 0.8207 (m) cc_final: 0.7694 (p) REVERT: B 586 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8205 (mtpt) REVERT: B 699 THR cc_start: 0.7642 (t) cc_final: 0.7386 (p) REVERT: C 890 ASP cc_start: 0.8410 (t0) cc_final: 0.7990 (t70) REVERT: C 910 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7624 (t80) REVERT: C 964 ASN cc_start: 0.7996 (t0) cc_final: 0.7721 (t0) REVERT: C 1035 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7100 (ttpp) REVERT: C 1117 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7537 (p) REVERT: C 1131 LEU cc_start: 0.8196 (pp) cc_final: 0.7922 (pt) REVERT: C 1185 CYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6947 (m) REVERT: C 1216 ASP cc_start: 0.7786 (t0) cc_final: 0.7450 (t0) REVERT: C 1218 SER cc_start: 0.8524 (t) cc_final: 0.8007 (p) REVERT: C 1227 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7226 (mtmm) REVERT: F 343 LYS cc_start: 0.8286 (mptt) cc_final: 0.7637 (ttpt) REVERT: F 371 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8051 (mtt180) REVERT: F 396 ASP cc_start: 0.8048 (t0) cc_final: 0.7366 (t0) REVERT: F 409 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: F 459 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8091 (ptp-170) REVERT: F 558 CYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6485 (t) REVERT: F 586 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7782 (mtpt) REVERT: F 634 GLU cc_start: 0.7263 (tp30) cc_final: 0.7038 (tp30) REVERT: G 870 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8064 (m) REVERT: G 903 MET cc_start: 0.7601 (ttt) cc_final: 0.7195 (mtp) REVERT: G 910 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: G 970 THR cc_start: 0.8701 (t) cc_final: 0.8376 (p) REVERT: G 986 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8095 (p) REVERT: I 115 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6549 (mt) REVERT: I 162 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8116 (tmtt) REVERT: I 167 ASP cc_start: 0.7590 (t0) cc_final: 0.7226 (t0) REVERT: I 194 ASN cc_start: 0.7104 (t0) cc_final: 0.6696 (t0) REVERT: I 208 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7552 (p) REVERT: I 240 GLU cc_start: 0.1784 (OUTLIER) cc_final: 0.0785 (tp30) REVERT: J 387 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7699 (mt) REVERT: J 498 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: J 502 MET cc_start: 0.7885 (mtp) cc_final: 0.7581 (mtt) REVERT: J 522 LYS cc_start: 0.8069 (tttp) cc_final: 0.7777 (tttp) REVERT: J 658 MET cc_start: 0.8042 (tmm) cc_final: 0.7622 (ttp) REVERT: J 707 SER cc_start: 0.7808 (t) cc_final: 0.7496 (p) REVERT: K 860 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: K 890 ASP cc_start: 0.8265 (t0) cc_final: 0.7946 (t70) REVERT: K 1056 LYS cc_start: 0.7841 (mmmm) cc_final: 0.7466 (mttm) REVERT: K 1069 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7879 (ttpp) REVERT: K 1093 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (p) REVERT: K 1136 LYS cc_start: 0.7795 (mttp) cc_final: 0.7176 (mtpp) REVERT: K 1150 ASN cc_start: 0.8359 (t0) cc_final: 0.7880 (t0) REVERT: K 1196 GLU cc_start: 0.7369 (mp0) cc_final: 0.6889 (mp0) REVERT: K 1200 ASP cc_start: 0.7477 (m-30) cc_final: 0.7252 (m-30) outliers start: 151 outliers final: 106 residues processed: 779 average time/residue: 0.1579 time to fit residues: 196.0695 Evaluate side-chains 800 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 677 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE 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 676 THR Chi-restraints excluded: chain B residue 694 LEU 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 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 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 1185 CYS 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 384 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 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 722 VAL Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1194 SER Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 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 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 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 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 1153 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 70 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 243 optimal weight: 0.0670 chunk 24 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN F 559 HIS F 686 GLN G1026 ASN J 406 HIS J 569 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090642 restraints weight = 40969.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.093419 restraints weight = 18894.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095225 restraints weight = 10704.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096417 restraints weight = 7070.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097188 restraints weight = 5260.142| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25251 Z= 0.110 Angle : 0.607 18.690 34425 Z= 0.295 Chirality : 0.043 0.315 3843 Planarity : 0.004 0.050 4416 Dihedral : 4.486 47.910 3732 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.59 % Allowed : 28.42 % Favored : 66.00 % 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 are not related in a simple way. whole: -0.35 (0.15), residues: 3141 helix: 2.82 (0.28), residues: 324 sheet: 0.05 (0.17), residues: 915 loop : -0.94 (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 E 166 PHE 0.028 0.001 PHE K1235 TRP 0.013 0.001 TRP A 195 HIS 0.004 0.001 HIS J 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (25185) covalent geometry : angle 0.58607 / 0.29 (34278) SS BOND : bond 0.00362 / 0.22 ( 51) SS BOND : angle 1.31781 / 0.90 ( 102) hydrogen bonds : bond 0.03587 / 2.44 ( 774) hydrogen bonds : angle 4.76934 / 3.33 ( 1986) link_BETA1-4 : bond 0.00487 / 0.35 ( 6) link_BETA1-4 : angle 1.12037 / 0.66 ( 18) link_NAG-ASN : bond 0.01127 / 0.63 ( 9) link_NAG-ASN : angle 5.13539 / 4.85 ( 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 840 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 690 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8222 (mppt) cc_final: 0.7916 (mppt) REVERT: A 139 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7194 (mmmt) REVERT: B 343 LYS cc_start: 0.8226 (mptt) cc_final: 0.7695 (ttmt) REVERT: B 345 THR cc_start: 0.8485 (m) cc_final: 0.7990 (p) REVERT: B 378 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7249 (tpp) REVERT: B 389 ILE cc_start: 0.8073 (mm) cc_final: 0.7797 (mt) REVERT: B 396 ASP cc_start: 0.8054 (t0) cc_final: 0.7597 (t0) REVERT: B 430 MET cc_start: 0.7606 (tmm) cc_final: 0.6843 (tmm) REVERT: B 490 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7311 (mm110) REVERT: B 492 THR cc_start: 0.8215 (m) cc_final: 0.7702 (p) REVERT: B 510 ASP cc_start: 0.8089 (t0) cc_final: 0.7883 (t0) REVERT: B 545 ASN cc_start: 0.8372 (t160) cc_final: 0.8166 (t0) REVERT: B 586 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8177 (mtpt) REVERT: B 699 THR cc_start: 0.7622 (t) cc_final: 0.7375 (p) REVERT: C 867 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8096 (pttm) REVERT: C 890 ASP cc_start: 0.8410 (t0) cc_final: 0.7979 (t70) REVERT: C 910 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7620 (t80) REVERT: C 964 ASN cc_start: 0.7984 (t0) cc_final: 0.7771 (t0) REVERT: C 1035 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7447 (ttpp) REVERT: C 1117 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7595 (p) REVERT: C 1131 LEU cc_start: 0.8180 (pp) cc_final: 0.7914 (pt) REVERT: C 1185 CYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6928 (m) REVERT: C 1216 ASP cc_start: 0.7755 (t0) cc_final: 0.7411 (t0) REVERT: C 1218 SER cc_start: 0.8525 (t) cc_final: 0.8006 (p) REVERT: C 1227 LYS cc_start: 0.7571 (ptpp) cc_final: 0.7202 (mtmm) REVERT: F 343 LYS cc_start: 0.8287 (mptt) cc_final: 0.7634 (ttpt) REVERT: F 354 ASP cc_start: 0.7769 (t0) cc_final: 0.7258 (t70) REVERT: F 371 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8064 (mtt180) REVERT: F 396 ASP cc_start: 0.8051 (t0) cc_final: 0.7463 (t0) REVERT: F 409 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: F 459 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: F 558 CYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6482 (t) REVERT: F 586 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7834 (mtpt) REVERT: F 634 GLU cc_start: 0.7257 (tp30) cc_final: 0.7047 (tp30) REVERT: G 870 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8056 (m) REVERT: G 892 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7486 (mm-40) REVERT: G 903 MET cc_start: 0.7611 (ttt) cc_final: 0.7211 (mtp) REVERT: G 910 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: G 970 THR cc_start: 0.8710 (t) cc_final: 0.8358 (p) REVERT: G 986 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8106 (p) REVERT: G 1021 ARG cc_start: 0.8912 (tpp-160) cc_final: 0.8570 (mmt-90) REVERT: G 1046 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (m) REVERT: G 1050 GLN cc_start: 0.7904 (tt0) cc_final: 0.7636 (tt0) REVERT: I 115 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6567 (mt) REVERT: I 162 LYS cc_start: 0.8361 (tmtt) cc_final: 0.8077 (tmtt) REVERT: I 167 ASP cc_start: 0.7579 (t0) cc_final: 0.7255 (t0) REVERT: I 193 TYR cc_start: 0.8433 (m-80) cc_final: 0.8105 (m-80) REVERT: I 194 ASN cc_start: 0.7123 (t0) cc_final: 0.6738 (t0) REVERT: I 208 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7523 (p) REVERT: I 240 GLU cc_start: 0.1980 (OUTLIER) cc_final: 0.0960 (tp30) REVERT: J 387 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (mt) REVERT: J 498 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: J 522 LYS cc_start: 0.8056 (tttp) cc_final: 0.7765 (tttp) REVERT: J 547 ASP cc_start: 0.7911 (m-30) cc_final: 0.7625 (m-30) REVERT: J 658 MET cc_start: 0.8046 (tmm) cc_final: 0.7640 (ttp) REVERT: J 707 SER cc_start: 0.7804 (t) cc_final: 0.7494 (p) REVERT: K 860 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: K 890 ASP cc_start: 0.8267 (t0) cc_final: 0.7947 (t70) REVERT: K 1056 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7454 (mttm) REVERT: K 1069 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7878 (ttpp) REVERT: K 1093 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (p) REVERT: K 1136 LYS cc_start: 0.7799 (mttp) cc_final: 0.7177 (mtpp) REVERT: K 1150 ASN cc_start: 0.8335 (t0) cc_final: 0.7721 (t0) REVERT: K 1196 GLU cc_start: 0.7369 (mp0) cc_final: 0.6888 (mp0) REVERT: K 1200 ASP cc_start: 0.7473 (m-30) cc_final: 0.7258 (m-30) outliers start: 150 outliers final: 113 residues processed: 780 average time/residue: 0.1577 time to fit residues: 195.5456 Evaluate side-chains 808 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 675 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 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 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 1169 LEU Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 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 722 VAL Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 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 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 447 SER Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 644 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 709 LEU Chi-restraints excluded: chain J residue 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 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 1122 THR Chi-restraints excluded: chain K residue 1153 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 7 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 237 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 957 GLN ** J 569 GLN ** 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 = 0.3283 r_free = 0.3283 target = 0.106960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.091915 restraints weight = 40410.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094673 restraints weight = 18819.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096460 restraints weight = 10755.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097635 restraints weight = 7175.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.098361 restraints weight = 5361.442| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25251 Z= 0.127 Angle : 0.617 17.974 34425 Z= 0.299 Chirality : 0.044 0.405 3843 Planarity : 0.004 0.049 4416 Dihedral : 4.487 48.017 3732 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.88 % Allowed : 27.82 % Favored : 66.29 % 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 are not related in a simple way. whole: -0.33 (0.15), residues: 3141 helix: 2.82 (0.28), residues: 324 sheet: 0.11 (0.18), residues: 867 loop : -0.94 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 930 TYR 0.018 0.001 TYR F 532 PHE 0.028 0.001 PHE K1235 TRP 0.011 0.001 TRP I 251 HIS 0.004 0.001 HIS J 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (25185) covalent geometry : angle 0.59634 / 0.29 (34278) SS BOND : bond 0.00398 / 0.26 ( 51) SS BOND : angle 1.33802 / 0.89 ( 102) hydrogen bonds : bond 0.03670 / 2.49 ( 774) hydrogen bonds : angle 4.73851 / 3.31 ( 1986) link_BETA1-4 : bond 0.00481 / 0.32 ( 6) link_BETA1-4 : angle 1.11058 / 0.67 ( 18) link_NAG-ASN : bond 0.00923 / 0.51 ( 9) link_NAG-ASN : angle 5.12277 / 4.78 ( 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 836 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 678 time to evaluate : 1.182 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: 0.8318 (mppt) cc_final: 0.8022 (mppt) REVERT: A 139 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7243 (mmmt) REVERT: B 343 LYS cc_start: 0.8250 (mptt) cc_final: 0.7714 (ttmt) REVERT: B 345 THR cc_start: 0.8506 (m) cc_final: 0.8022 (p) REVERT: B 378 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7300 (tpp) REVERT: B 389 ILE cc_start: 0.8107 (mm) cc_final: 0.7842 (mt) REVERT: B 396 ASP cc_start: 0.8068 (t0) cc_final: 0.7631 (t0) REVERT: B 430 MET cc_start: 0.7608 (tmm) cc_final: 0.6832 (tmm) REVERT: B 490 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7326 (mm110) REVERT: B 492 THR cc_start: 0.8252 (m) cc_final: 0.7747 (p) REVERT: B 545 ASN cc_start: 0.8315 (t160) cc_final: 0.8096 (t0) REVERT: B 586 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: B 699 THR cc_start: 0.7806 (t) cc_final: 0.7532 (p) REVERT: B 729 LEU cc_start: 0.8192 (tp) cc_final: 0.7943 (tt) REVERT: C 867 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8095 (pttm) REVERT: C 890 ASP cc_start: 0.8396 (t0) cc_final: 0.7960 (t70) REVERT: C 910 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 949 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7908 (ttm-80) REVERT: C 1035 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7476 (ttpp) REVERT: C 1117 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7652 (p) REVERT: C 1131 LEU cc_start: 0.8214 (pp) cc_final: 0.7960 (pt) REVERT: C 1185 CYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6892 (m) REVERT: C 1216 ASP cc_start: 0.7790 (t0) cc_final: 0.7455 (t0) REVERT: C 1218 SER cc_start: 0.8489 (t) cc_final: 0.7967 (p) REVERT: C 1227 LYS cc_start: 0.7588 (ptpp) cc_final: 0.7221 (mtmm) REVERT: F 343 LYS cc_start: 0.8312 (mptt) cc_final: 0.7651 (ttpt) REVERT: F 354 ASP cc_start: 0.7750 (t0) cc_final: 0.7260 (t70) REVERT: F 371 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8072 (mtt180) REVERT: F 396 ASP cc_start: 0.8067 (t0) cc_final: 0.7415 (t0) REVERT: F 409 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: F 459 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7946 (ptp-170) REVERT: F 483 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6591 (mm-30) REVERT: F 529 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7661 (ptpp) REVERT: F 558 CYS cc_start: 0.6886 (m) cc_final: 0.6439 (t) REVERT: F 586 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7742 (mtpt) REVERT: F 634 GLU cc_start: 0.7239 (tp30) cc_final: 0.7020 (tp30) REVERT: F 729 LEU cc_start: 0.8402 (tp) cc_final: 0.8141 (tt) REVERT: G 870 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8082 (m) REVERT: G 892 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7505 (mm-40) REVERT: G 903 MET cc_start: 0.7663 (ttt) cc_final: 0.7250 (mtp) REVERT: G 970 THR cc_start: 0.8701 (t) cc_final: 0.8394 (m) REVERT: G 986 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8128 (p) REVERT: G 1021 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8645 (tpt170) REVERT: G 1046 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8361 (m) REVERT: G 1050 GLN cc_start: 0.7929 (tt0) cc_final: 0.7663 (tt0) REVERT: I 115 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6565 (mt) REVERT: I 167 ASP cc_start: 0.7603 (t0) cc_final: 0.7260 (t0) REVERT: I 194 ASN cc_start: 0.7191 (t0) cc_final: 0.6814 (t0) REVERT: I 208 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7642 (p) REVERT: I 240 GLU cc_start: 0.1968 (OUTLIER) cc_final: 0.0929 (tp30) REVERT: J 387 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7728 (mt) REVERT: J 498 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: J 522 LYS cc_start: 0.8057 (tttp) cc_final: 0.7779 (tttp) REVERT: J 547 ASP cc_start: 0.7855 (m-30) cc_final: 0.7544 (m-30) REVERT: J 641 GLU cc_start: 0.7737 (pt0) cc_final: 0.7536 (pt0) REVERT: J 658 MET cc_start: 0.8059 (tmm) cc_final: 0.7643 (ttp) REVERT: J 707 SER cc_start: 0.7847 (t) cc_final: 0.7539 (p) REVERT: K 860 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: K 890 ASP cc_start: 0.8253 (t0) cc_final: 0.7909 (t70) REVERT: K 1056 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7494 (mttm) REVERT: K 1069 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7913 (ttpp) REVERT: K 1093 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8288 (p) REVERT: K 1136 LYS cc_start: 0.7808 (mttp) cc_final: 0.7193 (mtpp) REVERT: K 1150 ASN cc_start: 0.8302 (t0) cc_final: 0.7676 (t0) REVERT: K 1196 GLU cc_start: 0.7359 (mp0) cc_final: 0.6896 (mp0) REVERT: K 1200 ASP cc_start: 0.7446 (m-30) cc_final: 0.7240 (m-30) outliers start: 158 outliers final: 124 residues processed: 771 average time/residue: 0.1572 time to fit residues: 191.8014 Evaluate side-chains 816 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 672 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 694 LEU 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 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 949 ARG Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain 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 1244 VAL Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 252 ASN Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 447 SER 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 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 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 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 1114 LEU Chi-restraints excluded: chain K residue 1122 THR Chi-restraints excluded: chain K residue 1153 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1217 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 299 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 230 optimal weight: 0.8980 chunk 218 optimal weight: 0.0980 chunk 300 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 235 optimal weight: 0.1980 chunk 118 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 0.0050 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN ** F 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 957 GLN 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 = 0.3291 r_free = 0.3291 target = 0.107538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092372 restraints weight = 40996.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095181 restraints weight = 18910.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097013 restraints weight = 10700.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098172 restraints weight = 7065.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099005 restraints weight = 5257.418| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25251 Z= 0.095 Angle : 0.599 17.519 34425 Z= 0.290 Chirality : 0.043 0.399 3843 Planarity : 0.004 0.046 4416 Dihedral : 4.247 48.555 3731 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.62 % Allowed : 29.09 % Favored : 66.29 % 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 are not related in a simple way. whole: -0.22 (0.15), residues: 3141 helix: 2.88 (0.28), residues: 324 sheet: 0.19 (0.17), residues: 915 loop : -0.89 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 930 TYR 0.015 0.001 TYR F 532 PHE 0.027 0.001 PHE K1235 TRP 0.022 0.001 TRP A 251 HIS 0.013 0.001 HIS E 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.09 (25185) covalent geometry : angle 0.57991 / 0.28 (34278) SS BOND : bond 0.00248 / 0.16 ( 51) SS BOND : angle 1.21133 / 0.81 ( 102) hydrogen bonds : bond 0.03179 / 2.17 ( 774) hydrogen bonds : angle 4.62252 / 3.24 ( 1986) link_BETA1-4 : bond 0.00466 / 0.33 ( 6) link_BETA1-4 : angle 1.10337 / 0.68 ( 18) link_NAG-ASN : bond 0.00925 / 0.52 ( 9) link_NAG-ASN : angle 4.92481 / 4.64 ( 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 802 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 678 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7311 (mmmt) REVERT: A 152 ASN cc_start: 0.8737 (t0) cc_final: 0.8461 (t0) REVERT: B 343 LYS cc_start: 0.8331 (mptt) cc_final: 0.7743 (ttmt) REVERT: B 345 THR cc_start: 0.8483 (m) cc_final: 0.8026 (p) REVERT: B 368 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 378 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7234 (tpp) REVERT: B 396 ASP cc_start: 0.8021 (t0) cc_final: 0.7627 (t0) REVERT: B 430 MET cc_start: 0.7525 (tmm) cc_final: 0.6827 (tmm) REVERT: B 490 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7528 (mm110) REVERT: B 492 THR cc_start: 0.8283 (m) cc_final: 0.7788 (p) REVERT: B 545 ASN cc_start: 0.8174 (t160) cc_final: 0.7893 (t0) REVERT: B 586 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: B 729 LEU cc_start: 0.8223 (tp) cc_final: 0.7973 (tt) REVERT: C 867 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8221 (pttm) REVERT: C 890 ASP cc_start: 0.8364 (t0) cc_final: 0.7917 (t70) REVERT: C 910 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7644 (t80) REVERT: C 1117 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 1131 LEU cc_start: 0.8245 (pp) cc_final: 0.8043 (pt) REVERT: C 1216 ASP cc_start: 0.7741 (t0) cc_final: 0.7446 (t0) REVERT: C 1218 SER cc_start: 0.8315 (t) cc_final: 0.7852 (p) REVERT: C 1227 LYS cc_start: 0.7591 (ptpp) cc_final: 0.7186 (mtmm) REVERT: E 258 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: F 343 LYS cc_start: 0.8410 (mptt) cc_final: 0.7701 (ttpt) REVERT: F 371 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8057 (mtt-85) REVERT: F 396 ASP cc_start: 0.7939 (t0) cc_final: 0.7416 (t0) REVERT: F 409 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: F 459 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8290 (ptp-170) REVERT: F 483 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6535 (mm-30) REVERT: F 529 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7657 (ptpp) REVERT: F 558 CYS cc_start: 0.6704 (m) cc_final: 0.6325 (t) REVERT: F 634 GLU cc_start: 0.7192 (tp30) cc_final: 0.6973 (tp30) REVERT: F 729 LEU cc_start: 0.8238 (tp) cc_final: 0.7979 (tt) REVERT: G 819 SER cc_start: 0.8416 (m) cc_final: 0.8122 (p) REVERT: G 853 LEU cc_start: 0.7960 (tt) cc_final: 0.7730 (tt) REVERT: G 870 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8048 (m) REVERT: G 892 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7530 (mm-40) REVERT: G 903 MET cc_start: 0.7600 (ttt) cc_final: 0.7218 (mtp) REVERT: G 910 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: G 970 THR cc_start: 0.8732 (t) cc_final: 0.8432 (m) REVERT: G 986 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8154 (p) REVERT: G 1021 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8661 (mmt-90) REVERT: G 1046 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8388 (m) REVERT: G 1074 CYS cc_start: 0.5846 (m) cc_final: 0.5621 (m) REVERT: I 115 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6556 (mt) REVERT: I 167 ASP cc_start: 0.7509 (t0) cc_final: 0.7271 (t0) REVERT: I 194 ASN cc_start: 0.7169 (t0) cc_final: 0.6887 (t0) REVERT: I 208 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7654 (p) REVERT: I 240 GLU cc_start: 0.2230 (OUTLIER) cc_final: 0.1168 (tp30) REVERT: J 387 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7724 (mt) REVERT: J 490 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7605 (mm-40) REVERT: J 498 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: J 502 MET cc_start: 0.7890 (mtp) cc_final: 0.7473 (mtp) REVERT: J 522 LYS cc_start: 0.8161 (tttp) cc_final: 0.7745 (tttp) REVERT: J 547 ASP cc_start: 0.7642 (m-30) cc_final: 0.7432 (m-30) REVERT: J 658 MET cc_start: 0.8033 (tmm) cc_final: 0.7548 (ttp) REVERT: J 707 SER cc_start: 0.7844 (t) cc_final: 0.7541 (p) REVERT: J 714 ILE cc_start: 0.8401 (tp) cc_final: 0.8182 (tt) REVERT: K 860 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: K 890 ASP cc_start: 0.8238 (t0) cc_final: 0.7912 (t70) REVERT: K 1056 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7560 (mttm) REVERT: K 1069 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7936 (ttpp) REVERT: K 1079 ASN cc_start: 0.8387 (t0) cc_final: 0.8178 (t0) REVERT: K 1136 LYS cc_start: 0.7796 (mttp) cc_final: 0.7310 (mtpp) REVERT: K 1150 ASN cc_start: 0.8220 (t0) cc_final: 0.7600 (t0) REVERT: K 1196 GLU cc_start: 0.7303 (mp0) cc_final: 0.6909 (mp0) outliers start: 124 outliers final: 85 residues processed: 754 average time/residue: 0.1553 time to fit residues: 184.8753 Evaluate side-chains 765 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 661 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 586 LYS 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 694 LEU Chi-restraints excluded: chain B residue 718 CYS 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 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain 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 384 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 500 ILE Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain 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 986 THR Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1107 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 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 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 252 ASN Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 447 SER 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 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 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 870 VAL Chi-restraints excluded: chain K residue 923 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 22 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 225 optimal weight: 0.0570 chunk 187 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 964 ASN F 673 GLN G 957 GLN J 406 HIS ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090734 restraints weight = 40907.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.093506 restraints weight = 18914.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095317 restraints weight = 10718.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096499 restraints weight = 7097.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097145 restraints weight = 5280.845| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25251 Z= 0.130 Angle : 0.628 17.830 34425 Z= 0.304 Chirality : 0.044 0.435 3843 Planarity : 0.004 0.048 4416 Dihedral : 4.325 48.891 3731 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.28 % Allowed : 29.53 % Favored : 66.18 % 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 are not related in a simple way. whole: -0.26 (0.15), residues: 3141 helix: 2.87 (0.28), residues: 324 sheet: 0.16 (0.17), residues: 915 loop : -0.91 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 604 TYR 0.022 0.001 TYR F 397 PHE 0.025 0.001 PHE K1235 TRP 0.021 0.001 TRP A 251 HIS 0.005 0.001 HIS E 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (25185) covalent geometry : angle 0.60867 / 0.30 (34278) SS BOND : bond 0.00306 / 0.21 ( 51) SS BOND : angle 1.32489 / 0.92 ( 102) hydrogen bonds : bond 0.03509 / 2.38 ( 774) hydrogen bonds : angle 4.59707 / 3.22 ( 1986) link_BETA1-4 : bond 0.00446 / 0.32 ( 6) link_BETA1-4 : angle 1.04898 / 0.64 ( 18) link_NAG-ASN : bond 0.00884 / 0.49 ( 9) link_NAG-ASN : angle 5.03549 / 4.71 ( 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 790 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 675 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7337 (mmmt) REVERT: A 152 ASN cc_start: 0.8744 (t0) cc_final: 0.8470 (t0) REVERT: B 343 LYS cc_start: 0.8331 (mptt) cc_final: 0.7763 (ttmt) REVERT: B 345 THR cc_start: 0.8504 (m) cc_final: 0.8057 (p) REVERT: B 368 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 378 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7309 (tpp) REVERT: B 396 ASP cc_start: 0.8046 (t0) cc_final: 0.7667 (t0) REVERT: B 430 MET cc_start: 0.7568 (tmm) cc_final: 0.6817 (tmm) REVERT: B 490 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7552 (mm110) REVERT: B 492 THR cc_start: 0.8309 (m) cc_final: 0.7822 (p) REVERT: B 545 ASN cc_start: 0.8182 (t0) cc_final: 0.7911 (t0) REVERT: B 586 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8282 (mtpt) REVERT: B 729 LEU cc_start: 0.8280 (tp) cc_final: 0.8033 (tt) REVERT: C 890 ASP cc_start: 0.8353 (t0) cc_final: 0.7909 (t70) REVERT: C 1035 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7288 (ttpp) REVERT: C 1117 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 1131 LEU cc_start: 0.8291 (pp) cc_final: 0.8072 (pt) REVERT: C 1216 ASP cc_start: 0.7778 (t0) cc_final: 0.7483 (t0) REVERT: C 1218 SER cc_start: 0.8335 (t) cc_final: 0.7946 (p) REVERT: C 1227 LYS cc_start: 0.7644 (ptpp) cc_final: 0.7239 (mtmm) REVERT: C 1243 LEU cc_start: 0.7842 (tt) cc_final: 0.7600 (tp) REVERT: F 343 LYS cc_start: 0.8397 (mptt) cc_final: 0.7727 (ttpt) REVERT: F 371 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.8050 (mtt180) REVERT: F 396 ASP cc_start: 0.8002 (t0) cc_final: 0.7461 (t0) REVERT: F 409 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: F 459 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8235 (ptp-170) REVERT: F 529 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7718 (ptpp) REVERT: F 558 CYS cc_start: 0.6706 (m) cc_final: 0.6299 (t) REVERT: F 634 GLU cc_start: 0.7194 (tp30) cc_final: 0.6957 (tp30) REVERT: F 729 LEU cc_start: 0.8359 (tp) cc_final: 0.8099 (tt) REVERT: G 819 SER cc_start: 0.8439 (m) cc_final: 0.8117 (p) REVERT: G 870 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8086 (m) REVERT: G 892 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7529 (mm-40) REVERT: G 903 MET cc_start: 0.7691 (ttt) cc_final: 0.7302 (mtp) REVERT: G 970 THR cc_start: 0.8737 (t) cc_final: 0.8442 (m) REVERT: G 986 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8166 (p) REVERT: G 1021 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8651 (mmt-90) REVERT: G 1046 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8418 (m) REVERT: I 115 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6597 (mt) REVERT: I 167 ASP cc_start: 0.7556 (t0) cc_final: 0.7318 (t0) REVERT: I 194 ASN cc_start: 0.7218 (t0) cc_final: 0.6957 (t0) REVERT: I 208 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7683 (p) REVERT: I 240 GLU cc_start: 0.2478 (OUTLIER) cc_final: 0.1334 (tp30) REVERT: J 395 HIS cc_start: 0.7187 (t70) cc_final: 0.6701 (t70) REVERT: J 490 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7560 (mm-40) REVERT: J 498 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: J 522 LYS cc_start: 0.8167 (tttp) cc_final: 0.7753 (tttp) REVERT: J 547 ASP cc_start: 0.7650 (m-30) cc_final: 0.7404 (m-30) REVERT: J 548 MET cc_start: 0.6917 (ptt) cc_final: 0.6691 (ptt) REVERT: J 658 MET cc_start: 0.8063 (tmm) cc_final: 0.7549 (ttp) REVERT: J 707 SER cc_start: 0.7889 (t) cc_final: 0.7600 (p) REVERT: J 714 ILE cc_start: 0.8425 (tp) cc_final: 0.8202 (tt) REVERT: K 860 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: K 890 ASP cc_start: 0.8224 (t0) cc_final: 0.7915 (t70) REVERT: K 964 ASN cc_start: 0.8464 (p0) cc_final: 0.8123 (p0) REVERT: K 1022 THR cc_start: 0.8220 (m) cc_final: 0.7939 (t) REVERT: K 1056 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7613 (mttp) REVERT: K 1069 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7964 (ttpp) REVERT: K 1136 LYS cc_start: 0.7768 (mttp) cc_final: 0.7283 (mtpp) REVERT: K 1150 ASN cc_start: 0.8237 (t0) cc_final: 0.7549 (t0) REVERT: K 1196 GLU cc_start: 0.7304 (mp0) cc_final: 0.6915 (mp0) outliers start: 115 outliers final: 92 residues processed: 745 average time/residue: 0.1630 time to fit residues: 192.4077 Evaluate side-chains 769 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 664 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 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 543 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 586 LYS 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 708 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 744 LEU 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 975 GLN Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1156 GLU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain 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 551 ASN Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain G residue 910 PHE Chi-restraints excluded: chain G residue 923 VAL Chi-restraints excluded: chain G residue 975 GLN Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 1024 GLU Chi-restraints excluded: chain G residue 1040 SER Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1107 GLU Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1163 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1244 VAL Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 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 252 ASN Chi-restraints excluded: chain J residue 341 VAL 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 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 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 1046 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 60 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS F 686 GLN G 957 GLN I 145 HIS ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 467 GLN ** J 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089218 restraints weight = 40724.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.091966 restraints weight = 18862.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093763 restraints weight = 10723.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094935 restraints weight = 7121.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095705 restraints weight = 5321.741| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 25251 Z= 0.311 Angle : 0.750 18.886 34425 Z= 0.372 Chirality : 0.050 0.548 3843 Planarity : 0.005 0.053 4416 Dihedral : 5.000 48.020 3729 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.62 % Allowed : 29.39 % Favored : 66.00 % 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 are not related in a simple way. whole: -0.62 (0.15), residues: 3141 helix: 2.16 (0.28), residues: 348 sheet: 0.01 (0.17), residues: 906 loop : -1.17 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 604 TYR 0.025 0.003 TYR F 532 PHE 0.026 0.003 PHE K 910 TRP 0.018 0.002 TRP A 251 HIS 0.010 0.002 HIS E 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.31 (25185) covalent geometry : angle 0.72845 / 0.37 (34278) SS BOND : bond 0.00542 / 0.37 ( 51) SS BOND : angle 1.78731 / 1.18 ( 102) hydrogen bonds : bond 0.05089 / 3.41 ( 774) hydrogen bonds : angle 4.87689 / 3.42 ( 1986) link_BETA1-4 : bond 0.00620 / 0.41 ( 6) link_BETA1-4 : angle 1.37687 / 0.83 ( 18) link_NAG-ASN : bond 0.00881 / 0.49 ( 9) link_NAG-ASN : angle 5.50416 / 5.05 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5962.78 seconds wall clock time: 102 minutes 56.59 seconds (6176.59 seconds total)