Starting phenix.real_space_refine on Fri May 30 02:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9y_47821/05_2025/9e9y_47821.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.076 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 8 9.91 5 S 228 5.16 5 C 20684 2.51 5 N 5688 2.21 5 O 6228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 181 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32836 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 26, 'TRANS': 371} Chain: "C" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 370} Chain: "E" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1175 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "F" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1175 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "G" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "H" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 26, 'TRANS': 371} Chain: "I" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1175 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "K" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 26, 'TRANS': 371} Chain: "L" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1175 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "V" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.17, per 1000 atoms: 0.58 Number of scatterers: 32836 At special positions: 0 Unit cell: (175.122, 177.284, 198.904, 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 8 19.99 S 228 16.00 O 6228 8.00 N 5688 7.00 C 20684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.02 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.02 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.04 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.01 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 124 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 25 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 226 " distance=2.02 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.02 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.02 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.02 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.02 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.02 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.02 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.02 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS V 33 " - pdb=" SG CYS V 45 " distance=2.03 Simple disulfide: pdb=" SG CYS V 40 " - pdb=" SG CYS V 58 " distance=2.05 Simple disulfide: pdb=" SG CYS V 52 " - pdb=" SG CYS V 67 " distance=2.03 Simple disulfide: pdb=" SG CYS V 72 " - pdb=" SG CYS V 84 " distance=2.03 Simple disulfide: pdb=" SG CYS V 79 " - pdb=" SG CYS V 97 " distance=2.04 Simple disulfide: pdb=" SG CYS V 91 " - pdb=" SG CYS V 108 " distance=2.03 Simple disulfide: pdb=" SG CYS X 33 " - pdb=" SG CYS X 45 " distance=2.02 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 58 " distance=2.02 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 67 " distance=2.03 Simple disulfide: pdb=" SG CYS X 72 " - pdb=" SG CYS X 84 " distance=2.04 Simple disulfide: pdb=" SG CYS X 79 " - pdb=" SG CYS X 97 " distance=2.05 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 33 " - pdb=" SG CYS Y 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 40 " - pdb=" SG CYS Y 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 52 " - pdb=" SG CYS Y 67 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 72 " - pdb=" SG CYS Y 84 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 79 " - pdb=" SG CYS Y 97 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 91 " - pdb=" SG CYS Y 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 33 " - pdb=" SG CYS Z 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 40 " - pdb=" SG CYS Z 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 52 " - pdb=" SG CYS Z 67 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 72 " - pdb=" SG CYS Z 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 79 " - pdb=" SG CYS Z 97 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 91 " - pdb=" SG CYS Z 108 " 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 Time building additional restraints: 7.62 Conformation dependent library (CDL) restraints added in 3.8 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7872 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 99 sheets defined 14.9% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.546A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 403 through 437 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.685A pdb=" N ILE B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 391 Processing helix chain 'B' and resid 393 through 402 removed outlier: 3.556A pdb=" N THR B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 3.931A pdb=" N LEU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 403 through 438 removed outlier: 3.612A pdb=" N ASN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.794A pdb=" N GLY D 194 " --> pdb=" O PRO D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 351 through 363 removed outlier: 4.735A pdb=" N ILE D 357 " --> pdb=" O HIS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 402 Proline residue: D 399 - end of helix Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.627A pdb=" N LYS E 169 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 167 through 172 removed outlier: 4.059A pdb=" N SER F 170 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR F 172 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.094A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 397 through 401 Processing helix chain 'G' and resid 403 through 438 removed outlier: 3.588A pdb=" N ILE G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 191 through 195 removed outlier: 4.182A pdb=" N GLY H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 351 through 363 removed outlier: 4.004A pdb=" N ILE H 357 " --> pdb=" O HIS H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 403 Proline residue: H 399 - end of helix Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.825A pdb=" N LYS I 110 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 238 through 245 Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 283 through 287 Processing helix chain 'J' and resid 397 through 402 removed outlier: 3.534A pdb=" N VAL J 402 " --> pdb=" O PHE J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 437 removed outlier: 4.185A pdb=" N ILE J 435 " --> pdb=" O SER J 431 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN J 436 " --> pdb=" O SER J 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 191 through 195 removed outlier: 3.940A pdb=" N GLY K 194 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 363 removed outlier: 4.015A pdb=" N ILE K 357 " --> pdb=" O HIS K 353 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS K 358 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR K 359 " --> pdb=" O ILE K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 391 Processing helix chain 'K' and resid 391 through 398 Processing helix chain 'K' and resid 399 through 401 No H-bonds generated for 'chain 'K' and resid 399 through 401' Processing helix chain 'K' and resid 403 through 407 removed outlier: 4.362A pdb=" N ALA K 406 " --> pdb=" O ALA K 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 148 Processing helix chain 'L' and resid 155 through 157 No H-bonds generated for 'chain 'L' and resid 155 through 157' Processing helix chain 'L' and resid 168 through 172 Processing helix chain 'V' and resid 47 through 52 removed outlier: 3.746A pdb=" N CYS V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 65 removed outlier: 4.119A pdb=" N GLU V 64 " --> pdb=" O GLY V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 90 No H-bonds generated for 'chain 'V' and resid 88 through 90' Processing helix chain 'V' and resid 100 through 104 removed outlier: 3.506A pdb=" N SER V 104 " --> pdb=" O SER V 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 53 Processing helix chain 'X' and resid 61 through 65 removed outlier: 3.901A pdb=" N GLU X 64 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS X 65 " --> pdb=" O SER X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 65' Processing helix chain 'X' and resid 88 through 90 No H-bonds generated for 'chain 'X' and resid 88 through 90' Processing helix chain 'Y' and resid 47 through 53 removed outlier: 3.514A pdb=" N ASP Y 53 " --> pdb=" O TRP Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing helix chain 'Y' and resid 100 through 104 Processing helix chain 'Z' and resid 47 through 53 removed outlier: 3.772A pdb=" N CYS Z 52 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP Z 53 " --> pdb=" O TRP Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 removed outlier: 3.517A pdb=" N CYS Z 67 " --> pdb=" O GLU Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 3.644A pdb=" N TYR A 15 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 148 removed outlier: 4.433A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 303 removed outlier: 3.524A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 307 removed outlier: 6.798A pdb=" N CYS A 306 " --> pdb=" O LYS A 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.189A pdb=" N ARG B 291 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 311 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR B 293 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU B 309 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 295 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 307 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.970A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N SER B 48 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET B 67 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.970A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N ILE B 45 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N GLN B 104 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N VAL B 47 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N LEU B 102 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N ALA B 49 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 100 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.722A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 155 removed outlier: 3.508A pdb=" N LYS B 148 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 166 removed outlier: 3.755A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AC2, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC4, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.834A pdb=" N ASP C 281 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 14 through 19 removed outlier: 5.414A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 14 through 19 Processing sheet with id=AC7, first strand: chain 'C' and resid 42 through 48 removed outlier: 5.968A pdb=" N LYS C 44 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS C 123 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 46 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'C' and resid 59 through 63 removed outlier: 6.426A pdb=" N THR C 101 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD3, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 303 removed outlier: 7.932A pdb=" N PHE C 312 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR C 358 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AD6, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'C' and resid 387 through 388 removed outlier: 7.529A pdb=" N LEU D 285 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE D 319 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU D 287 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG D 317 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA D 289 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR D 315 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG D 291 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY D 313 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.819A pdb=" N GLN D 46 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 34 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 44 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N SER D 48 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET D 67 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS D 63 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.819A pdb=" N GLN D 46 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 34 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 44 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR D 99 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ALA D 49 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS D 97 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N PHE D 51 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N GLY D 95 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 14.773A pdb=" N TYR D 53 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 18.060A pdb=" N ARG D 93 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 86 removed outlier: 3.577A pdb=" N ASN D 122 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AE3, first strand: chain 'D' and resid 237 through 238 removed outlier: 3.658A pdb=" N LEU D 255 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY D 253 " --> pdb=" O MET D 168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 180 through 183 removed outlier: 3.627A pdb=" N THR D 215 " --> pdb=" O ILE D 189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 206 through 211 Processing sheet with id=AE6, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.589A pdb=" N LYS E 140 " --> pdb=" O MET E 115 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE E 112 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR E 123 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 114 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR E 123 " --> pdb=" O PRO E 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 159 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 248 through 250 removed outlier: 5.038A pdb=" N PHE E 198 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE E 214 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 248 through 250 removed outlier: 4.108A pdb=" N GLY E 227 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ALA E 223 " --> pdb=" O TRP E 242 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 140 through 141 removed outlier: 3.862A pdb=" N GLY F 122 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU F 116 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR F 123 " --> pdb=" O PRO F 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 159 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 248 through 251 removed outlier: 5.249A pdb=" N PHE F 198 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N ALA F 190 " --> pdb=" O PRO F 201 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE F 214 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 248 through 251 removed outlier: 6.603A pdb=" N VAL F 240 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL F 225 " --> pdb=" O VAL F 240 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TRP F 242 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA F 223 " --> pdb=" O TRP F 242 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AF4, first strand: chain 'G' and resid 14 through 19 removed outlier: 7.766A pdb=" N GLU G 30 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR G 137 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR G 32 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE G 135 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL G 34 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G 133 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER G 36 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 131 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU G 38 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 129 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 140 through 147 removed outlier: 3.952A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 129 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU G 38 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 131 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER G 36 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G 133 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL G 34 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE G 135 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR G 32 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR G 137 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU G 30 " --> pdb=" O TYR G 137 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF7, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.590A pdb=" N THR G 101 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AF9, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AG1, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AG2, first strand: chain 'G' and resid 296 through 304 removed outlier: 3.641A pdb=" N ALA G 304 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AG4, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AG5, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.404A pdb=" N ARG H 291 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE H 311 " --> pdb=" O ARG H 291 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR H 293 " --> pdb=" O GLU H 309 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU H 309 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU H 295 " --> pdb=" O THR H 307 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR H 307 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 14 through 16 Processing sheet with id=AG7, first strand: chain 'H' and resid 34 through 35 removed outlier: 7.262A pdb=" N PHE H 100 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS H 96 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU H 102 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 50 through 53 removed outlier: 12.027A pdb=" N GLN H 50 " --> pdb=" O THR H 62 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N THR H 62 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY H 52 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 83 through 86 removed outlier: 4.697A pdb=" N ASP H 109 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 148 through 155 Processing sheet with id=AH2, first strand: chain 'H' and resid 237 through 238 removed outlier: 3.547A pdb=" N LEU H 255 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY H 253 " --> pdb=" O MET H 168 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 180 through 182 Processing sheet with id=AH4, first strand: chain 'H' and resid 206 through 211 Processing sheet with id=AH5, first strand: chain 'I' and resid 140 through 141 removed outlier: 4.038A pdb=" N GLY I 122 " --> pdb=" O ILE I 114 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU I 116 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR I 123 " --> pdb=" O PRO I 134 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 174 through 175 removed outlier: 6.954A pdb=" N GLN I 174 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA I 223 " --> pdb=" O GLN I 174 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE I 214 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE I 198 " --> pdb=" O LEU I 237 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 174 through 175 removed outlier: 6.954A pdb=" N GLN I 174 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA I 223 " --> pdb=" O GLN I 174 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N VAL I 222 " --> pdb=" O TRP I 242 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP I 242 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER I 238 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY I 228 " --> pdb=" O ALA I 236 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA I 236 " --> pdb=" O GLY I 228 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.434A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 14 through 19 removed outlier: 5.367A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.514A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 51 through 53 removed outlier: 3.789A pdb=" N THR J 101 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 51 through 53 removed outlier: 5.285A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AI5, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AI6, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI7, first strand: chain 'J' and resid 296 through 304 removed outlier: 4.080A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AI9, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AJ1, first strand: chain 'K' and resid 14 through 16 removed outlier: 3.713A pdb=" N CYS K 25 " --> pdb=" O CYS K 16 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 31 through 35 removed outlier: 6.696A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N SER K 48 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N MET K 67 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS K 63 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 31 through 35 removed outlier: 6.696A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 13.606A pdb=" N TYR K 53 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 17.322A pdb=" N ARG K 93 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 83 through 86 Processing sheet with id=AJ5, first strand: chain 'K' and resid 148 through 155 removed outlier: 3.686A pdb=" N VAL K 150 " --> pdb=" O CYS K 266 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 237 through 238 removed outlier: 3.857A pdb=" N GLY K 164 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY K 253 " --> pdb=" O MET K 168 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 180 through 183 Processing sheet with id=AJ8, first strand: chain 'K' and resid 206 through 211 Processing sheet with id=AJ9, first strand: chain 'K' and resid 275 through 279 removed outlier: 3.800A pdb=" N THR K 275 " --> pdb=" O HIS K 286 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU K 285 " --> pdb=" O PHE K 319 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE K 319 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU K 287 " --> pdb=" O ARG K 317 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG K 317 " --> pdb=" O LEU K 287 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA K 289 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR K 315 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'K' and resid 275 through 279 removed outlier: 3.800A pdb=" N THR K 275 " --> pdb=" O HIS K 286 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 140 through 141 removed outlier: 4.280A pdb=" N GLY L 122 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU L 116 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR L 123 " --> pdb=" O PRO L 134 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 248 through 251 removed outlier: 4.872A pdb=" N PHE L 198 " --> pdb=" O LEU L 237 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE L 214 " --> pdb=" O VAL L 222 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 248 through 251 removed outlier: 6.344A pdb=" N ALA L 236 " --> pdb=" O GLY L 228 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY L 228 " --> pdb=" O ALA L 236 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER L 238 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE L 224 " --> pdb=" O VAL L 240 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP L 242 " --> pdb=" O VAL L 222 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N VAL L 222 " --> pdb=" O TRP L 242 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AK6, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AK7, first strand: chain 'Y' and resid 76 through 78 Processing sheet with id=AK8, first strand: chain 'Z' and resid 39 through 40 removed outlier: 3.763A pdb=" N ARG Z 44 " --> pdb=" O CYS Z 40 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Z' and resid 76 through 78 1241 hydrogen bonds defined for protein. 3129 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: 17.34 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10393 1.33 - 1.46: 7263 1.46 - 1.58: 15720 1.58 - 1.70: 0 1.70 - 1.83: 276 Bond restraints: 33652 Sorted by residual: bond pdb=" N ILE C 276 " pdb=" CA ILE C 276 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.04e+01 bond pdb=" N VAL D 111 " pdb=" CA VAL D 111 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.60e+00 bond pdb=" N VAL C 131 " pdb=" CA VAL C 131 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.78e+00 bond pdb=" N GLY K 322 " pdb=" CA GLY K 322 " ideal model delta sigma weight residual 1.447 1.475 -0.028 9.40e-03 1.13e+04 8.70e+00 bond pdb=" N VAL D 126 " pdb=" CA VAL D 126 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.18e-02 7.18e+03 8.65e+00 ... (remaining 33647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 42863 1.87 - 3.75: 2597 3.75 - 5.62: 279 5.62 - 7.49: 38 7.49 - 9.36: 7 Bond angle restraints: 45784 Sorted by residual: angle pdb=" CA GLY K 325 " pdb=" C GLY K 325 " pdb=" O GLY K 325 " ideal model delta sigma weight residual 122.23 118.24 3.99 6.90e-01 2.10e+00 3.34e+01 angle pdb=" N SER H 178 " pdb=" CA SER H 178 " pdb=" C SER H 178 " ideal model delta sigma weight residual 112.54 106.71 5.83 1.22e+00 6.72e-01 2.28e+01 angle pdb=" N THR B 407 " pdb=" CA THR B 407 " pdb=" C THR B 407 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" C SER X 104 " pdb=" N PRO X 105 " pdb=" CA PRO X 105 " ideal model delta sigma weight residual 119.56 123.87 -4.31 1.02e+00 9.61e-01 1.79e+01 angle pdb=" C TYR D 18 " pdb=" CA TYR D 18 " pdb=" CB TYR D 18 " ideal model delta sigma weight residual 109.71 117.30 -7.59 1.83e+00 2.99e-01 1.72e+01 ... (remaining 45779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18793 17.96 - 35.91: 1162 35.91 - 53.87: 222 53.87 - 71.83: 91 71.83 - 89.79: 28 Dihedral angle restraints: 20296 sinusoidal: 8004 harmonic: 12292 Sorted by residual: dihedral pdb=" CB CYS C 328 " pdb=" SG CYS C 328 " pdb=" SG CYS C 370 " pdb=" CB CYS C 370 " ideal model delta sinusoidal sigma weight residual -86.00 -137.24 51.24 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA SER V 62 " pdb=" C SER V 62 " pdb=" N ASP V 63 " pdb=" CA ASP V 63 " ideal model delta harmonic sigma weight residual 180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" C SER V 62 " pdb=" N SER V 62 " pdb=" CA SER V 62 " pdb=" CB SER V 62 " ideal model delta harmonic sigma weight residual -122.60 -136.13 13.53 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 20293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4640 0.093 - 0.186: 425 0.186 - 0.278: 21 0.278 - 0.371: 1 0.371 - 0.464: 1 Chirality restraints: 5088 Sorted by residual: chirality pdb=" CA SER V 62 " pdb=" N SER V 62 " pdb=" C SER V 62 " pdb=" CB SER V 62 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA GLU V 34 " pdb=" N GLU V 34 " pdb=" C GLU V 34 " pdb=" CB GLU V 34 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA CYS V 52 " pdb=" N CYS V 52 " pdb=" C CYS V 52 " pdb=" CB CYS V 52 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5085 not shown) Planarity restraints: 5928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 50 " -0.099 2.00e-02 2.50e+03 5.57e-02 7.76e+01 pdb=" CG TRP Y 50 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 50 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 50 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 50 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 50 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 50 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 50 " -0.070 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 50 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 50 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 89 " -0.075 2.00e-02 2.50e+03 4.71e-02 5.55e+01 pdb=" CG TRP X 89 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP X 89 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP X 89 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP X 89 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP X 89 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP X 89 " 0.075 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 89 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 89 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP X 89 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 85 " 0.072 2.00e-02 2.50e+03 4.39e-02 3.86e+01 pdb=" CG TYR G 85 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR G 85 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR G 85 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR G 85 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR G 85 " -0.038 2.00e-02 2.50e+03 pdb=" CZ TYR G 85 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR G 85 " 0.072 2.00e-02 2.50e+03 ... (remaining 5925 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 199 2.48 - 3.09: 24858 3.09 - 3.69: 51936 3.69 - 4.30: 71935 4.30 - 4.90: 119084 Nonbonded interactions: 268012 Sorted by model distance: nonbonded pdb=" O ASP Y 55 " pdb="CA CA Y 201 " model vdw 1.878 2.510 nonbonded pdb=" NZ LYS B 190 " pdb=" OD1 ASP Z 96 " model vdw 1.997 3.120 nonbonded pdb=" NZ LYS B 190 " pdb=" OD2 ASP Z 96 " model vdw 2.085 3.120 nonbonded pdb=" O PRO L 180 " pdb=" OH TYR L 184 " model vdw 2.129 3.040 nonbonded pdb=" ND2 ASN B 54 " pdb=" OG1 THR B 58 " model vdw 2.146 3.120 ... (remaining 268007 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 'C' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 77.410 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.006 0.111 33724 Z= 0.318 Angle : 0.950 9.364 45928 Z= 0.559 Chirality : 0.054 0.464 5088 Planarity : 0.008 0.125 5928 Dihedral : 13.042 89.786 12208 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.49 % Favored : 93.49 % Rotamer: Outliers : 0.88 % Allowed : 7.88 % Favored : 91.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4240 helix: -0.27 (0.23), residues: 406 sheet: -1.04 (0.14), residues: 1157 loop : -1.09 (0.11), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.005 TRP Y 50 HIS 0.019 0.002 HIS H 73 PHE 0.038 0.003 PHE V 38 TYR 0.072 0.006 TYR G 85 ARG 0.025 0.003 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.21302 ( 1159) hydrogen bonds : angle 9.34209 ( 3129) SS BOND : bond 0.00666 ( 72) SS BOND : angle 1.74179 ( 144) covalent geometry : bond 0.00616 (33652) covalent geometry : angle 0.94683 (45784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1471 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.9200 (t0) cc_final: 0.8501 (t0) REVERT: A 10 VAL cc_start: 0.9332 (t) cc_final: 0.9103 (m) REVERT: A 13 ILE cc_start: 0.9281 (mm) cc_final: 0.9070 (mm) REVERT: A 24 TYR cc_start: 0.8412 (m-80) cc_final: 0.8177 (m-80) REVERT: A 28 ASN cc_start: 0.9317 (p0) cc_final: 0.9028 (p0) REVERT: A 32 THR cc_start: 0.8292 (p) cc_final: 0.7715 (p) REVERT: A 75 ASP cc_start: 0.7779 (t0) cc_final: 0.7245 (t0) REVERT: A 102 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 103 LEU cc_start: 0.9294 (tp) cc_final: 0.9054 (tp) REVERT: A 133 LEU cc_start: 0.8437 (mt) cc_final: 0.8201 (mt) REVERT: A 140 THR cc_start: 0.8827 (m) cc_final: 0.8613 (p) REVERT: A 174 ASP cc_start: 0.7849 (m-30) cc_final: 0.7453 (m-30) REVERT: A 176 LYS cc_start: 0.8239 (mttt) cc_final: 0.7442 (mttm) REVERT: A 218 ASP cc_start: 0.8442 (t0) cc_final: 0.8205 (t0) REVERT: A 230 HIS cc_start: 0.8300 (t-90) cc_final: 0.7936 (t-90) REVERT: A 241 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 302 THR cc_start: 0.8797 (m) cc_final: 0.8426 (p) REVERT: A 341 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 409 TRP cc_start: 0.7772 (m100) cc_final: 0.7563 (m100) REVERT: B 80 MET cc_start: 0.8518 (mmt) cc_final: 0.8231 (mmm) REVERT: B 92 ARG cc_start: 0.2795 (mtt180) cc_final: 0.1166 (mmm160) REVERT: B 134 PHE cc_start: 0.9000 (p90) cc_final: 0.8434 (p90) REVERT: B 138 GLU cc_start: 0.7672 (tt0) cc_final: 0.7365 (tt0) REVERT: B 139 GLU cc_start: 0.8759 (tt0) cc_final: 0.8080 (tt0) REVERT: B 155 TYR cc_start: 0.7354 (m-80) cc_final: 0.6941 (m-80) REVERT: B 156 ASP cc_start: 0.8538 (t0) cc_final: 0.8113 (m-30) REVERT: B 161 THR cc_start: 0.8835 (p) cc_final: 0.8556 (p) REVERT: B 252 GLN cc_start: 0.7144 (mp10) cc_final: 0.6884 (mp10) REVERT: B 305 ASP cc_start: 0.8265 (t0) cc_final: 0.8025 (t0) REVERT: B 327 GLU cc_start: 0.8848 (tt0) cc_final: 0.8220 (tt0) REVERT: B 339 TRP cc_start: 0.9183 (m-90) cc_final: 0.8693 (m-90) REVERT: C 2 GLU cc_start: 0.8146 (tt0) cc_final: 0.7852 (tt0) REVERT: C 97 ASP cc_start: 0.7434 (m-30) cc_final: 0.7189 (m-30) REVERT: C 99 GLU cc_start: 0.8526 (tt0) cc_final: 0.8214 (tm-30) REVERT: C 109 GLU cc_start: 0.7116 (tt0) cc_final: 0.6695 (tt0) REVERT: C 146 THR cc_start: 0.8484 (t) cc_final: 0.8277 (t) REVERT: C 160 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8613 (tmtt) REVERT: C 204 GLN cc_start: 0.8634 (mt0) cc_final: 0.8296 (mt0) REVERT: C 208 LEU cc_start: 0.8981 (mp) cc_final: 0.8731 (mt) REVERT: C 218 ASP cc_start: 0.8473 (t70) cc_final: 0.7631 (t0) REVERT: C 233 TYR cc_start: 0.8672 (p90) cc_final: 0.8344 (p90) REVERT: C 257 PHE cc_start: 0.9055 (m-80) cc_final: 0.8685 (m-80) REVERT: C 264 GLU cc_start: 0.9100 (mp0) cc_final: 0.8607 (mp0) REVERT: C 277 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8170 (Cg_endo) REVERT: C 290 SER cc_start: 0.9022 (t) cc_final: 0.8773 (m) REVERT: C 324 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6734 (mtm-85) REVERT: C 325 GLU cc_start: 0.7748 (pp20) cc_final: 0.7515 (tm-30) REVERT: C 327 HIS cc_start: 0.5787 (t-90) cc_final: 0.5368 (t-90) REVERT: C 386 HIS cc_start: 0.8859 (m-70) cc_final: 0.8601 (m170) REVERT: D 27 SER cc_start: 0.9405 (t) cc_final: 0.8924 (m) REVERT: D 46 GLN cc_start: 0.8515 (tt0) cc_final: 0.8076 (tm-30) REVERT: D 55 GLN cc_start: 0.9130 (tt0) cc_final: 0.8654 (tp40) REVERT: D 87 THR cc_start: 0.9313 (p) cc_final: 0.9079 (p) REVERT: D 88 SER cc_start: 0.9262 (t) cc_final: 0.8989 (p) REVERT: D 138 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 168 MET cc_start: 0.9128 (mmp) cc_final: 0.8891 (mmt) REVERT: D 176 TYR cc_start: 0.7585 (m-80) cc_final: 0.6930 (m-80) REVERT: D 200 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7597 (mp0) REVERT: D 205 ASP cc_start: 0.8141 (t0) cc_final: 0.7616 (p0) REVERT: D 229 TYR cc_start: 0.7713 (p90) cc_final: 0.7151 (p90) REVERT: D 238 PHE cc_start: 0.9474 (t80) cc_final: 0.8346 (t80) REVERT: D 259 PHE cc_start: 0.8673 (m-80) cc_final: 0.8473 (m-80) REVERT: D 279 TRP cc_start: 0.8787 (p-90) cc_final: 0.7772 (p-90) REVERT: D 321 VAL cc_start: 0.9189 (t) cc_final: 0.8883 (p) REVERT: D 341 GLN cc_start: 0.8420 (mt0) cc_final: 0.8094 (mt0) REVERT: E 110 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8722 (mttt) REVERT: E 243 ASN cc_start: 0.9165 (t0) cc_final: 0.8888 (t0) REVERT: F 115 MET cc_start: 0.8541 (mmm) cc_final: 0.8170 (mmm) REVERT: F 116 LEU cc_start: 0.9126 (tp) cc_final: 0.8691 (tp) REVERT: F 186 TRP cc_start: 0.8505 (t60) cc_final: 0.8131 (t60) REVERT: F 216 ASP cc_start: 0.8500 (t0) cc_final: 0.7132 (t0) REVERT: F 218 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8120 (mtm180) REVERT: G 27 LEU cc_start: 0.8921 (tp) cc_final: 0.8702 (tp) REVERT: G 28 ASN cc_start: 0.9262 (p0) cc_final: 0.9009 (p0) REVERT: G 41 SER cc_start: 0.8774 (m) cc_final: 0.8152 (p) REVERT: G 55 ILE cc_start: 0.9480 (pt) cc_final: 0.9278 (pt) REVERT: G 100 ASN cc_start: 0.8181 (t0) cc_final: 0.7885 (t0) REVERT: G 101 THR cc_start: 0.9048 (p) cc_final: 0.8837 (t) REVERT: G 109 GLU cc_start: 0.8294 (tt0) cc_final: 0.8011 (tt0) REVERT: G 125 HIS cc_start: 0.6037 (m170) cc_final: 0.5767 (m170) REVERT: G 179 ILE cc_start: 0.9669 (mt) cc_final: 0.9429 (mm) REVERT: G 218 ASP cc_start: 0.8735 (t0) cc_final: 0.8436 (t70) REVERT: G 235 GLN cc_start: 0.8562 (pt0) cc_final: 0.8034 (pt0) REVERT: G 262 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7378 (mt-10) REVERT: G 311 ASP cc_start: 0.7803 (p0) cc_final: 0.7530 (p0) REVERT: G 341 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7934 (mp0) REVERT: G 357 SER cc_start: 0.8557 (t) cc_final: 0.8309 (t) REVERT: G 362 GLN cc_start: 0.8316 (pm20) cc_final: 0.8019 (pm20) REVERT: G 386 HIS cc_start: 0.7245 (m-70) cc_final: 0.5976 (m170) REVERT: G 387 ILE cc_start: 0.7051 (mp) cc_final: 0.6697 (mm) REVERT: G 395 ASP cc_start: 0.8425 (t0) cc_final: 0.7829 (t0) REVERT: H 32 GLU cc_start: 0.8005 (pt0) cc_final: 0.7760 (pt0) REVERT: H 39 ASP cc_start: 0.8807 (m-30) cc_final: 0.8401 (m-30) REVERT: H 46 GLN cc_start: 0.7950 (mt0) cc_final: 0.7715 (tt0) REVERT: H 67 MET cc_start: 0.7492 (tpp) cc_final: 0.7022 (tpp) REVERT: H 72 ASP cc_start: 0.8784 (m-30) cc_final: 0.8344 (t0) REVERT: H 109 ASP cc_start: 0.8541 (m-30) cc_final: 0.8311 (m-30) REVERT: H 156 ASP cc_start: 0.8163 (t0) cc_final: 0.7726 (t0) REVERT: H 161 THR cc_start: 0.7872 (p) cc_final: 0.7518 (p) REVERT: H 168 MET cc_start: 0.8411 (mmt) cc_final: 0.8148 (tpp) REVERT: H 186 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7767 (mm-30) REVERT: H 233 GLN cc_start: 0.8304 (pm20) cc_final: 0.7641 (tm-30) REVERT: H 272 HIS cc_start: 0.7567 (t70) cc_final: 0.6983 (t70) REVERT: H 280 PHE cc_start: 0.6955 (m-80) cc_final: 0.6350 (m-80) REVERT: H 309 GLU cc_start: 0.8189 (tt0) cc_final: 0.7696 (tt0) REVERT: H 337 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.7777 (mmt90) REVERT: H 347 ASP cc_start: 0.8473 (t0) cc_final: 0.8260 (t0) REVERT: H 396 CYS cc_start: 0.9499 (t) cc_final: 0.9046 (m) REVERT: I 125 CYS cc_start: 0.8544 (t) cc_final: 0.7927 (t) REVERT: I 157 TYR cc_start: 0.8716 (m-80) cc_final: 0.8302 (m-80) REVERT: I 160 GLU cc_start: 0.8083 (pt0) cc_final: 0.7354 (pt0) REVERT: I 161 TYR cc_start: 0.7896 (p90) cc_final: 0.7671 (p90) REVERT: I 184 TYR cc_start: 0.6221 (m-80) cc_final: 0.5985 (m-80) REVERT: I 209 ASP cc_start: 0.7116 (m-30) cc_final: 0.6179 (t70) REVERT: J 59 GLN cc_start: 0.8294 (tt0) cc_final: 0.7859 (tt0) REVERT: J 66 LEU cc_start: 0.9249 (mt) cc_final: 0.9029 (mp) REVERT: J 79 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7262 (mtt-85) REVERT: J 88 MET cc_start: 0.8165 (mtp) cc_final: 0.7600 (mtt) REVERT: J 145 ASP cc_start: 0.8130 (m-30) cc_final: 0.7642 (p0) REVERT: J 152 THR cc_start: 0.8401 (m) cc_final: 0.8109 (t) REVERT: J 209 ASP cc_start: 0.8836 (m-30) cc_final: 0.8463 (p0) REVERT: J 241 GLU cc_start: 0.9305 (tp30) cc_final: 0.8787 (tt0) REVERT: J 246 ASN cc_start: 0.8719 (m110) cc_final: 0.8161 (t0) REVERT: J 270 ASN cc_start: 0.9227 (m-40) cc_final: 0.9000 (m110) REVERT: J 305 ASP cc_start: 0.8874 (p0) cc_final: 0.8619 (p0) REVERT: J 381 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8272 (mttt) REVERT: K 33 ASN cc_start: 0.8820 (m-40) cc_final: 0.8588 (m-40) REVERT: K 46 GLN cc_start: 0.9169 (tt0) cc_final: 0.8905 (tt0) REVERT: K 70 ASP cc_start: 0.8727 (t0) cc_final: 0.8514 (t0) REVERT: K 75 ILE cc_start: 0.8743 (mp) cc_final: 0.8462 (mt) REVERT: K 80 MET cc_start: 0.8753 (mmp) cc_final: 0.8137 (mmp) REVERT: K 97 LYS cc_start: 0.8339 (tptm) cc_final: 0.7781 (tttp) REVERT: K 148 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8507 (ttmm) REVERT: K 165 TYR cc_start: 0.8910 (p90) cc_final: 0.8360 (p90) REVERT: K 168 MET cc_start: 0.9274 (mmp) cc_final: 0.8596 (mmm) REVERT: K 176 TYR cc_start: 0.8817 (m-80) cc_final: 0.8499 (m-10) REVERT: K 205 ASP cc_start: 0.8806 (t0) cc_final: 0.8434 (p0) REVERT: K 224 ARG cc_start: 0.7740 (mtm110) cc_final: 0.6931 (ttp80) REVERT: K 237 VAL cc_start: 0.9322 (t) cc_final: 0.9046 (t) REVERT: K 272 HIS cc_start: 0.8598 (t70) cc_final: 0.8102 (t-170) REVERT: K 279 TRP cc_start: 0.8976 (p-90) cc_final: 0.7986 (p-90) REVERT: K 280 PHE cc_start: 0.8794 (t80) cc_final: 0.8376 (t80) REVERT: K 309 GLU cc_start: 0.8976 (tt0) cc_final: 0.8579 (tt0) REVERT: K 327 GLU cc_start: 0.8260 (tt0) cc_final: 0.7732 (tt0) REVERT: K 330 TRP cc_start: 0.9376 (t-100) cc_final: 0.8785 (t-100) REVERT: K 334 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8100 (mm-30) REVERT: K 341 GLN cc_start: 0.9324 (mt0) cc_final: 0.8651 (mt0) REVERT: K 394 ARG cc_start: 0.8679 (ttp-170) cc_final: 0.8105 (mtt180) REVERT: L 115 MET cc_start: 0.8909 (mmm) cc_final: 0.8687 (mmm) REVERT: L 116 LEU cc_start: 0.9125 (tp) cc_final: 0.8798 (tt) REVERT: L 130 ARG cc_start: 0.8477 (mpt-90) cc_final: 0.8059 (mmm-85) REVERT: L 140 LYS cc_start: 0.8950 (tppt) cc_final: 0.8690 (tptp) REVERT: L 243 ASN cc_start: 0.8792 (t0) cc_final: 0.8564 (t0) REVERT: X 57 ASP cc_start: 0.7992 (m-30) cc_final: 0.7694 (m-30) REVERT: X 63 ASP cc_start: 0.6978 (m-30) cc_final: 0.6588 (m-30) REVERT: X 81 ASN cc_start: 0.8299 (p0) cc_final: 0.7932 (p0) REVERT: X 89 TRP cc_start: 0.7627 (m-10) cc_final: 0.7421 (m-10) REVERT: Y 38 PHE cc_start: 0.4659 (OUTLIER) cc_final: 0.4456 (p90) outliers start: 32 outliers final: 10 residues processed: 1488 average time/residue: 0.4238 time to fit residues: 1007.7442 Evaluate side-chains 1057 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1046 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain Y residue 38 PHE Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Z residue 66 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 59 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN C 275 HIS C 327 HIS C 408 ASN D 146 GLN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 188 HIS ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 143 HIS G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN H 96 HIS ** H 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 275 HIS ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 HIS J 364 ASN K 21 HIS ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN L 117 ASN V 83 GLN X 39 GLN Y 107 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129725 restraints weight = 65676.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133798 restraints weight = 32197.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136405 restraints weight = 19788.980| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 33724 Z= 0.211 Angle : 0.741 18.254 45928 Z= 0.391 Chirality : 0.048 0.216 5088 Planarity : 0.005 0.068 5928 Dihedral : 6.282 79.616 4629 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.23 % Allowed : 15.68 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4240 helix: 0.56 (0.24), residues: 416 sheet: -0.84 (0.14), residues: 1202 loop : -0.52 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 242 HIS 0.024 0.001 HIS D 349 PHE 0.042 0.002 PHE A 95 TYR 0.026 0.002 TYR E 175 ARG 0.011 0.001 ARG K 132 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1159) hydrogen bonds : angle 6.85123 ( 3129) SS BOND : bond 0.00539 ( 72) SS BOND : angle 1.58518 ( 144) covalent geometry : bond 0.00466 (33652) covalent geometry : angle 0.73649 (45784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1153 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.9508 (t0) cc_final: 0.9260 (t0) REVERT: A 13 ILE cc_start: 0.9360 (mm) cc_final: 0.9145 (mm) REVERT: A 37 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 102 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 123 LYS cc_start: 0.9516 (mtmt) cc_final: 0.9111 (mtpp) REVERT: A 137 TYR cc_start: 0.9313 (p90) cc_final: 0.8992 (p90) REVERT: A 140 THR cc_start: 0.9104 (m) cc_final: 0.8594 (m) REVERT: A 230 HIS cc_start: 0.8155 (t-90) cc_final: 0.7892 (t-90) REVERT: A 233 TYR cc_start: 0.9195 (p90) cc_final: 0.8836 (p90) REVERT: A 251 LEU cc_start: 0.9425 (tp) cc_final: 0.9051 (tp) REVERT: A 273 TYR cc_start: 0.8473 (p90) cc_final: 0.8104 (p90) REVERT: A 396 GLN cc_start: 0.8182 (pm20) cc_final: 0.7443 (pm20) REVERT: B 80 MET cc_start: 0.8346 (mmt) cc_final: 0.8027 (mmp) REVERT: B 92 ARG cc_start: 0.3001 (mtt180) cc_final: 0.1493 (mmm160) REVERT: B 104 GLN cc_start: 0.8101 (pp30) cc_final: 0.7745 (pp30) REVERT: B 138 GLU cc_start: 0.7312 (tt0) cc_final: 0.7040 (tt0) REVERT: B 156 ASP cc_start: 0.8624 (t0) cc_final: 0.8201 (m-30) REVERT: B 161 THR cc_start: 0.8951 (p) cc_final: 0.8724 (p) REVERT: B 179 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6243 (t80) REVERT: B 217 MET cc_start: 0.5374 (mmm) cc_final: 0.5163 (mmt) REVERT: B 239 ASN cc_start: 0.8468 (t0) cc_final: 0.8241 (t0) REVERT: B 293 THR cc_start: 0.9317 (m) cc_final: 0.8871 (m) REVERT: B 300 LEU cc_start: 0.8042 (mp) cc_final: 0.6944 (mp) REVERT: B 327 GLU cc_start: 0.8528 (tt0) cc_final: 0.8188 (tt0) REVERT: B 351 TRP cc_start: 0.6868 (m100) cc_final: 0.6630 (m-90) REVERT: C 2 GLU cc_start: 0.7819 (tt0) cc_final: 0.7576 (tt0) REVERT: C 27 LEU cc_start: 0.8678 (mt) cc_final: 0.8405 (mt) REVERT: C 93 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8764 (mm-40) REVERT: C 109 GLU cc_start: 0.7234 (tt0) cc_final: 0.6990 (tt0) REVERT: C 160 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8602 (tmtt) REVERT: C 212 ASP cc_start: 0.8268 (t0) cc_final: 0.8056 (t0) REVERT: C 218 ASP cc_start: 0.8806 (t70) cc_final: 0.8320 (t0) REVERT: C 233 TYR cc_start: 0.8636 (p90) cc_final: 0.8394 (p90) REVERT: C 238 SER cc_start: 0.9566 (t) cc_final: 0.9300 (p) REVERT: C 257 PHE cc_start: 0.9186 (m-80) cc_final: 0.8634 (m-80) REVERT: C 264 GLU cc_start: 0.8743 (mp0) cc_final: 0.8489 (mp0) REVERT: C 292 GLU cc_start: 0.8107 (pt0) cc_final: 0.7785 (tp30) REVERT: C 324 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7214 (mtm-85) REVERT: C 396 GLN cc_start: 0.7686 (pp30) cc_final: 0.6894 (pp30) REVERT: D 27 SER cc_start: 0.9226 (t) cc_final: 0.9025 (m) REVERT: D 50 GLN cc_start: 0.8140 (tp40) cc_final: 0.7800 (mm110) REVERT: D 55 GLN cc_start: 0.8707 (tt0) cc_final: 0.8491 (tp40) REVERT: D 99 TYR cc_start: 0.8801 (m-80) cc_final: 0.8565 (m-80) REVERT: D 176 TYR cc_start: 0.7782 (m-80) cc_final: 0.7212 (m-80) REVERT: D 189 ILE cc_start: 0.8361 (mt) cc_final: 0.8152 (mm) REVERT: D 200 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7723 (mp0) REVERT: D 205 ASP cc_start: 0.7970 (t0) cc_final: 0.7661 (p0) REVERT: D 211 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7366 (t) REVERT: D 229 TYR cc_start: 0.7937 (p90) cc_final: 0.7712 (p90) REVERT: D 238 PHE cc_start: 0.9326 (t80) cc_final: 0.8893 (t80) REVERT: D 294 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7608 (tp) REVERT: D 321 VAL cc_start: 0.9219 (t) cc_final: 0.8975 (p) REVERT: D 330 TRP cc_start: 0.9191 (t-100) cc_final: 0.8415 (t-100) REVERT: D 355 ILE cc_start: 0.8579 (mm) cc_final: 0.8266 (mm) REVERT: D 357 ILE cc_start: 0.8993 (tt) cc_final: 0.8731 (tp) REVERT: D 400 TYR cc_start: 0.8668 (m-80) cc_final: 0.8432 (m-80) REVERT: E 110 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8724 (mttt) REVERT: F 115 MET cc_start: 0.8519 (mmm) cc_final: 0.8004 (mmp) REVERT: F 119 GLN cc_start: 0.8498 (pm20) cc_final: 0.8068 (pm20) REVERT: F 161 TYR cc_start: 0.8312 (p90) cc_final: 0.7504 (p90) REVERT: F 186 TRP cc_start: 0.8314 (t60) cc_final: 0.8070 (t60) REVERT: F 242 TRP cc_start: 0.8658 (m-10) cc_final: 0.8399 (m-10) REVERT: G 41 SER cc_start: 0.8606 (m) cc_final: 0.8182 (p) REVERT: G 57 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8170 (p) REVERT: G 125 HIS cc_start: 0.6007 (m170) cc_final: 0.5526 (m170) REVERT: G 204 GLN cc_start: 0.8560 (mt0) cc_final: 0.8318 (mm-40) REVERT: G 218 ASP cc_start: 0.8381 (t0) cc_final: 0.8015 (t0) REVERT: G 273 TYR cc_start: 0.9047 (p90) cc_final: 0.8437 (p90) REVERT: G 362 GLN cc_start: 0.8260 (pm20) cc_final: 0.8041 (pm20) REVERT: G 379 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6643 (mt-10) REVERT: G 386 HIS cc_start: 0.7479 (m-70) cc_final: 0.6405 (m170) REVERT: G 395 ASP cc_start: 0.8469 (t0) cc_final: 0.7715 (t0) REVERT: H 32 GLU cc_start: 0.7768 (pt0) cc_final: 0.7362 (pt0) REVERT: H 46 GLN cc_start: 0.7821 (mt0) cc_final: 0.7373 (tt0) REVERT: H 67 MET cc_start: 0.7609 (tpp) cc_final: 0.7308 (tpp) REVERT: H 96 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7539 (p-80) REVERT: H 122 ASN cc_start: 0.8487 (m-40) cc_final: 0.8185 (m110) REVERT: H 168 MET cc_start: 0.8250 (mmt) cc_final: 0.7527 (mmt) REVERT: H 186 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7530 (mm-30) REVERT: H 233 GLN cc_start: 0.8265 (pm20) cc_final: 0.7726 (tm-30) REVERT: H 238 PHE cc_start: 0.8413 (t80) cc_final: 0.7835 (t80) REVERT: H 272 HIS cc_start: 0.7822 (t70) cc_final: 0.7523 (t-170) REVERT: H 280 PHE cc_start: 0.7234 (m-80) cc_final: 0.6071 (m-80) REVERT: H 337 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8346 (mmt90) REVERT: H 349 HIS cc_start: 0.6490 (m-70) cc_final: 0.6221 (m-70) REVERT: H 396 CYS cc_start: 0.9522 (t) cc_final: 0.9092 (m) REVERT: I 115 MET cc_start: 0.7903 (mmp) cc_final: 0.7691 (mmp) REVERT: I 116 LEU cc_start: 0.9179 (tp) cc_final: 0.8854 (mt) REVERT: I 133 LYS cc_start: 0.8512 (pptt) cc_final: 0.8185 (pptt) REVERT: I 161 TYR cc_start: 0.7607 (p90) cc_final: 0.7349 (p90) REVERT: I 169 LYS cc_start: 0.7238 (pttm) cc_final: 0.6772 (pttm) REVERT: I 179 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8247 (ptmm) REVERT: I 197 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8380 (mmt90) REVERT: I 220 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7744 (mtm-85) REVERT: J 2 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8164 (tm-30) REVERT: J 59 GLN cc_start: 0.8562 (tt0) cc_final: 0.8195 (tt0) REVERT: J 88 MET cc_start: 0.7863 (mtp) cc_final: 0.7271 (mtt) REVERT: J 145 ASP cc_start: 0.8083 (m-30) cc_final: 0.7482 (p0) REVERT: J 292 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7978 (mp0) REVERT: J 364 ASN cc_start: 0.8166 (t0) cc_final: 0.7957 (t0) REVERT: K 75 ILE cc_start: 0.9005 (mp) cc_final: 0.8751 (mt) REVERT: K 80 MET cc_start: 0.8581 (mmp) cc_final: 0.7959 (mmt) REVERT: K 86 SER cc_start: 0.8528 (t) cc_final: 0.8120 (p) REVERT: K 97 LYS cc_start: 0.8832 (tptm) cc_final: 0.8313 (tttp) REVERT: K 148 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8313 (ttmm) REVERT: K 176 TYR cc_start: 0.8578 (m-80) cc_final: 0.8309 (m-80) REVERT: K 240 SER cc_start: 0.8893 (t) cc_final: 0.8668 (p) REVERT: K 254 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8047 (pttp) REVERT: K 272 HIS cc_start: 0.8882 (t70) cc_final: 0.8287 (t70) REVERT: K 279 TRP cc_start: 0.9325 (p-90) cc_final: 0.8425 (p-90) REVERT: K 309 GLU cc_start: 0.9008 (tt0) cc_final: 0.8757 (tt0) REVERT: K 321 VAL cc_start: 0.9015 (t) cc_final: 0.8779 (p) REVERT: K 327 GLU cc_start: 0.8619 (tt0) cc_final: 0.8240 (tt0) REVERT: K 330 TRP cc_start: 0.9281 (t-100) cc_final: 0.8868 (t-100) REVERT: K 334 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7924 (mm-30) REVERT: L 116 LEU cc_start: 0.8993 (tp) cc_final: 0.8760 (tt) REVERT: L 130 ARG cc_start: 0.8482 (mpt-90) cc_final: 0.7983 (mmm-85) REVERT: L 140 LYS cc_start: 0.8960 (tppt) cc_final: 0.8581 (tptp) REVERT: L 161 TYR cc_start: 0.8619 (p90) cc_final: 0.8273 (p90) REVERT: L 243 ASN cc_start: 0.8877 (t0) cc_final: 0.8610 (t0) REVERT: V 83 GLN cc_start: 0.6873 (mm110) cc_final: 0.6632 (mm-40) REVERT: V 94 ASP cc_start: 0.7192 (m-30) cc_final: 0.6567 (t0) REVERT: X 81 ASN cc_start: 0.8396 (p0) cc_final: 0.8083 (p0) REVERT: Y 67 CYS cc_start: 0.1930 (p) cc_final: 0.1584 (m) outliers start: 153 outliers final: 100 residues processed: 1223 average time/residue: 0.4223 time to fit residues: 836.9532 Evaluate side-chains 1078 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 973 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain H residue 21 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain Z residue 66 ASN Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 228 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 250 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 392 optimal weight: 40.0000 chunk 222 optimal weight: 0.4980 chunk 172 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 HIS C 59 GLN C 102 GLN C 186 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN G 43 ASN ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN H 96 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS J 275 HIS ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 HIS ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN Z 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116742 restraints weight = 61723.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120210 restraints weight = 31659.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122492 restraints weight = 19873.664| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33724 Z= 0.249 Angle : 0.720 14.524 45928 Z= 0.377 Chirality : 0.047 0.239 5088 Planarity : 0.005 0.057 5928 Dihedral : 6.129 79.893 4622 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.95 % Allowed : 17.95 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4240 helix: 0.72 (0.25), residues: 421 sheet: -0.76 (0.14), residues: 1151 loop : -0.52 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 236 HIS 0.015 0.001 HIS B 349 PHE 0.030 0.002 PHE I 112 TYR 0.026 0.002 TYR B 206 ARG 0.010 0.001 ARG K 132 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1159) hydrogen bonds : angle 6.44600 ( 3129) SS BOND : bond 0.00453 ( 72) SS BOND : angle 1.41977 ( 144) covalent geometry : bond 0.00550 (33652) covalent geometry : angle 0.71716 (45784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1006 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.9536 (t0) cc_final: 0.9315 (t0) REVERT: A 44 LYS cc_start: 0.9327 (mtpt) cc_final: 0.8960 (ttmm) REVERT: A 66 LEU cc_start: 0.8561 (mt) cc_final: 0.8244 (mt) REVERT: A 102 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 123 LYS cc_start: 0.9538 (mtmt) cc_final: 0.9195 (mtpp) REVERT: A 230 HIS cc_start: 0.8310 (t-90) cc_final: 0.7986 (t-90) REVERT: A 251 LEU cc_start: 0.9440 (tp) cc_final: 0.9119 (tp) REVERT: A 284 ASP cc_start: 0.8766 (p0) cc_final: 0.8539 (p0) REVERT: A 364 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8473 (m-40) REVERT: A 377 ASN cc_start: 0.8474 (t0) cc_final: 0.8272 (t0) REVERT: A 379 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 395 ASP cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: A 396 GLN cc_start: 0.8314 (pm20) cc_final: 0.7470 (pm20) REVERT: B 50 GLN cc_start: 0.6553 (mt0) cc_final: 0.6221 (mp10) REVERT: B 80 MET cc_start: 0.8415 (mmt) cc_final: 0.8196 (mmm) REVERT: B 92 ARG cc_start: 0.2647 (mtt180) cc_final: 0.1403 (mmm160) REVERT: B 138 GLU cc_start: 0.7359 (tt0) cc_final: 0.7071 (tt0) REVERT: B 155 TYR cc_start: 0.7529 (m-80) cc_final: 0.7275 (m-80) REVERT: B 156 ASP cc_start: 0.8570 (t0) cc_final: 0.8013 (m-30) REVERT: B 161 THR cc_start: 0.8821 (p) cc_final: 0.8575 (p) REVERT: B 179 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 226 CYS cc_start: 0.6301 (m) cc_final: 0.6034 (m) REVERT: B 327 GLU cc_start: 0.8610 (tt0) cc_final: 0.8275 (tt0) REVERT: B 341 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8502 (mm110) REVERT: B 342 GLU cc_start: 0.8695 (tp30) cc_final: 0.8378 (tp30) REVERT: B 351 TRP cc_start: 0.7037 (m100) cc_final: 0.6820 (m-90) REVERT: C 27 LEU cc_start: 0.8824 (mt) cc_final: 0.8561 (mt) REVERT: C 45 GLU cc_start: 0.8706 (tp30) cc_final: 0.8501 (tp30) REVERT: C 103 LEU cc_start: 0.9251 (tp) cc_final: 0.8973 (tp) REVERT: C 109 GLU cc_start: 0.7278 (tt0) cc_final: 0.6984 (tt0) REVERT: C 160 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8672 (tmtt) REVERT: C 195 MET cc_start: 0.8800 (mpp) cc_final: 0.8457 (mpp) REVERT: C 204 GLN cc_start: 0.8647 (mt0) cc_final: 0.8387 (mt0) REVERT: C 212 ASP cc_start: 0.8426 (t0) cc_final: 0.8154 (t70) REVERT: C 218 ASP cc_start: 0.8769 (t70) cc_final: 0.7969 (t0) REVERT: C 238 SER cc_start: 0.9619 (t) cc_final: 0.9288 (p) REVERT: C 257 PHE cc_start: 0.9323 (m-80) cc_final: 0.8585 (m-80) REVERT: C 264 GLU cc_start: 0.8813 (mp0) cc_final: 0.8518 (mp0) REVERT: C 292 GLU cc_start: 0.8025 (pt0) cc_final: 0.7599 (tp30) REVERT: D 30 LYS cc_start: 0.9042 (tmtt) cc_final: 0.8502 (tmtt) REVERT: D 46 GLN cc_start: 0.8057 (tt0) cc_final: 0.7814 (tt0) REVERT: D 50 GLN cc_start: 0.8049 (tp40) cc_final: 0.7587 (mm110) REVERT: D 55 GLN cc_start: 0.8790 (tt0) cc_final: 0.8411 (tp40) REVERT: D 99 TYR cc_start: 0.8927 (m-80) cc_final: 0.8560 (m-80) REVERT: D 112 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8458 (p) REVERT: D 131 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8325 (mmt180) REVERT: D 176 TYR cc_start: 0.7937 (m-80) cc_final: 0.7242 (m-80) REVERT: D 200 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7735 (mp0) REVERT: D 259 PHE cc_start: 0.8912 (m-80) cc_final: 0.8635 (m-80) REVERT: D 321 VAL cc_start: 0.9197 (t) cc_final: 0.8901 (p) REVERT: D 339 TRP cc_start: 0.9069 (m-90) cc_final: 0.8746 (m-90) REVERT: D 357 ILE cc_start: 0.9027 (tt) cc_final: 0.8781 (tp) REVERT: D 393 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6330 (tpt170) REVERT: E 132 MET cc_start: 0.8774 (ptp) cc_final: 0.8430 (mpp) REVERT: E 172 THR cc_start: 0.8470 (t) cc_final: 0.7357 (m) REVERT: F 115 MET cc_start: 0.8534 (mmm) cc_final: 0.7986 (mmp) REVERT: F 119 GLN cc_start: 0.8457 (pm20) cc_final: 0.7976 (pm20) REVERT: F 161 TYR cc_start: 0.8368 (p90) cc_final: 0.7631 (p90) REVERT: F 186 TRP cc_start: 0.8329 (t60) cc_final: 0.8021 (t60) REVERT: F 188 HIS cc_start: 0.9128 (m-70) cc_final: 0.8358 (m170) REVERT: F 242 TRP cc_start: 0.8642 (m-10) cc_final: 0.8345 (m-10) REVERT: G 97 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: G 204 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8262 (mm-40) REVERT: G 218 ASP cc_start: 0.8643 (t0) cc_final: 0.7939 (t0) REVERT: G 253 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7149 (mt-10) REVERT: G 273 TYR cc_start: 0.8973 (p90) cc_final: 0.8516 (p90) REVERT: G 362 GLN cc_start: 0.8395 (pm20) cc_final: 0.8080 (pm20) REVERT: G 386 HIS cc_start: 0.7753 (m-70) cc_final: 0.6564 (m170) REVERT: G 395 ASP cc_start: 0.8406 (t0) cc_final: 0.7834 (t0) REVERT: H 32 GLU cc_start: 0.7991 (pt0) cc_final: 0.7153 (pt0) REVERT: H 46 GLN cc_start: 0.7760 (mt0) cc_final: 0.7129 (tt0) REVERT: H 67 MET cc_start: 0.7720 (tpp) cc_final: 0.7386 (tpp) REVERT: H 115 ILE cc_start: 0.8805 (pt) cc_final: 0.8462 (pt) REVERT: H 121 GLU cc_start: 0.8044 (tt0) cc_final: 0.7389 (tp30) REVERT: H 130 ILE cc_start: 0.9169 (tp) cc_final: 0.8827 (pt) REVERT: H 137 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8315 (mtp85) REVERT: H 199 TYR cc_start: 0.8112 (p90) cc_final: 0.7784 (p90) REVERT: H 233 GLN cc_start: 0.8372 (pm20) cc_final: 0.7744 (tm-30) REVERT: H 238 PHE cc_start: 0.8415 (t80) cc_final: 0.8044 (t80) REVERT: H 272 HIS cc_start: 0.8014 (t70) cc_final: 0.7439 (t70) REVERT: H 273 THR cc_start: 0.9237 (m) cc_final: 0.8742 (p) REVERT: H 280 PHE cc_start: 0.7275 (m-80) cc_final: 0.6271 (m-80) REVERT: H 337 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8421 (mmt90) REVERT: H 347 ASP cc_start: 0.9001 (t0) cc_final: 0.8790 (t0) REVERT: H 354 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8576 (pm20) REVERT: H 396 CYS cc_start: 0.9498 (t) cc_final: 0.9084 (m) REVERT: I 115 MET cc_start: 0.7648 (mmp) cc_final: 0.7435 (mmp) REVERT: I 116 LEU cc_start: 0.9115 (tp) cc_final: 0.8868 (mt) REVERT: I 153 LYS cc_start: 0.8517 (mppt) cc_final: 0.8248 (mmtm) REVERT: I 160 GLU cc_start: 0.7573 (pt0) cc_final: 0.6766 (pt0) REVERT: I 166 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5896 (tt0) REVERT: I 169 LYS cc_start: 0.7134 (pttm) cc_final: 0.6568 (pttm) REVERT: I 197 ARG cc_start: 0.8670 (mtt90) cc_final: 0.8060 (mmt90) REVERT: I 220 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7969 (mtm-85) REVERT: J 2 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8215 (tm-30) REVERT: J 59 GLN cc_start: 0.8513 (tt0) cc_final: 0.8157 (tt0) REVERT: J 88 MET cc_start: 0.8009 (mtp) cc_final: 0.7439 (mtt) REVERT: J 145 ASP cc_start: 0.8308 (m-30) cc_final: 0.7508 (p0) REVERT: K 30 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8465 (ttpt) REVERT: K 80 MET cc_start: 0.8632 (mmp) cc_final: 0.8072 (mmt) REVERT: K 86 SER cc_start: 0.8395 (t) cc_final: 0.8043 (p) REVERT: K 97 LYS cc_start: 0.8859 (tptm) cc_final: 0.8422 (tttp) REVERT: K 146 GLN cc_start: 0.9095 (tp40) cc_final: 0.8889 (tp-100) REVERT: K 148 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8389 (ttmm) REVERT: K 176 TYR cc_start: 0.8690 (m-80) cc_final: 0.8324 (m-10) REVERT: K 195 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: K 225 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7986 (tp-100) REVERT: K 254 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8023 (pttp) REVERT: K 272 HIS cc_start: 0.8894 (t70) cc_final: 0.8331 (t70) REVERT: K 321 VAL cc_start: 0.8957 (t) cc_final: 0.8744 (p) REVERT: K 330 TRP cc_start: 0.9352 (t-100) cc_final: 0.8928 (t-100) REVERT: K 334 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8065 (mm-30) REVERT: L 116 LEU cc_start: 0.9004 (tp) cc_final: 0.8785 (tt) REVERT: L 140 LYS cc_start: 0.9004 (tppt) cc_final: 0.8615 (tptp) REVERT: L 198 PHE cc_start: 0.7685 (m-10) cc_final: 0.7381 (m-10) REVERT: L 243 ASN cc_start: 0.8958 (t0) cc_final: 0.8676 (t0) REVERT: V 83 GLN cc_start: 0.6803 (mm110) cc_final: 0.6533 (mm-40) REVERT: V 94 ASP cc_start: 0.7168 (m-30) cc_final: 0.6368 (t0) REVERT: X 81 ASN cc_start: 0.8379 (p0) cc_final: 0.8032 (p0) REVERT: Y 67 CYS cc_start: 0.1648 (p) cc_final: 0.1243 (m) REVERT: Y 88 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8009 (ptp90) outliers start: 215 outliers final: 155 residues processed: 1107 average time/residue: 0.4093 time to fit residues: 737.6046 Evaluate side-chains 1082 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 918 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 195 LYS Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 372 optimal weight: 9.9990 chunk 363 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 120 optimal weight: 0.0010 chunk 84 optimal weight: 5.9990 overall best weight: 2.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 HIS C 59 GLN C 93 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 HIS J 364 ASN J 396 GLN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN K 363 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119328 restraints weight = 60680.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122787 restraints weight = 31356.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125047 restraints weight = 19656.003| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 33724 Z= 0.203 Angle : 0.681 12.248 45928 Z= 0.356 Chirality : 0.046 0.275 5088 Planarity : 0.005 0.065 5928 Dihedral : 6.081 84.274 4620 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.53 % Allowed : 19.50 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4240 helix: 0.89 (0.25), residues: 424 sheet: -0.78 (0.15), residues: 1130 loop : -0.49 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 236 HIS 0.018 0.001 HIS D 349 PHE 0.023 0.002 PHE H 134 TYR 0.021 0.002 TYR B 206 ARG 0.008 0.001 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1159) hydrogen bonds : angle 6.21373 ( 3129) SS BOND : bond 0.00498 ( 72) SS BOND : angle 1.49995 ( 144) covalent geometry : bond 0.00456 (33652) covalent geometry : angle 0.67705 (45784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1006 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 29 LEU cc_start: 0.9332 (tp) cc_final: 0.9099 (tp) REVERT: A 44 LYS cc_start: 0.9308 (mtpt) cc_final: 0.8916 (ttmm) REVERT: A 66 LEU cc_start: 0.8569 (mt) cc_final: 0.8265 (mt) REVERT: A 102 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 251 LEU cc_start: 0.9456 (tp) cc_final: 0.9123 (tp) REVERT: A 284 ASP cc_start: 0.8873 (p0) cc_final: 0.8555 (p0) REVERT: A 364 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8497 (m-40) REVERT: A 396 GLN cc_start: 0.8384 (pm20) cc_final: 0.7295 (pm20) REVERT: B 50 GLN cc_start: 0.6389 (mt0) cc_final: 0.6175 (mp10) REVERT: B 80 MET cc_start: 0.8365 (mmt) cc_final: 0.8110 (mmm) REVERT: B 92 ARG cc_start: 0.2496 (mtt180) cc_final: 0.1652 (mmm160) REVERT: B 138 GLU cc_start: 0.7405 (tt0) cc_final: 0.7155 (tt0) REVERT: B 156 ASP cc_start: 0.8576 (t0) cc_final: 0.7875 (m-30) REVERT: B 161 THR cc_start: 0.8866 (p) cc_final: 0.8609 (p) REVERT: B 179 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.6331 (t80) REVERT: B 327 GLU cc_start: 0.8590 (tt0) cc_final: 0.8297 (tt0) REVERT: B 341 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8583 (mm110) REVERT: B 342 GLU cc_start: 0.8693 (tp30) cc_final: 0.8356 (tp30) REVERT: B 351 TRP cc_start: 0.6990 (m100) cc_final: 0.6737 (m-90) REVERT: C 27 LEU cc_start: 0.8741 (mt) cc_final: 0.8539 (mt) REVERT: C 109 GLU cc_start: 0.7224 (tt0) cc_final: 0.7001 (tt0) REVERT: C 140 THR cc_start: 0.8612 (m) cc_final: 0.8379 (p) REVERT: C 195 MET cc_start: 0.8758 (mpp) cc_final: 0.8447 (mpp) REVERT: C 204 GLN cc_start: 0.8629 (mt0) cc_final: 0.8374 (mt0) REVERT: C 212 ASP cc_start: 0.8481 (t0) cc_final: 0.8185 (t0) REVERT: C 218 ASP cc_start: 0.8740 (t70) cc_final: 0.7962 (t0) REVERT: C 257 PHE cc_start: 0.9323 (m-80) cc_final: 0.8554 (m-80) REVERT: C 292 GLU cc_start: 0.8084 (pt0) cc_final: 0.7622 (tp30) REVERT: C 396 GLN cc_start: 0.7750 (pp30) cc_final: 0.7212 (pp30) REVERT: D 29 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8374 (mm) REVERT: D 30 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8261 (tmtt) REVERT: D 46 GLN cc_start: 0.8024 (tt0) cc_final: 0.7708 (tt0) REVERT: D 48 SER cc_start: 0.9297 (t) cc_final: 0.8930 (p) REVERT: D 50 GLN cc_start: 0.7864 (tp40) cc_final: 0.7572 (mm110) REVERT: D 55 GLN cc_start: 0.8756 (tt0) cc_final: 0.8325 (tp40) REVERT: D 99 TYR cc_start: 0.8984 (m-80) cc_final: 0.8610 (m-80) REVERT: D 131 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8194 (mmm-85) REVERT: D 137 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8019 (mtp180) REVERT: D 176 TYR cc_start: 0.7955 (m-80) cc_final: 0.7239 (m-80) REVERT: D 190 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8801 (mmtt) REVERT: D 200 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7710 (mp0) REVERT: D 211 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7336 (t) REVERT: D 217 MET cc_start: 0.6712 (tpp) cc_final: 0.6378 (tpp) REVERT: D 225 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6844 (tm-30) REVERT: D 259 PHE cc_start: 0.8897 (m-80) cc_final: 0.8628 (m-80) REVERT: D 321 VAL cc_start: 0.9134 (t) cc_final: 0.8799 (p) REVERT: D 357 ILE cc_start: 0.9029 (tt) cc_final: 0.8797 (tp) REVERT: D 393 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6434 (tpt170) REVERT: E 110 LYS cc_start: 0.8930 (mttt) cc_final: 0.8543 (mmtt) REVERT: E 192 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: E 250 LYS cc_start: 0.8635 (tttp) cc_final: 0.8300 (tmtt) REVERT: F 115 MET cc_start: 0.8548 (mmm) cc_final: 0.8071 (mmp) REVERT: F 119 GLN cc_start: 0.8504 (pm20) cc_final: 0.8027 (pm20) REVERT: F 161 TYR cc_start: 0.8331 (p90) cc_final: 0.7610 (p90) REVERT: F 186 TRP cc_start: 0.8282 (t60) cc_final: 0.8028 (t60) REVERT: F 188 HIS cc_start: 0.9096 (m-70) cc_final: 0.8373 (m170) REVERT: F 242 TRP cc_start: 0.8571 (m-10) cc_final: 0.8305 (m-10) REVERT: G 10 VAL cc_start: 0.9333 (p) cc_final: 0.9061 (m) REVERT: G 37 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7555 (mp0) REVERT: G 97 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: G 204 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8283 (mm-40) REVERT: G 218 ASP cc_start: 0.8596 (t0) cc_final: 0.7859 (t0) REVERT: G 253 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7257 (mt-10) REVERT: G 273 TYR cc_start: 0.8919 (p90) cc_final: 0.8515 (p90) REVERT: G 362 GLN cc_start: 0.8417 (pm20) cc_final: 0.8118 (pm20) REVERT: G 386 HIS cc_start: 0.7761 (m-70) cc_final: 0.6626 (m170) REVERT: G 395 ASP cc_start: 0.8391 (t0) cc_final: 0.7826 (t0) REVERT: H 100 PHE cc_start: 0.8557 (m-80) cc_final: 0.8323 (m-10) REVERT: H 115 ILE cc_start: 0.8824 (pt) cc_final: 0.8509 (pt) REVERT: H 121 GLU cc_start: 0.8084 (tt0) cc_final: 0.7493 (tp30) REVERT: H 130 ILE cc_start: 0.9169 (tp) cc_final: 0.8853 (pt) REVERT: H 137 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7873 (mtm180) REVERT: H 168 MET cc_start: 0.8670 (mpp) cc_final: 0.7646 (mmt) REVERT: H 186 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7527 (mm-30) REVERT: H 199 TYR cc_start: 0.8059 (p90) cc_final: 0.7796 (p90) REVERT: H 233 GLN cc_start: 0.8340 (pm20) cc_final: 0.7698 (tm-30) REVERT: H 238 PHE cc_start: 0.8472 (t80) cc_final: 0.7941 (t80) REVERT: H 272 HIS cc_start: 0.8002 (t70) cc_final: 0.7424 (t70) REVERT: H 273 THR cc_start: 0.9241 (m) cc_final: 0.8762 (p) REVERT: H 279 TRP cc_start: 0.9077 (p-90) cc_final: 0.8274 (p-90) REVERT: H 280 PHE cc_start: 0.7258 (m-80) cc_final: 0.6403 (m-80) REVERT: H 295 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8923 (tp) REVERT: H 337 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.8383 (mtt-85) REVERT: H 354 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8606 (pm20) REVERT: H 396 CYS cc_start: 0.9446 (t) cc_final: 0.9068 (m) REVERT: I 116 LEU cc_start: 0.9053 (tp) cc_final: 0.8845 (mt) REVERT: I 119 GLN cc_start: 0.8601 (pt0) cc_final: 0.8020 (pt0) REVERT: I 132 MET cc_start: 0.7922 (mpp) cc_final: 0.7573 (mpp) REVERT: I 153 LYS cc_start: 0.8519 (mppt) cc_final: 0.8302 (mmtm) REVERT: I 160 GLU cc_start: 0.7276 (pt0) cc_final: 0.6904 (pt0) REVERT: I 169 LYS cc_start: 0.7095 (pttm) cc_final: 0.6435 (pttm) REVERT: I 193 TYR cc_start: 0.8488 (t80) cc_final: 0.8160 (t80) REVERT: I 220 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7892 (mtm-85) REVERT: J 2 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8203 (tm-30) REVERT: J 59 GLN cc_start: 0.8497 (tt0) cc_final: 0.8033 (tt0) REVERT: J 88 MET cc_start: 0.8033 (mtp) cc_final: 0.7559 (mtp) REVERT: J 145 ASP cc_start: 0.8259 (m-30) cc_final: 0.7443 (p0) REVERT: J 181 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8579 (ttpt) REVERT: J 292 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7916 (mp0) REVERT: J 327 HIS cc_start: 0.6670 (m-70) cc_final: 0.4580 (m170) REVERT: K 46 GLN cc_start: 0.9134 (tt0) cc_final: 0.8901 (tt0) REVERT: K 54 ASN cc_start: 0.8878 (t0) cc_final: 0.8500 (t0) REVERT: K 80 MET cc_start: 0.8583 (mmp) cc_final: 0.8004 (mmt) REVERT: K 86 SER cc_start: 0.8218 (t) cc_final: 0.7868 (p) REVERT: K 97 LYS cc_start: 0.8832 (tptm) cc_final: 0.8440 (tttp) REVERT: K 148 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8356 (ttmm) REVERT: K 176 TYR cc_start: 0.8597 (m-80) cc_final: 0.8233 (m-80) REVERT: K 225 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8064 (tp-100) REVERT: K 238 PHE cc_start: 0.9206 (t80) cc_final: 0.8575 (t80) REVERT: K 254 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8009 (pttp) REVERT: K 272 HIS cc_start: 0.8887 (t70) cc_final: 0.8260 (t70) REVERT: K 321 VAL cc_start: 0.8907 (t) cc_final: 0.8704 (p) REVERT: K 330 TRP cc_start: 0.9356 (t-100) cc_final: 0.8843 (t-100) REVERT: K 334 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7941 (mm-30) REVERT: K 342 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7912 (tp30) REVERT: K 362 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8330 (ttp80) REVERT: L 140 LYS cc_start: 0.9034 (tppt) cc_final: 0.8640 (tptp) REVERT: L 198 PHE cc_start: 0.7681 (m-10) cc_final: 0.7429 (m-10) REVERT: L 243 ASN cc_start: 0.8920 (t0) cc_final: 0.8618 (t0) REVERT: V 83 GLN cc_start: 0.6673 (mm110) cc_final: 0.6371 (mm-40) REVERT: V 94 ASP cc_start: 0.7068 (m-30) cc_final: 0.6341 (t0) REVERT: X 81 ASN cc_start: 0.8282 (p0) cc_final: 0.7968 (p0) REVERT: Y 67 CYS cc_start: 0.1724 (p) cc_final: 0.1221 (m) REVERT: Y 89 TRP cc_start: 0.8057 (m-10) cc_final: 0.7577 (m-10) outliers start: 200 outliers final: 151 residues processed: 1108 average time/residue: 0.4261 time to fit residues: 771.3458 Evaluate side-chains 1103 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 942 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 90 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 chunk 365 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 407 optimal weight: 0.0000 chunk 234 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 HIS C 59 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** H 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN K 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121866 restraints weight = 60182.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125389 restraints weight = 30827.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127648 restraints weight = 19178.722| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33724 Z= 0.148 Angle : 0.657 13.971 45928 Z= 0.341 Chirality : 0.045 0.255 5088 Planarity : 0.005 0.050 5928 Dihedral : 5.897 87.736 4619 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.48 % Allowed : 20.85 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4240 helix: 1.27 (0.25), residues: 406 sheet: -0.80 (0.14), residues: 1161 loop : -0.36 (0.12), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 236 HIS 0.018 0.001 HIS D 349 PHE 0.023 0.002 PHE B 280 TYR 0.023 0.002 TYR A 76 ARG 0.009 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1159) hydrogen bonds : angle 6.00920 ( 3129) SS BOND : bond 0.00344 ( 72) SS BOND : angle 1.56179 ( 144) covalent geometry : bond 0.00333 (33652) covalent geometry : angle 0.65224 (45784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1041 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9278 (tp) cc_final: 0.9023 (tp) REVERT: A 44 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8848 (ttmm) REVERT: A 66 LEU cc_start: 0.8530 (mt) cc_final: 0.8296 (mt) REVERT: A 77 THR cc_start: 0.8780 (p) cc_final: 0.8528 (p) REVERT: A 102 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 176 LYS cc_start: 0.8767 (mttm) cc_final: 0.8484 (mttt) REVERT: A 186 ASN cc_start: 0.8919 (m-40) cc_final: 0.8680 (t0) REVERT: A 251 LEU cc_start: 0.9433 (tp) cc_final: 0.9099 (tp) REVERT: A 284 ASP cc_start: 0.8822 (p0) cc_final: 0.8488 (p0) REVERT: A 364 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8790 (m-40) REVERT: A 396 GLN cc_start: 0.8117 (pm20) cc_final: 0.7307 (pm20) REVERT: B 92 ARG cc_start: 0.2198 (mtt180) cc_final: 0.1805 (mmm160) REVERT: B 138 GLU cc_start: 0.7365 (tt0) cc_final: 0.7133 (tt0) REVERT: B 156 ASP cc_start: 0.8312 (t0) cc_final: 0.7794 (m-30) REVERT: B 161 THR cc_start: 0.8854 (p) cc_final: 0.8608 (p) REVERT: B 179 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6431 (t80) REVERT: B 217 MET cc_start: 0.4782 (mmt) cc_final: 0.4489 (mmt) REVERT: B 327 GLU cc_start: 0.8507 (tt0) cc_final: 0.8269 (tt0) REVERT: B 341 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8555 (mm110) REVERT: B 342 GLU cc_start: 0.8581 (tp30) cc_final: 0.8290 (tp30) REVERT: B 351 TRP cc_start: 0.7056 (m100) cc_final: 0.6819 (m-90) REVERT: C 9 ASN cc_start: 0.9174 (t0) cc_final: 0.8798 (t0) REVERT: C 27 LEU cc_start: 0.8710 (mt) cc_final: 0.8479 (mt) REVERT: C 88 MET cc_start: 0.7672 (ttm) cc_final: 0.7137 (ttm) REVERT: C 140 THR cc_start: 0.8563 (m) cc_final: 0.8331 (p) REVERT: C 212 ASP cc_start: 0.8436 (t0) cc_final: 0.8119 (t0) REVERT: C 218 ASP cc_start: 0.8721 (t70) cc_final: 0.8042 (t0) REVERT: C 257 PHE cc_start: 0.9314 (m-80) cc_final: 0.8558 (m-80) REVERT: C 292 GLU cc_start: 0.8060 (pt0) cc_final: 0.7545 (tp30) REVERT: C 381 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8567 (mtmt) REVERT: C 396 GLN cc_start: 0.7727 (pp30) cc_final: 0.7190 (pp30) REVERT: D 30 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8279 (tmtt) REVERT: D 48 SER cc_start: 0.9266 (t) cc_final: 0.8890 (p) REVERT: D 55 GLN cc_start: 0.8680 (tt0) cc_final: 0.8293 (tp40) REVERT: D 137 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7952 (mtp180) REVERT: D 176 TYR cc_start: 0.7964 (m-80) cc_final: 0.7264 (m-80) REVERT: D 200 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7720 (mp0) REVERT: D 211 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7280 (t) REVERT: D 217 MET cc_start: 0.6391 (tpp) cc_final: 0.6124 (mtp) REVERT: D 225 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6885 (tm-30) REVERT: D 259 PHE cc_start: 0.8790 (m-80) cc_final: 0.8561 (m-80) REVERT: D 357 ILE cc_start: 0.9023 (tt) cc_final: 0.8776 (tp) REVERT: D 393 ARG cc_start: 0.7296 (ttt180) cc_final: 0.6440 (tpt170) REVERT: E 110 LYS cc_start: 0.8885 (mttt) cc_final: 0.8606 (mmtt) REVERT: E 132 MET cc_start: 0.8531 (ptp) cc_final: 0.8101 (mpp) REVERT: E 152 LYS cc_start: 0.8808 (mttt) cc_final: 0.8493 (mtmt) REVERT: E 192 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: E 250 LYS cc_start: 0.8651 (tttp) cc_final: 0.8397 (tmtt) REVERT: F 115 MET cc_start: 0.8569 (mmm) cc_final: 0.8102 (mmp) REVERT: F 119 GLN cc_start: 0.8471 (pm20) cc_final: 0.7932 (pm20) REVERT: F 161 TYR cc_start: 0.8287 (p90) cc_final: 0.7561 (p90) REVERT: F 186 TRP cc_start: 0.8229 (t60) cc_final: 0.7986 (t60) REVERT: G 10 VAL cc_start: 0.9330 (p) cc_final: 0.9105 (m) REVERT: G 37 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7568 (mp0) REVERT: G 93 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8295 (mm110) REVERT: G 97 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: G 100 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: G 159 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7786 (mm) REVERT: G 204 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8292 (mm-40) REVERT: G 218 ASP cc_start: 0.8529 (t0) cc_final: 0.7734 (t0) REVERT: G 253 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7597 (mt-10) REVERT: G 273 TYR cc_start: 0.8892 (p90) cc_final: 0.8499 (p90) REVERT: G 386 HIS cc_start: 0.7752 (m-70) cc_final: 0.6461 (m170) REVERT: G 395 ASP cc_start: 0.8389 (t0) cc_final: 0.7814 (t0) REVERT: H 46 GLN cc_start: 0.7662 (mt0) cc_final: 0.7116 (mt0) REVERT: H 80 MET cc_start: 0.7471 (mmt) cc_final: 0.7147 (tpp) REVERT: H 100 PHE cc_start: 0.8478 (m-80) cc_final: 0.8265 (m-10) REVERT: H 130 ILE cc_start: 0.9162 (tp) cc_final: 0.8925 (pt) REVERT: H 137 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7921 (mtm180) REVERT: H 156 ASP cc_start: 0.8866 (t0) cc_final: 0.8666 (t0) REVERT: H 199 TYR cc_start: 0.8014 (p90) cc_final: 0.7776 (p90) REVERT: H 233 GLN cc_start: 0.8367 (pm20) cc_final: 0.7691 (tm-30) REVERT: H 242 ASP cc_start: 0.8820 (m-30) cc_final: 0.8428 (m-30) REVERT: H 272 HIS cc_start: 0.8067 (t70) cc_final: 0.7417 (t70) REVERT: H 279 TRP cc_start: 0.9138 (p-90) cc_final: 0.8343 (p-90) REVERT: H 280 PHE cc_start: 0.7277 (m-80) cc_final: 0.6420 (m-80) REVERT: H 337 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.8202 (mmt90) REVERT: H 343 SER cc_start: 0.9210 (t) cc_final: 0.8360 (t) REVERT: H 354 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8639 (pm20) REVERT: H 396 CYS cc_start: 0.9437 (t) cc_final: 0.9057 (m) REVERT: I 116 LEU cc_start: 0.9062 (tp) cc_final: 0.8855 (mt) REVERT: I 132 MET cc_start: 0.7877 (mpp) cc_final: 0.7547 (mpp) REVERT: I 151 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7933 (mm) REVERT: I 153 LYS cc_start: 0.8558 (mppt) cc_final: 0.8264 (mmtm) REVERT: J 2 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8205 (tm-30) REVERT: J 88 MET cc_start: 0.8026 (mtp) cc_final: 0.7629 (mtt) REVERT: J 145 ASP cc_start: 0.8260 (m-30) cc_final: 0.7400 (p0) REVERT: J 181 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8523 (ttpt) REVERT: J 207 SER cc_start: 0.9482 (t) cc_final: 0.9201 (p) REVERT: J 241 GLU cc_start: 0.8514 (tt0) cc_final: 0.8229 (mt-10) REVERT: J 246 ASN cc_start: 0.8327 (m110) cc_final: 0.7839 (t0) REVERT: J 270 ASN cc_start: 0.8992 (m-40) cc_final: 0.8658 (m-40) REVERT: J 352 ILE cc_start: 0.8662 (mm) cc_final: 0.8362 (mm) REVERT: K 44 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8543 (ttp-110) REVERT: K 54 ASN cc_start: 0.8601 (m-40) cc_final: 0.8397 (t0) REVERT: K 80 MET cc_start: 0.8483 (mmp) cc_final: 0.7909 (mmt) REVERT: K 86 SER cc_start: 0.8122 (t) cc_final: 0.7785 (p) REVERT: K 97 LYS cc_start: 0.8821 (tptm) cc_final: 0.8244 (tttp) REVERT: K 148 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8268 (ttmm) REVERT: K 168 MET cc_start: 0.9150 (mmt) cc_final: 0.8703 (mmt) REVERT: K 176 TYR cc_start: 0.8533 (m-80) cc_final: 0.8156 (m-80) REVERT: K 225 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8188 (tp-100) REVERT: K 254 LYS cc_start: 0.8914 (mtpt) cc_final: 0.7996 (pttp) REVERT: K 272 HIS cc_start: 0.8798 (t70) cc_final: 0.8069 (t70) REVERT: K 279 TRP cc_start: 0.9349 (p-90) cc_final: 0.8505 (p-90) REVERT: K 284 THR cc_start: 0.9503 (m) cc_final: 0.9082 (p) REVERT: K 321 VAL cc_start: 0.8866 (t) cc_final: 0.8613 (p) REVERT: K 330 TRP cc_start: 0.9274 (t-100) cc_final: 0.8856 (t-100) REVERT: K 334 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7874 (mm-30) REVERT: K 362 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8390 (ttp80) REVERT: L 140 LYS cc_start: 0.9043 (tppt) cc_final: 0.8663 (tptp) REVERT: L 243 ASN cc_start: 0.8834 (t0) cc_final: 0.8514 (t0) REVERT: V 83 GLN cc_start: 0.6861 (mm110) cc_final: 0.6540 (mm-40) REVERT: V 94 ASP cc_start: 0.6951 (m-30) cc_final: 0.6263 (t0) REVERT: X 81 ASN cc_start: 0.8242 (p0) cc_final: 0.7946 (p0) REVERT: Y 67 CYS cc_start: 0.1986 (p) cc_final: 0.1314 (m) REVERT: Y 88 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7716 (ptp90) outliers start: 198 outliers final: 145 residues processed: 1143 average time/residue: 0.4142 time to fit residues: 771.8343 Evaluate side-chains 1103 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 946 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 355 ILE Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 145 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 409 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 HIS E 192 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS G 392 HIS G 396 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN H 256 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115695 restraints weight = 61632.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119106 restraints weight = 31888.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121325 restraints weight = 20078.959| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 33724 Z= 0.291 Angle : 0.733 13.025 45928 Z= 0.382 Chirality : 0.047 0.257 5088 Planarity : 0.005 0.053 5928 Dihedral : 6.019 84.341 4617 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.39 % Allowed : 21.60 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4240 helix: 1.26 (0.25), residues: 409 sheet: -0.83 (0.14), residues: 1174 loop : -0.52 (0.12), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 236 HIS 0.022 0.002 HIS G 125 PHE 0.027 0.002 PHE E 112 TYR 0.029 0.002 TYR H 99 ARG 0.011 0.001 ARG K 323 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1159) hydrogen bonds : angle 6.07413 ( 3129) SS BOND : bond 0.00441 ( 72) SS BOND : angle 1.51089 ( 144) covalent geometry : bond 0.00643 (33652) covalent geometry : angle 0.72913 (45784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 939 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9264 (tp) cc_final: 0.9041 (tp) REVERT: A 44 LYS cc_start: 0.9285 (mtpt) cc_final: 0.8891 (ttmm) REVERT: A 102 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 251 LEU cc_start: 0.9454 (tp) cc_final: 0.9112 (tp) REVERT: A 284 ASP cc_start: 0.8906 (p0) cc_final: 0.8641 (p0) REVERT: A 364 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8915 (m-40) REVERT: A 396 GLN cc_start: 0.8338 (pm20) cc_final: 0.7363 (pm20) REVERT: B 92 ARG cc_start: 0.2726 (mtt180) cc_final: 0.2097 (mmm160) REVERT: B 138 GLU cc_start: 0.7568 (tt0) cc_final: 0.7279 (tt0) REVERT: B 156 ASP cc_start: 0.8361 (t0) cc_final: 0.7730 (m-30) REVERT: B 161 THR cc_start: 0.8901 (p) cc_final: 0.8661 (p) REVERT: B 179 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6473 (t80) REVERT: B 342 GLU cc_start: 0.8580 (tp30) cc_final: 0.8266 (tp30) REVERT: B 351 TRP cc_start: 0.7124 (m100) cc_final: 0.6894 (m-90) REVERT: C 2 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 27 LEU cc_start: 0.8857 (mt) cc_final: 0.8635 (mp) REVERT: C 97 ASP cc_start: 0.7867 (m-30) cc_final: 0.7639 (m-30) REVERT: C 140 THR cc_start: 0.8854 (m) cc_final: 0.8564 (p) REVERT: C 204 GLN cc_start: 0.8718 (mt0) cc_final: 0.8457 (mt0) REVERT: C 212 ASP cc_start: 0.8576 (t0) cc_final: 0.8278 (t0) REVERT: C 218 ASP cc_start: 0.8793 (t70) cc_final: 0.8014 (t0) REVERT: C 321 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9143 (mmmt) REVERT: C 381 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8508 (mtmt) REVERT: C 396 GLN cc_start: 0.8088 (pp30) cc_final: 0.7479 (pp30) REVERT: D 29 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8503 (mm) REVERT: D 30 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8405 (tptp) REVERT: D 32 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7809 (mm-30) REVERT: D 46 GLN cc_start: 0.7839 (tt0) cc_final: 0.7281 (tt0) REVERT: D 55 GLN cc_start: 0.8798 (tt0) cc_final: 0.8357 (tp40) REVERT: D 137 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: D 176 TYR cc_start: 0.8044 (m-80) cc_final: 0.7262 (m-80) REVERT: D 200 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7723 (mp0) REVERT: D 211 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7397 (t) REVERT: D 217 MET cc_start: 0.6430 (tpp) cc_final: 0.5806 (mtt) REVERT: D 225 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6312 (tp-100) REVERT: D 238 PHE cc_start: 0.9434 (t80) cc_final: 0.9069 (t80) REVERT: D 259 PHE cc_start: 0.8932 (m-80) cc_final: 0.8627 (m-80) REVERT: D 321 VAL cc_start: 0.9194 (t) cc_final: 0.8865 (p) REVERT: D 339 TRP cc_start: 0.9096 (m-90) cc_final: 0.8712 (m-90) REVERT: D 357 ILE cc_start: 0.9026 (tt) cc_final: 0.8781 (tp) REVERT: D 393 ARG cc_start: 0.7429 (ttt180) cc_final: 0.6501 (tpt170) REVERT: E 110 LYS cc_start: 0.8827 (mttt) cc_final: 0.8549 (mmtt) REVERT: E 132 MET cc_start: 0.8700 (ptp) cc_final: 0.8137 (mpp) REVERT: E 152 LYS cc_start: 0.8818 (mttt) cc_final: 0.8559 (mtmt) REVERT: E 192 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: E 250 LYS cc_start: 0.8788 (tttp) cc_final: 0.8407 (tmtt) REVERT: E 253 PRO cc_start: 0.7899 (Cg_exo) cc_final: 0.7647 (Cg_endo) REVERT: F 115 MET cc_start: 0.8637 (mmm) cc_final: 0.8135 (mmp) REVERT: F 119 GLN cc_start: 0.8481 (pm20) cc_final: 0.8005 (pm20) REVERT: F 169 LYS cc_start: 0.2670 (pttp) cc_final: 0.2457 (pttp) REVERT: F 188 HIS cc_start: 0.9038 (m-70) cc_final: 0.8531 (m-70) REVERT: G 10 VAL cc_start: 0.9452 (p) cc_final: 0.9220 (m) REVERT: G 24 TYR cc_start: 0.8724 (m-80) cc_final: 0.8026 (m-80) REVERT: G 37 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7928 (mp0) REVERT: G 75 ASP cc_start: 0.8093 (t0) cc_final: 0.7617 (t0) REVERT: G 97 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: G 100 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: G 204 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8326 (mm-40) REVERT: G 218 ASP cc_start: 0.8593 (t0) cc_final: 0.7703 (t0) REVERT: G 253 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7195 (mt-10) REVERT: G 273 TYR cc_start: 0.8933 (p90) cc_final: 0.8598 (p90) REVERT: G 386 HIS cc_start: 0.7814 (m90) cc_final: 0.6672 (m170) REVERT: G 395 ASP cc_start: 0.8475 (t0) cc_final: 0.7896 (t0) REVERT: H 96 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7190 (p90) REVERT: H 130 ILE cc_start: 0.9156 (tp) cc_final: 0.8903 (pt) REVERT: H 137 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8028 (mtp85) REVERT: H 199 TYR cc_start: 0.8172 (p90) cc_final: 0.7889 (p90) REVERT: H 233 GLN cc_start: 0.8464 (pm20) cc_final: 0.7768 (tm-30) REVERT: H 272 HIS cc_start: 0.8174 (t70) cc_final: 0.7461 (t70) REVERT: H 273 THR cc_start: 0.9270 (m) cc_final: 0.8744 (p) REVERT: H 279 TRP cc_start: 0.9097 (p-90) cc_final: 0.8300 (p-90) REVERT: H 280 PHE cc_start: 0.7366 (m-80) cc_final: 0.6513 (m-80) REVERT: H 337 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8291 (mmt90) REVERT: H 343 SER cc_start: 0.9357 (t) cc_final: 0.8571 (t) REVERT: H 347 ASP cc_start: 0.9034 (t0) cc_final: 0.8515 (t0) REVERT: H 396 CYS cc_start: 0.9476 (t) cc_final: 0.9083 (m) REVERT: I 116 LEU cc_start: 0.9100 (tp) cc_final: 0.8882 (mt) REVERT: I 130 ARG cc_start: 0.7910 (mpp80) cc_final: 0.7516 (mtm-85) REVERT: I 132 MET cc_start: 0.8008 (mpp) cc_final: 0.7670 (mpp) REVERT: I 153 LYS cc_start: 0.8561 (mppt) cc_final: 0.8314 (mmtm) REVERT: I 220 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7776 (mtm-85) REVERT: J 2 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8252 (tm-30) REVERT: J 24 TYR cc_start: 0.8513 (m-80) cc_final: 0.8277 (m-80) REVERT: J 88 MET cc_start: 0.8248 (mtp) cc_final: 0.7750 (mtt) REVERT: J 145 ASP cc_start: 0.8273 (m-30) cc_final: 0.7506 (p0) REVERT: J 234 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8748 (m) REVERT: J 270 ASN cc_start: 0.9092 (m-40) cc_final: 0.8785 (m-40) REVERT: J 302 THR cc_start: 0.9255 (m) cc_final: 0.8905 (p) REVERT: J 381 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8736 (mttt) REVERT: K 44 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8615 (ttp-110) REVERT: K 71 HIS cc_start: 0.8352 (m-70) cc_final: 0.8065 (m-70) REVERT: K 73 HIS cc_start: 0.7902 (t70) cc_final: 0.7599 (t70) REVERT: K 80 MET cc_start: 0.8674 (mmp) cc_final: 0.8170 (mmt) REVERT: K 86 SER cc_start: 0.8179 (t) cc_final: 0.7913 (p) REVERT: K 97 LYS cc_start: 0.8988 (tptm) cc_final: 0.8657 (tttp) REVERT: K 148 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8489 (ttmm) REVERT: K 225 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8219 (tp-100) REVERT: K 232 ASP cc_start: 0.7742 (m-30) cc_final: 0.6716 (m-30) REVERT: K 321 VAL cc_start: 0.8918 (t) cc_final: 0.8700 (p) REVERT: K 330 TRP cc_start: 0.9356 (t-100) cc_final: 0.9038 (t-100) REVERT: K 334 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8104 (mm-30) REVERT: K 341 GLN cc_start: 0.9564 (mm-40) cc_final: 0.8550 (mm110) REVERT: L 115 MET cc_start: 0.8554 (mmm) cc_final: 0.8271 (mmm) REVERT: L 140 LYS cc_start: 0.9038 (tppt) cc_final: 0.8705 (tptp) REVERT: L 243 ASN cc_start: 0.8900 (t0) cc_final: 0.8570 (t0) REVERT: V 83 GLN cc_start: 0.6973 (mm110) cc_final: 0.6614 (mm-40) REVERT: V 94 ASP cc_start: 0.7126 (m-30) cc_final: 0.6302 (t0) REVERT: X 81 ASN cc_start: 0.8218 (p0) cc_final: 0.7952 (p0) REVERT: Y 67 CYS cc_start: 0.1699 (p) cc_final: 0.1183 (m) REVERT: Z 89 TRP cc_start: 0.4255 (m-10) cc_final: 0.3370 (m100) outliers start: 231 outliers final: 177 residues processed: 1068 average time/residue: 0.4213 time to fit residues: 736.7001 Evaluate side-chains 1081 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 890 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 407 TRP Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 355 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 216 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN K 33 ASN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** 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 = 0.3862 r_free = 0.3862 target = 0.156117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123289 restraints weight = 60704.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126823 restraints weight = 30768.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129131 restraints weight = 19119.053| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33724 Z= 0.176 Angle : 0.685 12.691 45928 Z= 0.355 Chirality : 0.046 0.301 5088 Planarity : 0.005 0.059 5928 Dihedral : 5.894 80.476 4615 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.56 % Allowed : 23.17 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4240 helix: 1.35 (0.25), residues: 409 sheet: -0.91 (0.14), residues: 1230 loop : -0.41 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 236 HIS 0.031 0.001 HIS G 125 PHE 0.030 0.002 PHE E 112 TYR 0.022 0.002 TYR H 99 ARG 0.020 0.001 ARG L 234 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1159) hydrogen bonds : angle 5.96134 ( 3129) SS BOND : bond 0.00431 ( 72) SS BOND : angle 1.31533 ( 144) covalent geometry : bond 0.00397 (33652) covalent geometry : angle 0.68260 (45784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 957 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9219 (tp) cc_final: 0.8989 (tp) REVERT: A 44 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8871 (ttmm) REVERT: A 77 THR cc_start: 0.8807 (p) cc_final: 0.8573 (p) REVERT: A 88 MET cc_start: 0.6514 (tpp) cc_final: 0.6062 (mmt) REVERT: A 102 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 251 LEU cc_start: 0.9445 (tp) cc_final: 0.9092 (tp) REVERT: A 284 ASP cc_start: 0.8843 (p0) cc_final: 0.8481 (p0) REVERT: A 396 GLN cc_start: 0.8115 (pm20) cc_final: 0.7309 (pm20) REVERT: B 12 TYR cc_start: 0.8444 (p90) cc_final: 0.8244 (p90) REVERT: B 37 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 50 GLN cc_start: 0.6861 (mp10) cc_final: 0.6579 (mp10) REVERT: B 92 ARG cc_start: 0.2341 (mtt180) cc_final: 0.2041 (mmm160) REVERT: B 138 GLU cc_start: 0.7418 (tt0) cc_final: 0.7144 (tt0) REVERT: B 156 ASP cc_start: 0.8251 (t0) cc_final: 0.7682 (m-30) REVERT: B 161 THR cc_start: 0.8848 (p) cc_final: 0.8613 (p) REVERT: B 179 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6545 (t80) REVERT: B 182 GLU cc_start: 0.7618 (pp20) cc_final: 0.7288 (pp20) REVERT: B 254 LYS cc_start: 0.4088 (OUTLIER) cc_final: 0.3794 (pptt) REVERT: B 311 ILE cc_start: 0.9730 (tp) cc_final: 0.9493 (tp) REVERT: B 327 GLU cc_start: 0.8576 (tt0) cc_final: 0.8361 (pt0) REVERT: B 342 GLU cc_start: 0.8528 (tp30) cc_final: 0.8316 (tp30) REVERT: B 351 TRP cc_start: 0.7110 (m100) cc_final: 0.6890 (m-90) REVERT: C 2 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: C 9 ASN cc_start: 0.9249 (t0) cc_final: 0.8922 (t0) REVERT: C 140 THR cc_start: 0.8776 (m) cc_final: 0.8537 (p) REVERT: C 157 ARG cc_start: 0.7633 (tpp-160) cc_final: 0.7319 (tpp-160) REVERT: C 212 ASP cc_start: 0.8481 (t0) cc_final: 0.8205 (t0) REVERT: C 218 ASP cc_start: 0.8760 (t70) cc_final: 0.8054 (t0) REVERT: C 257 PHE cc_start: 0.9371 (m-80) cc_final: 0.8735 (m-80) REVERT: C 366 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9196 (tp) REVERT: C 381 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8656 (mtmt) REVERT: C 396 GLN cc_start: 0.7948 (pp30) cc_final: 0.7398 (pp30) REVERT: D 32 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 46 GLN cc_start: 0.7756 (tt0) cc_final: 0.7302 (tt0) REVERT: D 55 GLN cc_start: 0.8700 (tt0) cc_final: 0.8278 (tp40) REVERT: D 137 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7972 (mtp180) REVERT: D 176 TYR cc_start: 0.8087 (m-80) cc_final: 0.7210 (m-80) REVERT: D 200 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7678 (mp0) REVERT: D 211 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7305 (t) REVERT: D 217 MET cc_start: 0.6597 (tpp) cc_final: 0.6029 (mtt) REVERT: D 225 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6272 (tp-100) REVERT: D 259 PHE cc_start: 0.8825 (m-80) cc_final: 0.8625 (m-80) REVERT: D 321 VAL cc_start: 0.9185 (t) cc_final: 0.8845 (p) REVERT: D 357 ILE cc_start: 0.9021 (tt) cc_final: 0.8771 (tp) REVERT: D 393 ARG cc_start: 0.7400 (ttt180) cc_final: 0.6367 (tpt170) REVERT: E 110 LYS cc_start: 0.8801 (mttt) cc_final: 0.8588 (mmtp) REVERT: E 132 MET cc_start: 0.8693 (ptp) cc_final: 0.8186 (mpp) REVERT: E 152 LYS cc_start: 0.8825 (mttt) cc_final: 0.8569 (mtmt) REVERT: E 192 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7820 (mp-120) REVERT: E 250 LYS cc_start: 0.8713 (tttp) cc_final: 0.8398 (tmtt) REVERT: E 253 PRO cc_start: 0.7932 (Cg_exo) cc_final: 0.7577 (Cg_endo) REVERT: F 115 MET cc_start: 0.8608 (mmm) cc_final: 0.8099 (mmp) REVERT: F 119 GLN cc_start: 0.8475 (pm20) cc_final: 0.7988 (pm20) REVERT: F 188 HIS cc_start: 0.9004 (m-70) cc_final: 0.8522 (m-70) REVERT: F 218 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8316 (mmm160) REVERT: G 10 VAL cc_start: 0.9422 (p) cc_final: 0.9212 (m) REVERT: G 24 TYR cc_start: 0.8618 (m-80) cc_final: 0.7884 (m-80) REVERT: G 37 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8012 (mp0) REVERT: G 75 ASP cc_start: 0.7969 (t0) cc_final: 0.7454 (t0) REVERT: G 97 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: G 100 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8400 (m-40) REVERT: G 159 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7651 (mm) REVERT: G 204 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: G 218 ASP cc_start: 0.8481 (t0) cc_final: 0.7615 (t0) REVERT: G 253 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6946 (mt-10) REVERT: G 273 TYR cc_start: 0.8899 (p90) cc_final: 0.8584 (p90) REVERT: G 386 HIS cc_start: 0.7748 (m90) cc_final: 0.6622 (m170) REVERT: G 395 ASP cc_start: 0.8422 (t0) cc_final: 0.7859 (t0) REVERT: H 44 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7718 (ptp90) REVERT: H 80 MET cc_start: 0.8111 (mmt) cc_final: 0.7551 (mmt) REVERT: H 94 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (tp) REVERT: H 96 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7272 (p-80) REVERT: H 130 ILE cc_start: 0.9161 (tp) cc_final: 0.8940 (pt) REVERT: H 137 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8037 (mtp85) REVERT: H 199 TYR cc_start: 0.8084 (p90) cc_final: 0.7808 (p90) REVERT: H 233 GLN cc_start: 0.8407 (pm20) cc_final: 0.7714 (tm-30) REVERT: H 272 HIS cc_start: 0.8200 (t70) cc_final: 0.7520 (t70) REVERT: H 279 TRP cc_start: 0.9131 (p-90) cc_final: 0.8335 (p-90) REVERT: H 280 PHE cc_start: 0.7310 (m-80) cc_final: 0.6421 (m-80) REVERT: H 337 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8307 (mmt90) REVERT: H 343 SER cc_start: 0.9363 (t) cc_final: 0.8587 (t) REVERT: H 396 CYS cc_start: 0.9431 (t) cc_final: 0.9024 (m) REVERT: I 130 ARG cc_start: 0.7739 (mpp80) cc_final: 0.7227 (mtm-85) REVERT: I 153 LYS cc_start: 0.8613 (mppt) cc_final: 0.8353 (mmtm) REVERT: I 195 ASN cc_start: 0.8593 (t0) cc_final: 0.8330 (t0) REVERT: J 2 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8207 (tm-30) REVERT: J 24 TYR cc_start: 0.8466 (m-80) cc_final: 0.8243 (m-80) REVERT: J 88 MET cc_start: 0.8018 (mtp) cc_final: 0.7413 (mtt) REVERT: J 145 ASP cc_start: 0.8206 (m-30) cc_final: 0.7434 (p0) REVERT: J 207 SER cc_start: 0.9500 (t) cc_final: 0.9201 (p) REVERT: J 241 GLU cc_start: 0.8461 (tt0) cc_final: 0.8028 (mt-10) REVERT: J 246 ASN cc_start: 0.8320 (m110) cc_final: 0.7836 (t0) REVERT: J 270 ASN cc_start: 0.8994 (m-40) cc_final: 0.8641 (m-40) REVERT: J 302 THR cc_start: 0.9273 (m) cc_final: 0.8943 (p) REVERT: J 352 ILE cc_start: 0.8724 (mm) cc_final: 0.8471 (mm) REVERT: K 44 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8572 (ttp-110) REVERT: K 69 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7673 (t80) REVERT: K 71 HIS cc_start: 0.8262 (m-70) cc_final: 0.7967 (m-70) REVERT: K 73 HIS cc_start: 0.7690 (t70) cc_final: 0.7437 (t-170) REVERT: K 75 ILE cc_start: 0.9010 (mt) cc_final: 0.8776 (mt) REVERT: K 80 MET cc_start: 0.8413 (mmp) cc_final: 0.7871 (mmt) REVERT: K 82 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7218 (ttpt) REVERT: K 86 SER cc_start: 0.8159 (t) cc_final: 0.7872 (p) REVERT: K 97 LYS cc_start: 0.8945 (tptm) cc_final: 0.8260 (tttt) REVERT: K 148 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8450 (ttmm) REVERT: K 217 MET cc_start: 0.8279 (tpp) cc_final: 0.7857 (mmt) REVERT: K 225 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8321 (tp-100) REVERT: K 232 ASP cc_start: 0.7317 (m-30) cc_final: 0.6594 (m-30) REVERT: K 330 TRP cc_start: 0.9290 (t-100) cc_final: 0.8976 (t-100) REVERT: K 334 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8003 (mm-30) REVERT: K 341 GLN cc_start: 0.9513 (mm-40) cc_final: 0.9292 (mm-40) REVERT: L 115 MET cc_start: 0.8544 (mmm) cc_final: 0.8267 (mmm) REVERT: L 140 LYS cc_start: 0.8983 (tppt) cc_final: 0.8707 (tptp) REVERT: L 243 ASN cc_start: 0.8842 (t0) cc_final: 0.8550 (t0) REVERT: V 83 GLN cc_start: 0.6915 (mm110) cc_final: 0.6555 (mm-40) REVERT: V 94 ASP cc_start: 0.7007 (m-30) cc_final: 0.6226 (t0) REVERT: X 81 ASN cc_start: 0.8115 (p0) cc_final: 0.7839 (p0) REVERT: Y 67 CYS cc_start: 0.1791 (p) cc_final: 0.1114 (m) REVERT: Z 69 LYS cc_start: 0.7842 (tptt) cc_final: 0.7015 (mptt) REVERT: Z 89 TRP cc_start: 0.4422 (m-10) cc_final: 0.3414 (m100) outliers start: 201 outliers final: 155 residues processed: 1068 average time/residue: 0.4125 time to fit residues: 721.4125 Evaluate side-chains 1098 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 925 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 355 ILE Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 40 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 181 optimal weight: 0.9990 chunk 387 optimal weight: 4.9990 chunk 263 optimal weight: 0.0270 chunk 290 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 388 optimal weight: 0.6980 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 100 ASN C 186 ASN C 204 GLN C 270 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127073 restraints weight = 60658.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130722 restraints weight = 30490.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133089 restraints weight = 18801.838| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33724 Z= 0.133 Angle : 0.691 11.928 45928 Z= 0.352 Chirality : 0.046 0.259 5088 Planarity : 0.005 0.056 5928 Dihedral : 5.771 79.063 4615 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.73 % Allowed : 23.98 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4240 helix: 1.42 (0.25), residues: 409 sheet: -0.83 (0.14), residues: 1230 loop : -0.37 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 236 HIS 0.013 0.001 HIS G 125 PHE 0.025 0.002 PHE H 238 TYR 0.018 0.001 TYR J 46 ARG 0.011 0.001 ARG L 234 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1159) hydrogen bonds : angle 5.85457 ( 3129) SS BOND : bond 0.00306 ( 72) SS BOND : angle 1.43587 ( 144) covalent geometry : bond 0.00304 (33652) covalent geometry : angle 0.68768 (45784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1026 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9140 (tp) cc_final: 0.8841 (tp) REVERT: A 44 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8845 (ttmm) REVERT: A 77 THR cc_start: 0.8706 (p) cc_final: 0.8343 (p) REVERT: A 102 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: A 251 LEU cc_start: 0.9405 (tp) cc_final: 0.9082 (tp) REVERT: A 284 ASP cc_start: 0.8788 (p0) cc_final: 0.8570 (p0) REVERT: A 396 GLN cc_start: 0.7974 (pm20) cc_final: 0.7188 (pm20) REVERT: B 37 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 50 GLN cc_start: 0.6747 (mp10) cc_final: 0.6375 (mp10) REVERT: B 80 MET cc_start: 0.8483 (tpp) cc_final: 0.7878 (mmt) REVERT: B 138 GLU cc_start: 0.7346 (tt0) cc_final: 0.7106 (tt0) REVERT: B 161 THR cc_start: 0.8823 (p) cc_final: 0.8606 (p) REVERT: B 179 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.6500 (t80) REVERT: B 254 LYS cc_start: 0.3842 (OUTLIER) cc_final: 0.3580 (pptt) REVERT: B 311 ILE cc_start: 0.9720 (tp) cc_final: 0.9469 (tp) REVERT: B 327 GLU cc_start: 0.8510 (tt0) cc_final: 0.8298 (pt0) REVERT: B 342 GLU cc_start: 0.8537 (tp30) cc_final: 0.8327 (tp30) REVERT: C 2 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: C 97 ASP cc_start: 0.7768 (m-30) cc_final: 0.7567 (m-30) REVERT: C 158 ASP cc_start: 0.9198 (m-30) cc_final: 0.8517 (m-30) REVERT: C 212 ASP cc_start: 0.8482 (t0) cc_final: 0.8213 (t0) REVERT: C 218 ASP cc_start: 0.8680 (t70) cc_final: 0.8042 (t0) REVERT: C 241 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8763 (mm-30) REVERT: C 257 PHE cc_start: 0.9357 (m-80) cc_final: 0.8710 (m-80) REVERT: C 321 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9194 (mmmt) REVERT: C 390 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 396 GLN cc_start: 0.7803 (pp30) cc_final: 0.7281 (pp30) REVERT: D 30 LYS cc_start: 0.8676 (tptp) cc_final: 0.8431 (tmtt) REVERT: D 55 GLN cc_start: 0.8732 (tt0) cc_final: 0.8250 (tp40) REVERT: D 137 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: D 176 TYR cc_start: 0.8042 (m-80) cc_final: 0.7341 (m-80) REVERT: D 200 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7699 (mp0) REVERT: D 211 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7117 (t) REVERT: D 217 MET cc_start: 0.6584 (tpp) cc_final: 0.6182 (mtt) REVERT: D 225 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6228 (tp-100) REVERT: D 259 PHE cc_start: 0.8719 (m-80) cc_final: 0.8447 (m-80) REVERT: D 321 VAL cc_start: 0.9175 (t) cc_final: 0.8873 (p) REVERT: D 393 ARG cc_start: 0.7326 (ttt180) cc_final: 0.6300 (tpt170) REVERT: E 110 LYS cc_start: 0.8715 (mttt) cc_final: 0.8482 (mmtp) REVERT: E 132 MET cc_start: 0.8703 (ptp) cc_final: 0.8249 (mpp) REVERT: E 152 LYS cc_start: 0.8824 (mttt) cc_final: 0.8579 (mtmt) REVERT: E 212 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7509 (mmt-90) REVERT: E 250 LYS cc_start: 0.8583 (tttp) cc_final: 0.8332 (tmtt) REVERT: F 115 MET cc_start: 0.8593 (mmm) cc_final: 0.8032 (mmp) REVERT: F 119 GLN cc_start: 0.8493 (pm20) cc_final: 0.7836 (pm20) REVERT: F 188 HIS cc_start: 0.9000 (m-70) cc_final: 0.8558 (m-70) REVERT: F 218 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8263 (mmm160) REVERT: G 10 VAL cc_start: 0.9330 (p) cc_final: 0.9100 (m) REVERT: G 24 TYR cc_start: 0.8456 (m-80) cc_final: 0.7808 (m-80) REVERT: G 30 GLU cc_start: 0.8075 (tt0) cc_final: 0.7737 (tt0) REVERT: G 37 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8009 (mp0) REVERT: G 75 ASP cc_start: 0.7885 (t0) cc_final: 0.7378 (t0) REVERT: G 97 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: G 100 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8538 (m-40) REVERT: G 130 LYS cc_start: 0.8391 (tppt) cc_final: 0.7672 (tppt) REVERT: G 218 ASP cc_start: 0.8398 (t0) cc_final: 0.7787 (t0) REVERT: G 253 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7039 (mt-10) REVERT: G 273 TYR cc_start: 0.8866 (p90) cc_final: 0.8634 (p90) REVERT: G 341 GLU cc_start: 0.8626 (mp0) cc_final: 0.8406 (mt-10) REVERT: G 386 HIS cc_start: 0.7743 (m90) cc_final: 0.6659 (m170) REVERT: H 42 SER cc_start: 0.9075 (m) cc_final: 0.8588 (p) REVERT: H 44 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7508 (ptp90) REVERT: H 80 MET cc_start: 0.7932 (mmt) cc_final: 0.7571 (tpp) REVERT: H 94 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8680 (tt) REVERT: H 137 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7983 (mtp85) REVERT: H 146 GLN cc_start: 0.7583 (pt0) cc_final: 0.6987 (pp30) REVERT: H 168 MET cc_start: 0.8118 (mpp) cc_final: 0.7540 (tpp) REVERT: H 199 TYR cc_start: 0.8023 (p90) cc_final: 0.7771 (p90) REVERT: H 233 GLN cc_start: 0.8364 (pm20) cc_final: 0.7693 (tm-30) REVERT: H 272 HIS cc_start: 0.8088 (t70) cc_final: 0.7446 (t70) REVERT: H 279 TRP cc_start: 0.9105 (p-90) cc_final: 0.8319 (p-90) REVERT: H 337 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8223 (mmt90) REVERT: H 343 SER cc_start: 0.9360 (t) cc_final: 0.8907 (t) REVERT: H 396 CYS cc_start: 0.9404 (t) cc_final: 0.8883 (m) REVERT: I 116 LEU cc_start: 0.8945 (mt) cc_final: 0.8708 (mt) REVERT: I 132 MET cc_start: 0.7910 (mpp) cc_final: 0.7568 (mpp) REVERT: I 134 PRO cc_start: 0.9014 (Cg_exo) cc_final: 0.8809 (Cg_endo) REVERT: I 153 LYS cc_start: 0.8623 (mppt) cc_final: 0.8371 (mmtm) REVERT: J 2 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8236 (tm-30) REVERT: J 88 MET cc_start: 0.7730 (mtp) cc_final: 0.7335 (mtt) REVERT: J 139 ASN cc_start: 0.8138 (t0) cc_final: 0.7633 (m110) REVERT: J 145 ASP cc_start: 0.8228 (m-30) cc_final: 0.7391 (p0) REVERT: J 207 SER cc_start: 0.9499 (t) cc_final: 0.9202 (p) REVERT: J 241 GLU cc_start: 0.8432 (tt0) cc_final: 0.8062 (mt-10) REVERT: J 246 ASN cc_start: 0.8294 (m110) cc_final: 0.7808 (t0) REVERT: J 352 ILE cc_start: 0.8689 (mm) cc_final: 0.8454 (mm) REVERT: J 410 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8994 (tm) REVERT: K 44 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8332 (ttp-110) REVERT: K 69 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7556 (t80) REVERT: K 71 HIS cc_start: 0.8211 (m-70) cc_final: 0.7935 (m-70) REVERT: K 80 MET cc_start: 0.8337 (mmp) cc_final: 0.7985 (mmt) REVERT: K 86 SER cc_start: 0.8066 (t) cc_final: 0.7795 (p) REVERT: K 97 LYS cc_start: 0.8821 (tptm) cc_final: 0.8089 (tttt) REVERT: K 148 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8274 (ttmm) REVERT: K 168 MET cc_start: 0.9018 (mmt) cc_final: 0.8532 (mmt) REVERT: K 176 TYR cc_start: 0.8530 (m-10) cc_final: 0.8246 (m-80) REVERT: K 217 MET cc_start: 0.8143 (tpp) cc_final: 0.7846 (mmt) REVERT: K 225 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8314 (tp-100) REVERT: K 254 LYS cc_start: 0.8946 (mtpt) cc_final: 0.7977 (pttm) REVERT: K 279 TRP cc_start: 0.9409 (p-90) cc_final: 0.8662 (p-90) REVERT: K 280 PHE cc_start: 0.8607 (t80) cc_final: 0.8286 (t80) REVERT: K 284 THR cc_start: 0.9485 (m) cc_final: 0.9069 (p) REVERT: K 321 VAL cc_start: 0.8811 (t) cc_final: 0.8533 (p) REVERT: K 334 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7900 (mm-30) REVERT: K 362 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8253 (mmm-85) REVERT: L 115 MET cc_start: 0.8566 (mmm) cc_final: 0.8247 (mmm) REVERT: L 140 LYS cc_start: 0.9018 (tppt) cc_final: 0.8712 (tptp) REVERT: L 192 GLN cc_start: 0.7222 (tm-30) cc_final: 0.7011 (tm-30) REVERT: L 243 ASN cc_start: 0.8805 (t0) cc_final: 0.8520 (t0) REVERT: V 83 GLN cc_start: 0.6858 (mm110) cc_final: 0.6505 (mm-40) REVERT: V 94 ASP cc_start: 0.6919 (m-30) cc_final: 0.6239 (t0) REVERT: X 81 ASN cc_start: 0.7985 (p0) cc_final: 0.7692 (p0) REVERT: Y 67 CYS cc_start: 0.2177 (p) cc_final: 0.1335 (m) REVERT: Z 69 LYS cc_start: 0.7779 (tptt) cc_final: 0.7145 (mptt) REVERT: Z 89 TRP cc_start: 0.4317 (m-10) cc_final: 0.3287 (m100) outliers start: 171 outliers final: 131 residues processed: 1113 average time/residue: 0.4230 time to fit residues: 770.4435 Evaluate side-chains 1074 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 929 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 325 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 141 optimal weight: 0.0070 chunk 177 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 408 optimal weight: 0.9990 chunk 360 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 100 ASN G 186 ASN G 345 HIS H 96 HIS ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN J 364 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.160545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127963 restraints weight = 60398.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131582 restraints weight = 30455.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133943 restraints weight = 18829.269| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33724 Z= 0.140 Angle : 0.698 11.452 45928 Z= 0.357 Chirality : 0.046 0.252 5088 Planarity : 0.005 0.059 5928 Dihedral : 5.689 78.786 4615 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.42 % Allowed : 25.50 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4240 helix: 1.43 (0.25), residues: 409 sheet: -0.79 (0.14), residues: 1241 loop : -0.36 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP K 330 HIS 0.015 0.001 HIS H 349 PHE 0.029 0.002 PHE K 259 TYR 0.040 0.002 TYR C 320 ARG 0.016 0.001 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1159) hydrogen bonds : angle 5.79190 ( 3129) SS BOND : bond 0.00341 ( 72) SS BOND : angle 1.29818 ( 144) covalent geometry : bond 0.00323 (33652) covalent geometry : angle 0.69498 (45784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 969 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9097 (tp) cc_final: 0.8803 (tp) REVERT: A 44 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8843 (ttmm) REVERT: A 45 GLU cc_start: 0.8949 (tp30) cc_final: 0.8617 (tt0) REVERT: A 77 THR cc_start: 0.8712 (p) cc_final: 0.8439 (p) REVERT: A 102 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: A 251 LEU cc_start: 0.9395 (tp) cc_final: 0.9057 (tp) REVERT: A 264 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 284 ASP cc_start: 0.8867 (p0) cc_final: 0.8657 (p0) REVERT: A 396 GLN cc_start: 0.7917 (pm20) cc_final: 0.7185 (pm20) REVERT: B 12 TYR cc_start: 0.8367 (p90) cc_final: 0.8119 (p90) REVERT: B 37 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 50 GLN cc_start: 0.6697 (mp10) cc_final: 0.6272 (mp10) REVERT: B 138 GLU cc_start: 0.7308 (tt0) cc_final: 0.7070 (tt0) REVERT: B 156 ASP cc_start: 0.7743 (t0) cc_final: 0.7464 (m-30) REVERT: B 161 THR cc_start: 0.8820 (p) cc_final: 0.8595 (p) REVERT: B 179 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6464 (t80) REVERT: B 311 ILE cc_start: 0.9724 (tp) cc_final: 0.9524 (tp) REVERT: B 327 GLU cc_start: 0.8461 (tt0) cc_final: 0.8257 (pt0) REVERT: B 341 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9052 (mm-40) REVERT: B 342 GLU cc_start: 0.8422 (tp30) cc_final: 0.8203 (tp30) REVERT: C 9 ASN cc_start: 0.9230 (t0) cc_final: 0.8959 (t0) REVERT: C 157 ARG cc_start: 0.7225 (tpp-160) cc_final: 0.6845 (tpp-160) REVERT: C 158 ASP cc_start: 0.8983 (m-30) cc_final: 0.8677 (m-30) REVERT: C 212 ASP cc_start: 0.8453 (t0) cc_final: 0.8178 (t0) REVERT: C 218 ASP cc_start: 0.8713 (t70) cc_final: 0.8101 (t0) REVERT: C 257 PHE cc_start: 0.9353 (m-80) cc_final: 0.8721 (m-80) REVERT: C 325 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: C 390 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 396 GLN cc_start: 0.7810 (pp30) cc_final: 0.7273 (pp30) REVERT: D 30 LYS cc_start: 0.8604 (tptp) cc_final: 0.8166 (tmtt) REVERT: D 55 GLN cc_start: 0.8723 (tt0) cc_final: 0.8252 (tp40) REVERT: D 137 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: D 176 TYR cc_start: 0.8050 (m-80) cc_final: 0.7322 (m-80) REVERT: D 200 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7705 (mp0) REVERT: D 211 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7099 (t) REVERT: D 225 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6833 (tp40) REVERT: D 259 PHE cc_start: 0.8706 (m-80) cc_final: 0.8403 (m-80) REVERT: D 321 VAL cc_start: 0.9188 (t) cc_final: 0.8878 (p) REVERT: D 393 ARG cc_start: 0.7345 (ttt180) cc_final: 0.6368 (tpt170) REVERT: E 110 LYS cc_start: 0.8729 (mttt) cc_final: 0.8467 (mttp) REVERT: E 115 MET cc_start: 0.7808 (tpp) cc_final: 0.7448 (tpp) REVERT: E 119 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8420 (tp-100) REVERT: E 132 MET cc_start: 0.8682 (ptp) cc_final: 0.8275 (mpp) REVERT: E 152 LYS cc_start: 0.8821 (mttt) cc_final: 0.8371 (mtmt) REVERT: E 250 LYS cc_start: 0.8609 (tttp) cc_final: 0.8374 (tmtt) REVERT: F 115 MET cc_start: 0.8595 (mmm) cc_final: 0.8026 (mmp) REVERT: F 119 GLN cc_start: 0.8537 (pm20) cc_final: 0.7999 (pm20) REVERT: F 188 HIS cc_start: 0.8970 (m-70) cc_final: 0.8524 (m-70) REVERT: F 218 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8236 (mmm160) REVERT: G 10 VAL cc_start: 0.9355 (p) cc_final: 0.9120 (m) REVERT: G 24 TYR cc_start: 0.8338 (m-80) cc_final: 0.7811 (m-80) REVERT: G 37 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8058 (mp0) REVERT: G 75 ASP cc_start: 0.7863 (t0) cc_final: 0.7428 (t0) REVERT: G 100 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8431 (m110) REVERT: G 113 ASP cc_start: 0.7995 (m-30) cc_final: 0.7270 (m-30) REVERT: G 130 LYS cc_start: 0.8393 (tppt) cc_final: 0.7689 (tppt) REVERT: G 202 ASP cc_start: 0.9070 (p0) cc_final: 0.8553 (p0) REVERT: G 218 ASP cc_start: 0.8361 (t0) cc_final: 0.7497 (t0) REVERT: G 253 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7108 (mt-10) REVERT: G 261 ILE cc_start: 0.8766 (mp) cc_final: 0.8390 (mm) REVERT: G 273 TYR cc_start: 0.8867 (p90) cc_final: 0.8658 (p90) REVERT: G 386 HIS cc_start: 0.7749 (m90) cc_final: 0.6768 (m170) REVERT: G 395 ASP cc_start: 0.8233 (t0) cc_final: 0.7472 (t0) REVERT: H 42 SER cc_start: 0.9069 (m) cc_final: 0.8616 (p) REVERT: H 44 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7329 (ptp90) REVERT: H 67 MET cc_start: 0.7624 (tpp) cc_final: 0.7150 (tpp) REVERT: H 80 MET cc_start: 0.8004 (mmt) cc_final: 0.7764 (tpp) REVERT: H 94 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8560 (tt) REVERT: H 137 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7955 (mtp180) REVERT: H 168 MET cc_start: 0.8103 (mpp) cc_final: 0.7358 (tpp) REVERT: H 233 GLN cc_start: 0.8413 (pm20) cc_final: 0.7687 (tm-30) REVERT: H 272 HIS cc_start: 0.8158 (t70) cc_final: 0.7454 (t70) REVERT: H 279 TRP cc_start: 0.9083 (p-90) cc_final: 0.8293 (p-90) REVERT: H 334 GLU cc_start: 0.8320 (mp0) cc_final: 0.8120 (mm-30) REVERT: H 337 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8216 (mmt90) REVERT: H 396 CYS cc_start: 0.9396 (t) cc_final: 0.8876 (m) REVERT: I 116 LEU cc_start: 0.8974 (mt) cc_final: 0.8677 (mt) REVERT: I 130 ARG cc_start: 0.8170 (mpp80) cc_final: 0.7805 (mtm-85) REVERT: I 153 LYS cc_start: 0.8654 (mppt) cc_final: 0.8399 (mmtm) REVERT: J 2 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8190 (tm-30) REVERT: J 88 MET cc_start: 0.7611 (mtp) cc_final: 0.7069 (mtt) REVERT: J 139 ASN cc_start: 0.8049 (t0) cc_final: 0.7579 (m110) REVERT: J 145 ASP cc_start: 0.8181 (m-30) cc_final: 0.7414 (p0) REVERT: J 204 GLN cc_start: 0.9092 (mt0) cc_final: 0.8578 (mt0) REVERT: J 207 SER cc_start: 0.9504 (t) cc_final: 0.9185 (p) REVERT: J 241 GLU cc_start: 0.8408 (tt0) cc_final: 0.8038 (mt-10) REVERT: J 246 ASN cc_start: 0.8306 (m110) cc_final: 0.7811 (t0) REVERT: J 352 ILE cc_start: 0.8721 (mm) cc_final: 0.8452 (mm) REVERT: J 410 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8988 (tm) REVERT: K 69 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7550 (t80) REVERT: K 71 HIS cc_start: 0.8198 (m-70) cc_final: 0.7918 (m-70) REVERT: K 80 MET cc_start: 0.8398 (mmp) cc_final: 0.8148 (mmt) REVERT: K 86 SER cc_start: 0.8096 (t) cc_final: 0.7865 (p) REVERT: K 97 LYS cc_start: 0.8840 (tptm) cc_final: 0.8155 (tttt) REVERT: K 132 ARG cc_start: 0.7645 (tmm160) cc_final: 0.7335 (tmm160) REVERT: K 146 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8801 (tp-100) REVERT: K 148 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8201 (ttmm) REVERT: K 176 TYR cc_start: 0.8512 (m-10) cc_final: 0.8103 (m-80) REVERT: K 217 MET cc_start: 0.8100 (tpp) cc_final: 0.7862 (mmt) REVERT: K 225 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8290 (tp-100) REVERT: K 254 LYS cc_start: 0.8787 (mtpt) cc_final: 0.7908 (pttm) REVERT: K 279 TRP cc_start: 0.9406 (p-90) cc_final: 0.8680 (p-90) REVERT: K 280 PHE cc_start: 0.8627 (t80) cc_final: 0.8268 (t80) REVERT: K 284 THR cc_start: 0.9510 (m) cc_final: 0.9044 (p) REVERT: K 321 VAL cc_start: 0.8849 (t) cc_final: 0.8581 (p) REVERT: K 334 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7912 (mm-30) REVERT: K 342 GLU cc_start: 0.8799 (tp30) cc_final: 0.8509 (tp30) REVERT: L 115 MET cc_start: 0.8573 (mmm) cc_final: 0.8249 (mmm) REVERT: L 140 LYS cc_start: 0.9037 (tppt) cc_final: 0.8730 (tptp) REVERT: L 243 ASN cc_start: 0.8734 (t0) cc_final: 0.8449 (t0) REVERT: V 83 GLN cc_start: 0.6982 (mm110) cc_final: 0.6630 (mm-40) REVERT: V 94 ASP cc_start: 0.6908 (m-30) cc_final: 0.6221 (t0) REVERT: X 81 ASN cc_start: 0.7991 (p0) cc_final: 0.7734 (p0) REVERT: Y 67 CYS cc_start: 0.2075 (p) cc_final: 0.1252 (m) REVERT: Z 69 LYS cc_start: 0.7815 (tptt) cc_final: 0.7208 (mptt) REVERT: Z 89 TRP cc_start: 0.4334 (m-10) cc_final: 0.3187 (m100) outliers start: 160 outliers final: 129 residues processed: 1052 average time/residue: 0.4056 time to fit residues: 700.1441 Evaluate side-chains 1090 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 950 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 359 SER Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 96 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 338 optimal weight: 0.8980 chunk 351 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 186 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 186 ASN G 345 HIS ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124502 restraints weight = 60798.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128026 restraints weight = 30916.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130330 restraints weight = 19138.767| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33724 Z= 0.222 Angle : 0.724 10.617 45928 Z= 0.373 Chirality : 0.047 0.258 5088 Planarity : 0.005 0.062 5928 Dihedral : 5.774 76.478 4615 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.12 % Allowed : 25.94 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4240 helix: 1.45 (0.25), residues: 406 sheet: -0.83 (0.14), residues: 1247 loop : -0.40 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 330 HIS 0.015 0.001 HIS H 349 PHE 0.025 0.002 PHE H 238 TYR 0.041 0.002 TYR C 320 ARG 0.010 0.001 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1159) hydrogen bonds : angle 5.83935 ( 3129) SS BOND : bond 0.00369 ( 72) SS BOND : angle 1.33135 ( 144) covalent geometry : bond 0.00503 (33652) covalent geometry : angle 0.72113 (45784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 919 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8459 (ttm170) REVERT: A 29 LEU cc_start: 0.9110 (tp) cc_final: 0.8893 (tp) REVERT: A 44 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8899 (ttmm) REVERT: A 45 GLU cc_start: 0.9022 (tp30) cc_final: 0.8698 (tt0) REVERT: A 77 THR cc_start: 0.8804 (p) cc_final: 0.8532 (p) REVERT: A 251 LEU cc_start: 0.9401 (tp) cc_final: 0.9101 (tp) REVERT: A 264 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 284 ASP cc_start: 0.8930 (p0) cc_final: 0.8673 (p0) REVERT: A 396 GLN cc_start: 0.8016 (pm20) cc_final: 0.7181 (pm20) REVERT: B 37 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 50 GLN cc_start: 0.6809 (mp10) cc_final: 0.6417 (mp10) REVERT: B 80 MET cc_start: 0.8490 (tpp) cc_final: 0.7849 (mmt) REVERT: B 138 GLU cc_start: 0.7377 (tt0) cc_final: 0.7095 (tt0) REVERT: B 156 ASP cc_start: 0.7796 (t0) cc_final: 0.7491 (m-30) REVERT: B 161 THR cc_start: 0.8857 (p) cc_final: 0.8635 (p) REVERT: B 179 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.6500 (t80) REVERT: B 311 ILE cc_start: 0.9751 (tp) cc_final: 0.9537 (tp) REVERT: B 327 GLU cc_start: 0.8532 (tt0) cc_final: 0.8317 (pt0) REVERT: B 341 GLN cc_start: 0.9310 (mm-40) cc_final: 0.9032 (mm-40) REVERT: B 342 GLU cc_start: 0.8427 (tp30) cc_final: 0.8154 (tp30) REVERT: C 212 ASP cc_start: 0.8502 (t0) cc_final: 0.8222 (t0) REVERT: C 218 ASP cc_start: 0.8731 (t70) cc_final: 0.7977 (t0) REVERT: C 257 PHE cc_start: 0.9381 (m-80) cc_final: 0.8753 (m-80) REVERT: C 325 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 390 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7747 (tm-30) REVERT: C 396 GLN cc_start: 0.7782 (pp30) cc_final: 0.7243 (pp30) REVERT: D 30 LYS cc_start: 0.8722 (tptp) cc_final: 0.8285 (tmtt) REVERT: D 55 GLN cc_start: 0.8757 (tt0) cc_final: 0.8259 (tp40) REVERT: D 137 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7843 (mtp180) REVERT: D 176 TYR cc_start: 0.8102 (m-80) cc_final: 0.7388 (m-80) REVERT: D 200 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7682 (mp0) REVERT: D 211 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7219 (t) REVERT: D 225 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6349 (tp40) REVERT: D 259 PHE cc_start: 0.8795 (m-80) cc_final: 0.8522 (m-80) REVERT: D 321 VAL cc_start: 0.9218 (t) cc_final: 0.8895 (p) REVERT: D 393 ARG cc_start: 0.7399 (ttt180) cc_final: 0.6416 (tpt170) REVERT: E 110 LYS cc_start: 0.8711 (mttt) cc_final: 0.8462 (mttp) REVERT: E 119 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8404 (tp-100) REVERT: E 132 MET cc_start: 0.8691 (ptp) cc_final: 0.8178 (mpp) REVERT: E 152 LYS cc_start: 0.8818 (mttt) cc_final: 0.8369 (mtmt) REVERT: E 250 LYS cc_start: 0.8680 (tttp) cc_final: 0.8368 (tmtt) REVERT: F 115 MET cc_start: 0.8641 (mmm) cc_final: 0.8107 (mmp) REVERT: F 119 GLN cc_start: 0.8480 (pm20) cc_final: 0.8049 (pm20) REVERT: F 188 HIS cc_start: 0.9055 (m-70) cc_final: 0.8509 (m-70) REVERT: F 218 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8305 (mmm160) REVERT: G 10 VAL cc_start: 0.9462 (p) cc_final: 0.9224 (m) REVERT: G 24 TYR cc_start: 0.8419 (m-80) cc_final: 0.7968 (m-80) REVERT: G 37 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8100 (mp0) REVERT: G 75 ASP cc_start: 0.7949 (t0) cc_final: 0.7552 (t0) REVERT: G 100 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8643 (m110) REVERT: G 113 ASP cc_start: 0.8110 (m-30) cc_final: 0.7539 (m-30) REVERT: G 130 LYS cc_start: 0.8479 (tppt) cc_final: 0.7790 (tppt) REVERT: G 202 ASP cc_start: 0.9063 (p0) cc_final: 0.8578 (p0) REVERT: G 218 ASP cc_start: 0.8462 (t0) cc_final: 0.7597 (t0) REVERT: G 253 GLU cc_start: 0.7775 (mt-10) cc_final: 0.6879 (mt-10) REVERT: G 273 TYR cc_start: 0.8911 (p90) cc_final: 0.8687 (p90) REVERT: G 298 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8418 (tm-30) REVERT: G 386 HIS cc_start: 0.7750 (m90) cc_final: 0.6735 (m170) REVERT: G 395 ASP cc_start: 0.8225 (t0) cc_final: 0.7478 (t0) REVERT: H 42 SER cc_start: 0.9087 (m) cc_final: 0.8880 (m) REVERT: H 44 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7257 (ptp90) REVERT: H 67 MET cc_start: 0.7738 (tpp) cc_final: 0.7201 (tpp) REVERT: H 80 MET cc_start: 0.8143 (mmt) cc_final: 0.7911 (tpp) REVERT: H 94 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8672 (tt) REVERT: H 137 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8007 (mtp85) REVERT: H 146 GLN cc_start: 0.7890 (pt0) cc_final: 0.6997 (tm-30) REVERT: H 233 GLN cc_start: 0.8446 (pm20) cc_final: 0.7737 (tm-30) REVERT: H 272 HIS cc_start: 0.8234 (t70) cc_final: 0.7476 (t70) REVERT: H 279 TRP cc_start: 0.9105 (p-90) cc_final: 0.8328 (p-90) REVERT: H 337 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8282 (mmt90) REVERT: H 396 CYS cc_start: 0.9395 (t) cc_final: 0.8882 (m) REVERT: I 116 LEU cc_start: 0.8940 (mt) cc_final: 0.8651 (mt) REVERT: I 130 ARG cc_start: 0.8170 (mpp80) cc_final: 0.7820 (mtm-85) REVERT: I 153 LYS cc_start: 0.8623 (mppt) cc_final: 0.8334 (mmtm) REVERT: I 169 LYS cc_start: 0.7237 (pttm) cc_final: 0.6537 (pttm) REVERT: J 2 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8185 (tm-30) REVERT: J 88 MET cc_start: 0.7828 (mtp) cc_final: 0.7319 (mtt) REVERT: J 145 ASP cc_start: 0.8188 (m-30) cc_final: 0.7506 (p0) REVERT: J 207 SER cc_start: 0.9503 (t) cc_final: 0.9190 (p) REVERT: J 241 GLU cc_start: 0.8505 (tt0) cc_final: 0.8212 (mt-10) REVERT: J 246 ASN cc_start: 0.8314 (m110) cc_final: 0.7830 (t0) REVERT: J 302 THR cc_start: 0.9317 (m) cc_final: 0.8926 (p) REVERT: J 352 ILE cc_start: 0.8741 (mm) cc_final: 0.8505 (mm) REVERT: J 410 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9017 (tm) REVERT: K 69 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7726 (t80) REVERT: K 71 HIS cc_start: 0.8261 (m-70) cc_final: 0.8021 (m-70) REVERT: K 80 MET cc_start: 0.8307 (mmp) cc_final: 0.7883 (mmt) REVERT: K 86 SER cc_start: 0.8102 (t) cc_final: 0.7857 (p) REVERT: K 97 LYS cc_start: 0.8995 (tptm) cc_final: 0.8346 (tttp) REVERT: K 148 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8435 (ttmm) REVERT: K 176 TYR cc_start: 0.8517 (m-10) cc_final: 0.8138 (m-80) REVERT: K 217 MET cc_start: 0.8087 (tpp) cc_final: 0.7862 (mmt) REVERT: K 225 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8258 (tp-100) REVERT: K 284 THR cc_start: 0.9495 (m) cc_final: 0.9007 (p) REVERT: K 334 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8014 (mm-30) REVERT: L 115 MET cc_start: 0.8574 (mmm) cc_final: 0.8244 (mmm) REVERT: L 140 LYS cc_start: 0.8989 (tppt) cc_final: 0.8699 (tptp) REVERT: L 243 ASN cc_start: 0.8820 (t0) cc_final: 0.8524 (t0) REVERT: V 83 GLN cc_start: 0.6977 (mm110) cc_final: 0.6610 (mm-40) REVERT: V 94 ASP cc_start: 0.7059 (m-30) cc_final: 0.6210 (t0) REVERT: X 81 ASN cc_start: 0.7977 (p0) cc_final: 0.7754 (p0) REVERT: Y 67 CYS cc_start: 0.2203 (p) cc_final: 0.1375 (m) REVERT: Z 69 LYS cc_start: 0.7904 (tptt) cc_final: 0.7304 (mptt) REVERT: Z 89 TRP cc_start: 0.4451 (m-10) cc_final: 0.3291 (m100) outliers start: 149 outliers final: 131 residues processed: 1001 average time/residue: 0.4141 time to fit residues: 679.0051 Evaluate side-chains 1032 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 891 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain J residue 315 SER Chi-restraints excluded: chain J residue 328 CYS Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 359 SER Chi-restraints excluded: chain J residue 395 ASP Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 174 GLN Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 72 CYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 184 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 407 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 186 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 186 ASN G 345 HIS H 96 HIS ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125240 restraints weight = 60343.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128760 restraints weight = 30643.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131078 restraints weight = 19043.841| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33724 Z= 0.197 Angle : 0.726 12.817 45928 Z= 0.373 Chirality : 0.046 0.220 5088 Planarity : 0.005 0.058 5928 Dihedral : 5.794 75.264 4615 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.26 % Allowed : 26.13 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4240 helix: 1.44 (0.25), residues: 406 sheet: -0.83 (0.14), residues: 1245 loop : -0.41 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 330 HIS 0.013 0.001 HIS H 349 PHE 0.031 0.002 PHE K 259 TYR 0.041 0.002 TYR C 320 ARG 0.010 0.001 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1159) hydrogen bonds : angle 5.84746 ( 3129) SS BOND : bond 0.00343 ( 72) SS BOND : angle 1.34399 ( 144) covalent geometry : bond 0.00449 (33652) covalent geometry : angle 0.72327 (45784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14792.55 seconds wall clock time: 258 minutes 9.45 seconds (15489.45 seconds total)