Starting phenix.real_space_refine on Fri May 30 02:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9z_47822/05_2025/9e9z_47822.cif" } resolution = 3.95 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= 0.071 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 224 5.16 5 C 20692 2.51 5 N 5676 2.21 5 O 6232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32832 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3121 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 26, 'TRANS': 371} Chain: "C" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3121 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: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "H" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3121 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: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "K" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3121 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: "W" 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: "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: "W" 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} Time building chain proxies: 18.71, per 1000 atoms: 0.57 Number of scatterers: 32832 At special positions: 0 Unit cell: (175.122, 174.041, 190.256, 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 224 16.00 O 6232 8.00 N 5676 7.00 C 20692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=73, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.04 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.02 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.04 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.02 Simple disulfide: pdb=" SG CYS V 33 " - pdb=" SG CYS V 45 " distance=2.02 Simple disulfide: pdb=" SG CYS V 40 " - pdb=" SG CYS V 58 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS V 91 " - pdb=" SG CYS V 108 " distance=2.02 Simple disulfide: pdb=" SG CYS W 33 " - pdb=" SG CYS W 45 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 58 " distance=2.03 Simple disulfide: pdb=" SG CYS W 52 " - pdb=" SG CYS W 67 " distance=2.04 Simple disulfide: pdb=" SG CYS W 72 " - pdb=" SG CYS W 84 " distance=2.03 Simple disulfide: pdb=" SG CYS W 79 " - pdb=" SG CYS W 97 " distance=2.02 Simple disulfide: pdb=" SG CYS W 91 " - pdb=" SG CYS W 108 " distance=2.03 Simple disulfide: pdb=" SG CYS X 33 " - pdb=" SG CYS X 45 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 67 " distance=2.04 Simple disulfide: pdb=" SG CYS X 72 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 79 " - pdb=" SG CYS X 97 " distance=2.02 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 108 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 33 " - pdb=" SG CYS Y 45 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 40 " - pdb=" SG CYS Y 58 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 52 " - pdb=" SG CYS Y 67 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 72 " - pdb=" SG CYS Y 84 " distance=2.04 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 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: 8.77 Conformation dependent library (CDL) restraints added in 4.4 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: 75 helices and 96 sheets defined 15.6% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 113 through 118 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 removed outlier: 3.839A pdb=" N SER A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 182 through 186 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 232 through 235 removed outlier: 3.690A pdb=" N LYS B 235 " --> pdb=" O ASP B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 363 through 391 removed outlier: 3.535A pdb=" N ILE B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 402 removed outlier: 4.042A pdb=" N THR B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Proline residue: B 399 - end of helix Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.683A pdb=" N VAL C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 438 removed outlier: 3.931A pdb=" N MET C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 191 through 195 removed outlier: 4.237A 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 Processing helix chain 'D' and resid 363 through 402 Proline residue: D 399 - end of helix Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.814A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 172 removed outlier: 3.593A pdb=" N THR E 172 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 4.180A pdb=" N LYS F 110 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 154 through 157 Processing helix chain 'F' and resid 165 through 172 removed outlier: 5.677A pdb=" N SER F 170 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR F 172 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 289 through 293 Processing helix chain 'G' and resid 403 through 438 removed outlier: 4.130A pdb=" N TRP G 409 " --> pdb=" O THR G 405 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN G 436 " --> pdb=" O SER G 432 " (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: 3.755A 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 Processing helix chain 'H' and resid 363 through 403 Proline residue: H 399 - end of helix Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 165 through 171 removed outlier: 4.122A pdb=" N SER I 170 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 238 through 247 Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.881A pdb=" N GLY J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 287 Processing helix chain 'J' and resid 289 through 293 Processing helix chain 'J' and resid 397 through 402 removed outlier: 3.905A pdb=" N VAL J 402 " --> pdb=" O PHE J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 417 removed outlier: 4.471A pdb=" N TRP J 409 " --> pdb=" O THR J 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU J 410 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY J 415 " --> pdb=" O LEU J 411 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY J 416 " --> pdb=" O ALA J 412 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 417 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 439 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: 3.603A 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: 4.086A pdb=" N ILE K 357 " --> pdb=" O HIS K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 391 Processing helix chain 'K' and resid 391 through 402 Proline residue: K 399 - end of helix removed outlier: 3.892A pdb=" N LEU K 402 " --> pdb=" O THR K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 removed outlier: 4.299A pdb=" N ALA K 406 " --> pdb=" O ALA K 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 149 Processing helix chain 'L' and resid 165 through 170 removed outlier: 4.437A pdb=" N SER L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 51 Processing helix chain 'V' and resid 100 through 104 Processing helix chain 'W' and resid 47 through 52 removed outlier: 3.810A pdb=" N LYS W 51 " --> pdb=" O THR W 47 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS W 52 " --> pdb=" O LEU W 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 47 through 52' Processing helix chain 'W' and resid 61 through 65 Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'W' and resid 100 through 104 Processing helix chain 'X' and resid 47 through 51 Processing helix chain 'X' and resid 61 through 65 Processing helix chain 'X' and resid 86 through 90 removed outlier: 4.348A pdb=" N LYS X 90 " --> pdb=" O SER X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 104 removed outlier: 3.584A pdb=" N SER X 104 " --> pdb=" O SER X 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 52 removed outlier: 4.334A pdb=" N CYS Y 52 " --> pdb=" O LEU Y 48 " (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 sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 5.278A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.735A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.278A 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 removed outlier: 3.646A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 303 removed outlier: 7.843A pdb=" N PHE A 312 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 358 " --> pdb=" O PHE A 312 " (cutoff:3.500A) 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: 6.069A pdb=" N ARG B 291 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 311 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR B 293 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU B 309 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 295 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 307 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.953A pdb=" N TYR B 18 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 117 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 35 removed outlier: 10.122A pdb=" N SER B 48 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET B 67 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.665A pdb=" N TYR B 99 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA B 49 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B 97 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N PHE B 51 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N GLY B 95 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 162 through 166 removed outlier: 3.837A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 166 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 255 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AC1, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC3, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.630A pdb=" N ASP C 281 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 15 through 19 removed outlier: 5.327A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 128 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AC6, first strand: chain 'C' and resid 43 through 48 removed outlier: 6.708A pdb=" N LYS C 44 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 123 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 46 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 63 removed outlier: 5.803A pdb=" N THR C 101 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD1, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD2, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'C' and resid 296 through 303 Processing sheet with id=AD4, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.904A pdb=" N ILE C 366 " --> pdb=" O HIS C 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AD6, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.157A pdb=" N ARG D 291 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 311 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR D 293 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU D 309 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 295 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR D 307 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AD8, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.853A pdb=" N GLN D 46 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL D 34 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG D 44 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.473A 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: 6.853A pdb=" N GLN D 46 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL D 34 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG D 44 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.028A 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: 7.962A pdb=" N LYS D 97 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N PHE D 51 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLY D 95 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 16.520A pdb=" N TYR D 53 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 18.184A pdb=" N ARG D 93 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.741A pdb=" N SER D 110 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS D 128 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR D 112 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 126 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 147 through 155 Processing sheet with id=AE3, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AE4, first strand: chain 'D' and resid 180 through 183 Processing sheet with id=AE5, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AE6, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.792A pdb=" N GLY E 122 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU E 116 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR E 123 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 248 through 251 removed outlier: 3.759A pdb=" N VAL E 200 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE E 198 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 9.825A pdb=" N ALA E 190 " --> pdb=" O PRO E 201 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 223 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 248 through 251 removed outlier: 6.702A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 9.155A 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: 7.018A pdb=" N PHE F 112 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR F 123 " --> pdb=" O PHE F 112 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 114 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR F 123 " --> pdb=" O PRO F 134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 248 through 251 removed outlier: 6.574A pdb=" N ALA F 236 " --> pdb=" O GLY F 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY F 228 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER F 238 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP F 242 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL F 222 " --> pdb=" O TRP F 242 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 214 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE F 198 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR F 235 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 8 removed outlier: 4.478A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.665A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.232A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 54 removed outlier: 5.728A pdb=" N VAL G 108 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP G 75 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AF8, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AF9, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AG1, first strand: chain 'G' and resid 296 through 304 removed outlier: 3.503A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 304 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.658A pdb=" N LYS G 372 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.613A pdb=" N THR H 275 " --> pdb=" O HIS H 286 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.300A pdb=" N ARG H 291 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 311 " --> pdb=" O ARG H 291 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR H 293 " --> pdb=" O GLU H 309 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU H 309 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU H 295 " --> pdb=" O THR H 307 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR H 307 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 14 through 16 Processing sheet with id=AG6, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.133A pdb=" N TYR H 18 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP H 109 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 33 through 35 removed outlier: 4.313A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N SER H 48 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET H 67 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS H 63 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 33 through 35 removed outlier: 4.313A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR H 99 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N ALA H 49 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LYS H 97 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N PHE H 51 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N GLY H 95 " --> pdb=" O PHE H 51 " (cutoff:3.500A) removed outlier: 15.154A pdb=" N TYR H 53 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 18.516A pdb=" N ARG H 93 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 148 through 155 Processing sheet with id=AH1, first strand: chain 'H' and resid 162 through 166 removed outlier: 6.059A pdb=" N ILE H 257 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR H 165 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU H 255 " --> pdb=" O TYR H 165 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 168 through 169 Processing sheet with id=AH3, first strand: chain 'H' and resid 180 through 183 Processing sheet with id=AH4, first strand: chain 'H' and resid 207 through 211 Processing sheet with id=AH5, first strand: chain 'I' and resid 140 through 141 removed outlier: 6.627A pdb=" N LEU I 116 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR I 123 " --> pdb=" O PRO I 134 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 247 through 251 removed outlier: 4.762A pdb=" N PHE I 198 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE I 214 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY I 228 " --> pdb=" O GLU I 257 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 247 through 251 removed outlier: 6.595A pdb=" N ALA I 236 " --> pdb=" O GLY I 228 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY I 228 " --> pdb=" O ALA I 236 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER I 238 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE I 224 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP I 242 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL I 222 " --> pdb=" O TRP I 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY I 228 " --> pdb=" O GLU I 257 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.113A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.370A pdb=" N ALA J 127 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR J 42 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N HIS J 125 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.894A pdb=" N LYS J 130 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER J 36 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 59 through 61 removed outlier: 3.578A pdb=" N THR J 101 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AI4, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AI5, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI6, first strand: chain 'J' and resid 296 through 304 removed outlier: 3.545A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AI8, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AI9, first strand: chain 'K' and resid 14 through 16 Processing sheet with id=AJ1, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.621A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG K 44 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE K 51 " --> pdb=" O ARG K 65 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG K 65 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS K 63 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.621A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG K 44 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 14.396A pdb=" N TYR K 53 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 17.590A pdb=" N ARG K 93 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE K 85 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG K 93 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N ILE K 83 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL K 126 " --> pdb=" O VAL K 111 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 149 through 155 removed outlier: 3.536A pdb=" N VAL K 150 " --> pdb=" O CYS K 266 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 237 through 238 removed outlier: 3.890A pdb=" N GLY K 164 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU K 255 " --> pdb=" O ILE K 166 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 180 through 183 Processing sheet with id=AJ6, first strand: chain 'K' and resid 206 through 211 Processing sheet with id=AJ7, first strand: chain 'K' and resid 275 through 279 Processing sheet with id=AJ8, first strand: chain 'L' and resid 140 through 141 removed outlier: 6.480A pdb=" N PHE L 112 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR L 123 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE L 114 " --> pdb=" O ASN L 121 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR L 123 " --> pdb=" O PRO L 134 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 248 through 251 removed outlier: 6.057A pdb=" N VAL L 240 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL L 225 " --> pdb=" O VAL L 240 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP L 242 " --> pdb=" O ALA L 223 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA L 223 " --> pdb=" O TRP L 242 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE L 214 " --> pdb=" O VAL L 222 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE L 198 " --> pdb=" O LEU L 237 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'V' and resid 38 through 39 Processing sheet with id=AK2, first strand: chain 'V' and resid 76 through 77 Processing sheet with id=AK3, first strand: chain 'W' and resid 38 through 39 removed outlier: 3.593A pdb=" N PHE W 38 " --> pdb=" O ILE W 46 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AK5, first strand: chain 'X' and resid 77 through 78 Processing sheet with id=AK6, first strand: chain 'Y' and resid 76 through 77 1266 hydrogen bonds defined for protein. 3135 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: 15.19 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7369 1.33 - 1.45: 8372 1.45 - 1.58: 17651 1.58 - 1.71: 0 1.71 - 1.83: 268 Bond restraints: 33660 Sorted by residual: bond pdb=" N ILE B 389 " pdb=" CA ILE B 389 " ideal model delta sigma weight residual 1.458 1.493 -0.035 9.00e-03 1.23e+04 1.55e+01 bond pdb=" N CYS D 19 " pdb=" CA CYS D 19 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" N ARG D 20 " pdb=" CA ARG D 20 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" N ILE D 115 " pdb=" CA ILE D 115 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.01e+01 bond pdb=" N VAL D 126 " pdb=" CA VAL D 126 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.23e-02 6.61e+03 9.37e+00 ... (remaining 33655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 41264 1.66 - 3.32: 3767 3.32 - 4.98: 641 4.98 - 6.64: 107 6.64 - 8.30: 17 Bond angle restraints: 45796 Sorted by residual: angle pdb=" CA ASP C 97 " pdb=" CB ASP C 97 " pdb=" CG ASP C 97 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" O TYR D 18 " pdb=" C TYR D 18 " pdb=" N CYS D 19 " ideal model delta sigma weight residual 123.48 116.27 7.21 1.14e+00 7.69e-01 4.00e+01 angle pdb=" CA ASP V 63 " pdb=" CB ASP V 63 " pdb=" CG ASP V 63 " ideal model delta sigma weight residual 112.60 118.65 -6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" N TYR K 69 " pdb=" CA TYR K 69 " pdb=" CB TYR K 69 " ideal model delta sigma weight residual 110.45 117.49 -7.04 1.26e+00 6.30e-01 3.12e+01 angle pdb=" CA PHE V 38 " pdb=" CB PHE V 38 " pdb=" CG PHE V 38 " ideal model delta sigma weight residual 113.80 119.21 -5.41 1.00e+00 1.00e+00 2.93e+01 ... (remaining 45791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18734 17.86 - 35.72: 1206 35.72 - 53.58: 230 53.58 - 71.44: 76 71.44 - 89.29: 33 Dihedral angle restraints: 20279 sinusoidal: 7983 harmonic: 12296 Sorted by residual: dihedral pdb=" CA GLY Y 61 " pdb=" C GLY Y 61 " pdb=" N SER Y 62 " pdb=" CA SER Y 62 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" C VAL K 80 " pdb=" N VAL K 80 " pdb=" CA VAL K 80 " pdb=" CB VAL K 80 " ideal model delta harmonic sigma weight residual -122.00 -135.55 13.55 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA GLU V 56 " pdb=" C GLU V 56 " pdb=" N ASP V 57 " pdb=" CA ASP V 57 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 20276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4477 0.089 - 0.177: 546 0.177 - 0.266: 50 0.266 - 0.355: 6 0.355 - 0.443: 1 Chirality restraints: 5080 Sorted by residual: chirality pdb=" CA VAL K 80 " pdb=" N VAL K 80 " pdb=" C VAL K 80 " pdb=" CB VAL K 80 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA PHE V 38 " pdb=" N PHE V 38 " pdb=" C PHE V 38 " pdb=" CB PHE V 38 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA SER K 79 " pdb=" N SER K 79 " pdb=" C SER K 79 " pdb=" CB SER K 79 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 5077 not shown) Planarity restraints: 5924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 89 " 0.116 2.00e-02 2.50e+03 5.73e-02 8.20e+01 pdb=" CG TRP J 89 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP J 89 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP J 89 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP J 89 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP J 89 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 89 " -0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 89 " 0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 89 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP J 89 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 89 " -0.068 2.00e-02 2.50e+03 3.55e-02 3.15e+01 pdb=" CG TRP G 89 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP G 89 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP G 89 " 0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP G 89 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP G 89 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP G 89 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 89 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 89 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 89 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 89 " -0.056 2.00e-02 2.50e+03 3.45e-02 2.98e+01 pdb=" CG TRP X 89 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP X 89 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP X 89 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP X 89 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP X 89 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP X 89 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 89 " -0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 89 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP X 89 " -0.038 2.00e-02 2.50e+03 ... (remaining 5921 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 499 2.62 - 3.19: 31645 3.19 - 3.76: 51999 3.76 - 4.33: 70391 4.33 - 4.90: 115001 Nonbonded interactions: 269535 Sorted by model distance: nonbonded pdb=" OG SER D 68 " pdb=" OD1 ASP D 70 " model vdw 2.047 3.040 nonbonded pdb=" O TRP Y 89 " pdb="CA CA Y 202 " model vdw 2.110 2.510 nonbonded pdb=" O TRP X 50 " pdb="CA CA X 201 " model vdw 2.135 2.510 nonbonded pdb=" OH TYR K 12 " pdb=" OE2 GLU K 32 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" OG1 THR B 307 " model vdw 2.173 3.040 ... (remaining 269530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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 'W' selection = chain 'X' selection = chain 'Y' } 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 77.560 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.220 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.007 0.094 33733 Z= 0.360 Angle : 1.035 8.302 45942 Z= 0.631 Chirality : 0.058 0.443 5080 Planarity : 0.008 0.106 5924 Dihedral : 12.944 89.294 12188 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.71 % Favored : 92.24 % Rotamer: Outliers : 1.16 % Allowed : 7.70 % Favored : 91.14 % Cbeta Deviations : 0.05 % 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: -1.56 (0.12), residues: 4240 helix: -0.83 (0.23), residues: 402 sheet: -0.82 (0.15), residues: 1044 loop : -1.17 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.005 TRP J 89 HIS 0.009 0.002 HIS F 187 PHE 0.066 0.003 PHE V 38 TYR 0.049 0.005 TYR E 175 ARG 0.024 0.003 ARG H 245 Details of bonding type rmsd hydrogen bonds : bond 0.21630 ( 1197) hydrogen bonds : angle 9.27592 ( 3135) SS BOND : bond 0.00589 ( 73) SS BOND : angle 1.51313 ( 146) covalent geometry : bond 0.00655 (33660) covalent geometry : angle 1.03349 (45796) *********************** 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 1485 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 1443 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 8 PRO cc_start: 0.9585 (Cg_exo) cc_final: 0.9059 (Cg_endo) REVERT: A 20 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8443 (mt-10) REVERT: A 24 TYR cc_start: 0.8917 (m-80) cc_final: 0.8558 (m-80) REVERT: A 27 LEU cc_start: 0.8692 (tp) cc_final: 0.8311 (tp) REVERT: A 37 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 67 GLU cc_start: 0.8115 (pm20) cc_final: 0.7849 (pm20) REVERT: A 75 ASP cc_start: 0.8504 (t0) cc_final: 0.7339 (t0) REVERT: A 77 THR cc_start: 0.8881 (m) cc_final: 0.8622 (m) REVERT: A 97 ASP cc_start: 0.7980 (m-30) cc_final: 0.7656 (t0) REVERT: A 117 ASP cc_start: 0.8466 (t0) cc_final: 0.7949 (t0) REVERT: A 136 VAL cc_start: 0.8225 (p) cc_final: 0.7880 (p) REVERT: A 191 GLU cc_start: 0.8622 (tp30) cc_final: 0.8001 (tp30) REVERT: A 218 ASP cc_start: 0.8806 (t0) cc_final: 0.8302 (t0) REVERT: A 219 ILE cc_start: 0.9477 (mt) cc_final: 0.9277 (mt) REVERT: A 237 VAL cc_start: 0.9425 (t) cc_final: 0.9194 (p) REVERT: A 242 MET cc_start: 0.8164 (tpt) cc_final: 0.7694 (tmm) REVERT: A 252 GLN cc_start: 0.8917 (mp10) cc_final: 0.8480 (mm-40) REVERT: A 284 ASP cc_start: 0.8829 (m-30) cc_final: 0.8376 (m-30) REVERT: A 316 LEU cc_start: 0.9020 (pt) cc_final: 0.8728 (pt) REVERT: A 354 LEU cc_start: 0.9272 (mt) cc_final: 0.9042 (mt) REVERT: A 357 SER cc_start: 0.9320 (p) cc_final: 0.8797 (m) REVERT: A 367 VAL cc_start: 0.9395 (t) cc_final: 0.9126 (p) REVERT: A 397 GLU cc_start: 0.7725 (tp30) cc_final: 0.7474 (tp30) REVERT: B 15 PHE cc_start: 0.8526 (t80) cc_final: 0.8232 (t80) REVERT: B 39 ASP cc_start: 0.7835 (m-30) cc_final: 0.7321 (m-30) REVERT: B 92 ARG cc_start: 0.2541 (mtt180) cc_final: 0.1755 (mtp180) REVERT: B 114 SER cc_start: 0.9047 (m) cc_final: 0.8766 (p) REVERT: B 122 ASN cc_start: 0.8592 (m110) cc_final: 0.8191 (m110) REVERT: B 131 ARG cc_start: 0.8358 (ptm160) cc_final: 0.7920 (mtm110) REVERT: B 138 GLU cc_start: 0.7738 (tt0) cc_final: 0.7255 (tt0) REVERT: B 156 ASP cc_start: 0.8297 (t0) cc_final: 0.8075 (t0) REVERT: B 168 MET cc_start: 0.7464 (pmm) cc_final: 0.6925 (pmm) REVERT: B 217 MET cc_start: 0.6391 (tpp) cc_final: 0.4978 (tpp) REVERT: B 261 LEU cc_start: 0.9186 (tp) cc_final: 0.8953 (tp) REVERT: B 305 ASP cc_start: 0.8964 (t0) cc_final: 0.8547 (t0) REVERT: B 327 GLU cc_start: 0.7894 (tt0) cc_final: 0.7428 (tt0) REVERT: B 332 ASN cc_start: 0.9182 (m-40) cc_final: 0.8889 (m-40) REVERT: B 342 GLU cc_start: 0.8459 (tp30) cc_final: 0.8246 (tp30) REVERT: B 354 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 367 THR cc_start: 0.9069 (m) cc_final: 0.8784 (p) REVERT: C 7 VAL cc_start: 0.9392 (t) cc_final: 0.8941 (m) REVERT: C 32 THR cc_start: 0.8818 (m) cc_final: 0.8185 (p) REVERT: C 95 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8085 (p90) REVERT: C 99 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8433 (mt-10) REVERT: C 139 ASN cc_start: 0.8356 (t0) cc_final: 0.7855 (m-40) REVERT: C 151 VAL cc_start: 0.8716 (t) cc_final: 0.8452 (p) REVERT: C 191 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 209 ASP cc_start: 0.8868 (p0) cc_final: 0.8643 (p0) REVERT: C 228 ASN cc_start: 0.9291 (m110) cc_final: 0.9020 (m110) REVERT: C 230 HIS cc_start: 0.8613 (t-90) cc_final: 0.7922 (t-90) REVERT: C 231 VAL cc_start: 0.9547 (OUTLIER) cc_final: 0.9306 (p) REVERT: C 307 ILE cc_start: 0.5867 (mt) cc_final: 0.5447 (tt) REVERT: C 308 TYR cc_start: 0.8310 (p90) cc_final: 0.7853 (p90) REVERT: C 362 GLN cc_start: 0.8251 (pt0) cc_final: 0.7975 (pm20) REVERT: C 373 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8566 (mttp) REVERT: C 404 LYS cc_start: 0.8546 (tppt) cc_final: 0.8333 (tppt) REVERT: C 409 TRP cc_start: 0.7997 (m100) cc_final: 0.7196 (m100) REVERT: D 26 PHE cc_start: 0.8916 (m-80) cc_final: 0.8173 (m-10) REVERT: D 33 ASN cc_start: 0.8456 (m-40) cc_final: 0.8084 (m110) REVERT: D 37 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8518 (mp0) REVERT: D 58 THR cc_start: 0.9249 (m) cc_final: 0.8991 (p) REVERT: D 125 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7764 (t) REVERT: D 134 PHE cc_start: 0.9007 (p90) cc_final: 0.8779 (p90) REVERT: D 139 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 158 LEU cc_start: 0.8488 (mt) cc_final: 0.8283 (mt) REVERT: D 160 GLU cc_start: 0.8636 (mp0) cc_final: 0.8424 (mp0) REVERT: D 169 HIS cc_start: 0.6975 (m90) cc_final: 0.6119 (m170) REVERT: D 176 TYR cc_start: 0.8676 (m-80) cc_final: 0.8330 (m-80) REVERT: D 180 LEU cc_start: 0.8466 (mp) cc_final: 0.8087 (mt) REVERT: D 195 LYS cc_start: 0.8818 (mttt) cc_final: 0.8361 (mttt) REVERT: D 210 ILE cc_start: 0.8942 (pt) cc_final: 0.8721 (mp) REVERT: D 242 ASP cc_start: 0.8980 (m-30) cc_final: 0.8773 (m-30) REVERT: D 254 LYS cc_start: 0.4150 (pptt) cc_final: 0.3041 (pttm) REVERT: D 273 THR cc_start: 0.9192 (m) cc_final: 0.8629 (p) REVERT: D 339 TRP cc_start: 0.9015 (m-90) cc_final: 0.8610 (m-90) REVERT: D 355 ILE cc_start: 0.8318 (mm) cc_final: 0.8106 (mm) REVERT: D 366 TYR cc_start: 0.7895 (m-80) cc_final: 0.7659 (m-80) REVERT: E 174 GLN cc_start: 0.8750 (pm20) cc_final: 0.8539 (pm20) REVERT: E 257 GLU cc_start: 0.8865 (pt0) cc_final: 0.8656 (mp0) REVERT: F 112 PHE cc_start: 0.8560 (m-80) cc_final: 0.8329 (m-80) REVERT: F 119 GLN cc_start: 0.8052 (pt0) cc_final: 0.7617 (pm20) REVERT: F 177 SER cc_start: 0.9035 (p) cc_final: 0.8289 (p) REVERT: F 186 TRP cc_start: 0.8150 (t60) cc_final: 0.7557 (t60) REVERT: F 188 HIS cc_start: 0.6845 (m-70) cc_final: 0.5557 (m-70) REVERT: F 226 LEU cc_start: 0.8164 (mm) cc_final: 0.7810 (mm) REVERT: G 21 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7788 (tmm-80) REVERT: G 27 LEU cc_start: 0.8049 (tp) cc_final: 0.7684 (tp) REVERT: G 62 CYS cc_start: 0.4265 (m) cc_final: 0.3207 (m) REVERT: G 79 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7836 (ttt180) REVERT: G 129 LEU cc_start: 0.8188 (tp) cc_final: 0.7912 (tt) REVERT: G 133 LEU cc_start: 0.9265 (mt) cc_final: 0.9028 (mp) REVERT: G 140 THR cc_start: 0.9003 (m) cc_final: 0.8797 (p) REVERT: G 148 VAL cc_start: 0.8921 (t) cc_final: 0.8694 (t) REVERT: G 161 VAL cc_start: 0.9139 (t) cc_final: 0.8916 (m) REVERT: G 203 ILE cc_start: 0.9108 (tt) cc_final: 0.8858 (tt) REVERT: G 206 SER cc_start: 0.9595 (m) cc_final: 0.9303 (t) REVERT: G 218 ASP cc_start: 0.7964 (t0) cc_final: 0.7369 (t0) REVERT: G 220 ARG cc_start: 0.8920 (ptp-170) cc_final: 0.8407 (ptp90) REVERT: G 223 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9340 (ttmm) REVERT: G 230 HIS cc_start: 0.8708 (t-90) cc_final: 0.7691 (t-90) REVERT: G 235 GLN cc_start: 0.9045 (pt0) cc_final: 0.8664 (pt0) REVERT: G 241 GLU cc_start: 0.9312 (tp30) cc_final: 0.9050 (tp30) REVERT: G 341 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7509 (tp30) REVERT: H 32 GLU cc_start: 0.8067 (pt0) cc_final: 0.7822 (pm20) REVERT: H 36 ASP cc_start: 0.8752 (p0) cc_final: 0.8461 (p0) REVERT: H 37 GLU cc_start: 0.8706 (tp30) cc_final: 0.8249 (mm-30) REVERT: H 46 GLN cc_start: 0.7110 (mt0) cc_final: 0.6875 (mt0) REVERT: H 82 LYS cc_start: 0.8643 (mttt) cc_final: 0.8286 (mtmm) REVERT: H 115 ILE cc_start: 0.8305 (pt) cc_final: 0.8031 (pt) REVERT: H 122 ASN cc_start: 0.7256 (t0) cc_final: 0.6953 (t0) REVERT: H 139 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6943 (tm-30) REVERT: H 167 THR cc_start: 0.9207 (p) cc_final: 0.8907 (t) REVERT: H 168 MET cc_start: 0.8409 (mmt) cc_final: 0.8058 (tpp) REVERT: H 180 LEU cc_start: 0.8774 (mt) cc_final: 0.8442 (mp) REVERT: H 236 TRP cc_start: 0.8703 (m-90) cc_final: 0.7893 (m-90) REVERT: H 272 HIS cc_start: 0.7369 (t70) cc_final: 0.6879 (t70) REVERT: H 303 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8482 (ptp-110) REVERT: H 305 ASP cc_start: 0.8668 (t0) cc_final: 0.8419 (t0) REVERT: H 332 ASN cc_start: 0.8989 (m-40) cc_final: 0.8700 (m110) REVERT: H 334 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8796 (mm-30) REVERT: H 337 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8572 (mmm-85) REVERT: H 362 ARG cc_start: 0.9239 (mtp180) cc_final: 0.8942 (mtp180) REVERT: I 145 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7080 (mp10) REVERT: I 192 GLN cc_start: 0.8705 (tp40) cc_final: 0.8393 (tp40) REVERT: I 194 GLU cc_start: 0.8381 (tt0) cc_final: 0.7762 (tt0) REVERT: I 235 THR cc_start: 0.3994 (m) cc_final: 0.3673 (m) REVERT: J 9 ASN cc_start: 0.9007 (t0) cc_final: 0.8400 (t0) REVERT: J 15 TYR cc_start: 0.8754 (t80) cc_final: 0.8020 (t80) REVERT: J 87 PHE cc_start: 0.8200 (m-80) cc_final: 0.7935 (m-80) REVERT: J 117 ASP cc_start: 0.9033 (t70) cc_final: 0.8703 (t0) REVERT: J 173 PHE cc_start: 0.8741 (m-80) cc_final: 0.8487 (m-10) REVERT: J 181 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8634 (ttmt) REVERT: J 256 PRO cc_start: 0.9305 (Cg_exo) cc_final: 0.8808 (Cg_endo) REVERT: J 257 PHE cc_start: 0.8611 (m-80) cc_final: 0.7658 (m-80) REVERT: J 277 PRO cc_start: 0.9030 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: J 307 ILE cc_start: 0.8399 (mt) cc_final: 0.8121 (mm) REVERT: J 311 ASP cc_start: 0.8293 (t0) cc_final: 0.7956 (t70) REVERT: J 341 GLU cc_start: 0.8298 (mp0) cc_final: 0.7601 (mp0) REVERT: J 355 HIS cc_start: 0.7398 (m-70) cc_final: 0.6986 (m-70) REVERT: J 387 ILE cc_start: 0.8796 (mm) cc_final: 0.8522 (mm) REVERT: J 398 PHE cc_start: 0.9000 (t80) cc_final: 0.8780 (t80) REVERT: J 409 TRP cc_start: 0.8489 (m100) cc_final: 0.8207 (m100) REVERT: K 33 ASN cc_start: 0.8255 (m110) cc_final: 0.7935 (m110) REVERT: K 43 ILE cc_start: 0.9257 (pp) cc_final: 0.8919 (pt) REVERT: K 100 PHE cc_start: 0.8990 (m-80) cc_final: 0.8496 (m-80) REVERT: K 104 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7807 (tm-30) REVERT: K 121 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: K 146 HIS cc_start: 0.4369 (m-70) cc_final: 0.3928 (m-70) REVERT: K 170 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.7928 (ptm160) REVERT: K 200 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8051 (mt-10) REVERT: K 229 TYR cc_start: 0.8525 (p90) cc_final: 0.8137 (p90) REVERT: K 272 HIS cc_start: 0.8568 (t70) cc_final: 0.7640 (t70) REVERT: K 279 TRP cc_start: 0.9020 (p-90) cc_final: 0.8475 (p-90) REVERT: K 311 ILE cc_start: 0.9349 (mm) cc_final: 0.8944 (mm) REVERT: K 342 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7780 (mm-30) REVERT: K 347 ASP cc_start: 0.8839 (t0) cc_final: 0.8593 (t0) REVERT: K 366 TYR cc_start: 0.8358 (m-80) cc_final: 0.8098 (m-80) REVERT: L 143 ASN cc_start: 0.8242 (t0) cc_final: 0.7451 (m-40) REVERT: L 156 MET cc_start: 0.8432 (pmm) cc_final: 0.8134 (ppp) REVERT: L 191 VAL cc_start: 0.7722 (m) cc_final: 0.7519 (t) REVERT: L 224 ILE cc_start: 0.7975 (mm) cc_final: 0.7722 (mm) REVERT: L 230 ASN cc_start: 0.8230 (p0) cc_final: 0.8003 (t0) REVERT: V 99 ASP cc_start: 0.6636 (p0) cc_final: 0.6304 (p0) REVERT: W 90 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7431 (tmtt) REVERT: W 96 ASP cc_start: 0.7937 (m-30) cc_final: 0.7729 (m-30) REVERT: X 96 ASP cc_start: 0.8207 (m-30) cc_final: 0.7878 (m-30) REVERT: Y 79 CYS cc_start: 0.5006 (m) cc_final: 0.4274 (m) outliers start: 42 outliers final: 12 residues processed: 1463 average time/residue: 0.4511 time to fit residues: 1066.1084 Evaluate side-chains 1005 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 989 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain K residue 53 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 33 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 59 GLN C 100 ASN D 233 GLN D 361 HIS D 405 ASN E 119 GLN F 188 HIS G 59 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS H 169 HIS I 117 ASN I 188 HIS J 143 HIS ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 218 ASN ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN W 37 GLN X 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121642 restraints weight = 64340.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125409 restraints weight = 31776.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127831 restraints weight = 19811.979| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33733 Z= 0.265 Angle : 0.788 11.864 45942 Z= 0.421 Chirality : 0.050 0.245 5080 Planarity : 0.005 0.071 5924 Dihedral : 6.972 80.395 4630 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 4.76 % Allowed : 15.03 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4240 helix: -0.05 (0.24), residues: 424 sheet: -0.80 (0.14), residues: 1138 loop : -0.70 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 89 HIS 0.013 0.002 HIS D 146 PHE 0.030 0.002 PHE H 259 TYR 0.027 0.002 TYR F 157 ARG 0.009 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 1197) hydrogen bonds : angle 6.97049 ( 3135) SS BOND : bond 0.00667 ( 73) SS BOND : angle 2.01674 ( 146) covalent geometry : bond 0.00588 (33660) covalent geometry : angle 0.78064 (45796) *********************** 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 1227 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1055 time to evaluate : 3.958 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 75 ASP cc_start: 0.8250 (t0) cc_final: 0.7442 (t0) REVERT: A 125 HIS cc_start: 0.7718 (m90) cc_final: 0.7468 (m90) REVERT: A 129 LEU cc_start: 0.8385 (tt) cc_final: 0.8174 (tt) REVERT: A 158 ASP cc_start: 0.8753 (t0) cc_final: 0.8366 (t0) REVERT: A 160 LYS cc_start: 0.8605 (mptt) cc_final: 0.8153 (mmtm) REVERT: A 252 GLN cc_start: 0.9211 (mp10) cc_final: 0.8241 (mm-40) REVERT: A 367 VAL cc_start: 0.9574 (t) cc_final: 0.9366 (p) REVERT: A 395 ASP cc_start: 0.8390 (t0) cc_final: 0.8106 (t0) REVERT: B 32 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7743 (tp30) REVERT: B 33 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7378 (t0) REVERT: B 39 ASP cc_start: 0.7809 (m-30) cc_final: 0.7528 (m-30) REVERT: B 50 GLN cc_start: 0.7223 (mt0) cc_final: 0.6902 (mt0) REVERT: B 51 PHE cc_start: 0.8283 (m-80) cc_final: 0.8001 (m-80) REVERT: B 70 ASP cc_start: 0.7927 (p0) cc_final: 0.7283 (p0) REVERT: B 92 ARG cc_start: 0.2714 (mtt180) cc_final: 0.1790 (mtp180) REVERT: B 114 SER cc_start: 0.9150 (m) cc_final: 0.8756 (p) REVERT: B 122 ASN cc_start: 0.8619 (m110) cc_final: 0.8401 (m110) REVERT: B 138 GLU cc_start: 0.7629 (tt0) cc_final: 0.7398 (tt0) REVERT: B 156 ASP cc_start: 0.8749 (t0) cc_final: 0.8372 (t0) REVERT: B 176 TYR cc_start: 0.7371 (m-80) cc_final: 0.6739 (m-80) REVERT: B 278 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9016 (mttm) REVERT: B 284 THR cc_start: 0.8946 (m) cc_final: 0.8682 (p) REVERT: B 305 ASP cc_start: 0.8858 (t0) cc_final: 0.8589 (t0) REVERT: B 327 GLU cc_start: 0.7801 (tt0) cc_final: 0.7413 (tt0) REVERT: B 330 TRP cc_start: 0.9099 (t-100) cc_final: 0.8817 (t-100) REVERT: B 332 ASN cc_start: 0.9179 (m-40) cc_final: 0.8952 (m110) REVERT: B 334 GLU cc_start: 0.8671 (tp30) cc_final: 0.8418 (mm-30) REVERT: C 32 THR cc_start: 0.9086 (m) cc_final: 0.8704 (p) REVERT: C 99 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 100 ASN cc_start: 0.8305 (m-40) cc_final: 0.7985 (m-40) REVERT: C 103 LEU cc_start: 0.9232 (tp) cc_final: 0.9024 (tt) REVERT: C 139 ASN cc_start: 0.8239 (t0) cc_final: 0.7961 (m-40) REVERT: C 228 ASN cc_start: 0.9372 (m110) cc_final: 0.9034 (m-40) REVERT: C 231 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9430 (m) REVERT: C 307 ILE cc_start: 0.6259 (mt) cc_final: 0.5647 (tt) REVERT: C 308 TYR cc_start: 0.8426 (p90) cc_final: 0.8131 (p90) REVERT: C 373 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8655 (mttp) REVERT: C 396 GLN cc_start: 0.7596 (tt0) cc_final: 0.7333 (tt0) REVERT: C 409 TRP cc_start: 0.8311 (m100) cc_final: 0.7547 (m100) REVERT: D 18 TYR cc_start: 0.8483 (t80) cc_final: 0.8235 (t80) REVERT: D 33 ASN cc_start: 0.8387 (m-40) cc_final: 0.8149 (m-40) REVERT: D 134 PHE cc_start: 0.8948 (p90) cc_final: 0.8571 (p90) REVERT: D 139 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 193 SER cc_start: 0.8330 (p) cc_final: 0.7902 (p) REVERT: D 195 LYS cc_start: 0.9124 (mttt) cc_final: 0.8745 (mttt) REVERT: D 227 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7834 (mm) REVERT: D 273 THR cc_start: 0.9322 (m) cc_final: 0.8819 (p) REVERT: D 305 ASP cc_start: 0.8156 (t0) cc_final: 0.7938 (t70) REVERT: D 339 TRP cc_start: 0.9026 (m-90) cc_final: 0.8728 (m-90) REVERT: E 132 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7577 (mtp) REVERT: E 186 TRP cc_start: 0.7533 (t60) cc_final: 0.6944 (t60) REVERT: E 194 GLU cc_start: 0.8907 (tp30) cc_final: 0.8475 (tp30) REVERT: F 112 PHE cc_start: 0.8681 (m-80) cc_final: 0.8450 (m-80) REVERT: G 10 VAL cc_start: 0.9069 (t) cc_final: 0.8797 (m) REVERT: G 27 LEU cc_start: 0.8363 (tp) cc_final: 0.7969 (tp) REVERT: G 62 CYS cc_start: 0.4489 (m) cc_final: 0.4140 (m) REVERT: G 140 THR cc_start: 0.8762 (m) cc_final: 0.8511 (p) REVERT: G 170 PHE cc_start: 0.7912 (t80) cc_final: 0.7367 (t80) REVERT: G 203 ILE cc_start: 0.9154 (tt) cc_final: 0.8892 (tt) REVERT: G 206 SER cc_start: 0.9643 (m) cc_final: 0.9322 (t) REVERT: G 218 ASP cc_start: 0.7701 (t0) cc_final: 0.7153 (t0) REVERT: G 220 ARG cc_start: 0.8629 (ptp-170) cc_final: 0.8214 (ptp90) REVERT: G 257 PHE cc_start: 0.8598 (m-80) cc_final: 0.8187 (m-80) REVERT: G 261 ILE cc_start: 0.9360 (mt) cc_final: 0.8993 (mm) REVERT: G 324 ARG cc_start: 0.7723 (ptp-170) cc_final: 0.7365 (ptp90) REVERT: G 362 GLN cc_start: 0.8111 (pm20) cc_final: 0.7867 (pm20) REVERT: G 364 ASN cc_start: 0.8965 (t0) cc_final: 0.8704 (t0) REVERT: H 51 PHE cc_start: 0.7948 (m-80) cc_final: 0.7681 (m-80) REVERT: H 82 LYS cc_start: 0.8717 (mttt) cc_final: 0.8427 (mtmm) REVERT: H 104 GLN cc_start: 0.8792 (tt0) cc_final: 0.8468 (tt0) REVERT: H 117 SER cc_start: 0.8411 (t) cc_final: 0.8132 (p) REVERT: H 121 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7460 (tm-30) REVERT: H 139 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: H 158 LEU cc_start: 0.8970 (mt) cc_final: 0.8658 (mt) REVERT: H 180 LEU cc_start: 0.9000 (mt) cc_final: 0.8764 (mt) REVERT: H 200 GLU cc_start: 0.7631 (tt0) cc_final: 0.7171 (tt0) REVERT: H 236 TRP cc_start: 0.8399 (m-90) cc_final: 0.8113 (m-90) REVERT: H 303 ARG cc_start: 0.8674 (mtt180) cc_final: 0.8388 (ttm-80) REVERT: H 337 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8590 (mtt-85) REVERT: H 362 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8697 (mmm-85) REVERT: I 115 MET cc_start: 0.6146 (mmp) cc_final: 0.5850 (mmm) REVERT: I 152 LYS cc_start: 0.8532 (ttpt) cc_final: 0.7839 (mmtt) REVERT: I 161 TYR cc_start: 0.9005 (p90) cc_final: 0.8682 (p90) REVERT: I 186 TRP cc_start: 0.8249 (t60) cc_final: 0.7743 (t60) REVERT: I 192 GLN cc_start: 0.8449 (tp40) cc_final: 0.8236 (tp40) REVERT: I 194 GLU cc_start: 0.8361 (tt0) cc_final: 0.7749 (tt0) REVERT: I 212 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: J 9 ASN cc_start: 0.9297 (t0) cc_final: 0.8728 (t0) REVERT: J 15 TYR cc_start: 0.8175 (t80) cc_final: 0.7971 (t80) REVERT: J 133 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8502 (mm) REVERT: J 251 LEU cc_start: 0.9413 (tp) cc_final: 0.8863 (tp) REVERT: J 257 PHE cc_start: 0.8509 (m-80) cc_final: 0.7895 (m-80) REVERT: J 271 CYS cc_start: 0.6598 (m) cc_final: 0.6353 (m) REVERT: J 277 PRO cc_start: 0.9224 (Cg_exo) cc_final: 0.9018 (Cg_endo) REVERT: J 307 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8188 (mm) REVERT: J 319 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7320 (mm-40) REVERT: J 372 LYS cc_start: 0.8848 (tptt) cc_final: 0.8602 (tppt) REVERT: J 398 PHE cc_start: 0.9115 (t80) cc_final: 0.8886 (t80) REVERT: J 409 TRP cc_start: 0.8599 (m100) cc_final: 0.8181 (m100) REVERT: K 78 ASP cc_start: 0.8617 (t0) cc_final: 0.8353 (t70) REVERT: K 100 PHE cc_start: 0.9217 (m-80) cc_final: 0.8675 (m-80) REVERT: K 121 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: K 170 ARG cc_start: 0.8263 (ptp-170) cc_final: 0.7960 (ptp-170) REVERT: K 218 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8418 (p0) REVERT: K 279 TRP cc_start: 0.9136 (p-90) cc_final: 0.8691 (p-90) REVERT: K 339 TRP cc_start: 0.8973 (m-90) cc_final: 0.7807 (m-90) REVERT: L 143 ASN cc_start: 0.8299 (t0) cc_final: 0.7379 (m-40) REVERT: W 90 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7530 (tmtt) REVERT: X 96 ASP cc_start: 0.8020 (m-30) cc_final: 0.7817 (m-30) REVERT: Y 83 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5436 (pm20) outliers start: 172 outliers final: 117 residues processed: 1134 average time/residue: 0.4221 time to fit residues: 778.5397 Evaluate side-chains 1033 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 906 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 278 LYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 117 ASN Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 218 ASN Chi-restraints excluded: chain K residue 314 THR Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 195 ASN Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 75 SER Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 157 optimal weight: 4.9990 chunk 405 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 228 optimal weight: 0.0470 chunk 223 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 392 optimal weight: 20.0000 overall best weight: 1.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 204 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 408 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 272 HIS F 187 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN ** L 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124534 restraints weight = 64775.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128465 restraints weight = 31701.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130977 restraints weight = 19577.070| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33733 Z= 0.160 Angle : 0.712 10.495 45942 Z= 0.373 Chirality : 0.047 0.262 5080 Planarity : 0.005 0.050 5924 Dihedral : 6.647 79.519 4621 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 4.49 % Allowed : 18.58 % Favored : 76.94 % 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: -0.84 (0.13), residues: 4240 helix: 0.22 (0.24), residues: 424 sheet: -0.81 (0.14), residues: 1165 loop : -0.50 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 89 HIS 0.010 0.001 HIS H 272 PHE 0.025 0.002 PHE J 87 TYR 0.027 0.002 TYR J 233 ARG 0.006 0.001 ARG G 21 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1197) hydrogen bonds : angle 6.54568 ( 3135) SS BOND : bond 0.00349 ( 73) SS BOND : angle 1.80025 ( 146) covalent geometry : bond 0.00365 (33660) covalent geometry : angle 0.70585 (45796) *********************** 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 1199 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1037 time to evaluate : 3.631 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: A 16 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8249 (mtpt) REVERT: A 24 TYR cc_start: 0.8439 (m-80) cc_final: 0.8000 (m-80) REVERT: A 69 LYS cc_start: 0.9011 (ptmm) cc_final: 0.8708 (ptmt) REVERT: A 75 ASP cc_start: 0.7961 (t0) cc_final: 0.6950 (t0) REVERT: A 143 HIS cc_start: 0.8408 (m90) cc_final: 0.8086 (m-70) REVERT: A 158 ASP cc_start: 0.8707 (t0) cc_final: 0.8226 (t0) REVERT: A 160 LYS cc_start: 0.8589 (mptt) cc_final: 0.8231 (mmtm) REVERT: A 280 ILE cc_start: 0.9382 (mp) cc_final: 0.8824 (mp) REVERT: A 367 VAL cc_start: 0.9549 (t) cc_final: 0.9347 (p) REVERT: A 395 ASP cc_start: 0.8426 (t0) cc_final: 0.8108 (t0) REVERT: B 32 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7639 (tp30) REVERT: B 33 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7422 (t0) REVERT: B 37 GLU cc_start: 0.8128 (tp30) cc_final: 0.7892 (tp30) REVERT: B 70 ASP cc_start: 0.7885 (p0) cc_final: 0.7235 (p0) REVERT: B 92 ARG cc_start: 0.2523 (mtt180) cc_final: 0.1771 (mtm180) REVERT: B 114 SER cc_start: 0.9124 (m) cc_final: 0.8679 (p) REVERT: B 122 ASN cc_start: 0.8718 (m110) cc_final: 0.8476 (m-40) REVERT: B 131 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7307 (mtm110) REVERT: B 146 HIS cc_start: 0.5158 (OUTLIER) cc_final: 0.4737 (m170) REVERT: B 156 ASP cc_start: 0.8656 (t0) cc_final: 0.8410 (t70) REVERT: B 176 TYR cc_start: 0.7282 (m-80) cc_final: 0.6681 (m-80) REVERT: B 257 ILE cc_start: 0.8326 (mt) cc_final: 0.8064 (pt) REVERT: B 278 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9074 (mttm) REVERT: B 305 ASP cc_start: 0.8849 (t0) cc_final: 0.8546 (t0) REVERT: B 329 VAL cc_start: 0.9409 (t) cc_final: 0.9165 (m) REVERT: B 330 TRP cc_start: 0.8980 (t-100) cc_final: 0.8671 (t-100) REVERT: B 332 ASN cc_start: 0.9179 (m-40) cc_final: 0.8941 (m110) REVERT: C 32 THR cc_start: 0.9087 (m) cc_final: 0.8669 (p) REVERT: C 97 ASP cc_start: 0.8012 (p0) cc_final: 0.7780 (p0) REVERT: C 100 ASN cc_start: 0.8395 (m-40) cc_final: 0.7939 (m-40) REVERT: C 133 LEU cc_start: 0.9323 (mt) cc_final: 0.9103 (mt) REVERT: C 139 ASN cc_start: 0.8215 (t0) cc_final: 0.7807 (m-40) REVERT: C 262 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7562 (pt0) REVERT: C 307 ILE cc_start: 0.6482 (mt) cc_final: 0.5913 (tt) REVERT: C 308 TYR cc_start: 0.8323 (p90) cc_final: 0.8057 (p90) REVERT: C 373 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8711 (mttp) REVERT: C 409 TRP cc_start: 0.8273 (m100) cc_final: 0.7478 (m100) REVERT: D 32 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8072 (mm-30) REVERT: D 121 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7188 (tp30) REVERT: D 134 PHE cc_start: 0.8942 (p90) cc_final: 0.8606 (p90) REVERT: D 139 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8085 (mm-30) REVERT: D 193 SER cc_start: 0.8273 (p) cc_final: 0.7889 (p) REVERT: D 195 LYS cc_start: 0.9096 (mttt) cc_final: 0.8739 (mttt) REVERT: D 227 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7843 (mm) REVERT: D 273 THR cc_start: 0.9260 (m) cc_final: 0.8767 (p) REVERT: D 327 GLU cc_start: 0.8305 (tt0) cc_final: 0.8082 (tt0) REVERT: D 339 TRP cc_start: 0.8862 (m-90) cc_final: 0.8517 (m-90) REVERT: E 112 PHE cc_start: 0.8143 (m-80) cc_final: 0.7629 (m-10) REVERT: E 119 GLN cc_start: 0.7987 (pt0) cc_final: 0.7748 (pm20) REVERT: E 160 GLU cc_start: 0.7017 (pm20) cc_final: 0.6512 (mp0) REVERT: E 186 TRP cc_start: 0.7512 (t60) cc_final: 0.6911 (t60) REVERT: E 194 GLU cc_start: 0.8812 (tp30) cc_final: 0.8416 (tp30) REVERT: F 127 VAL cc_start: 0.8934 (t) cc_final: 0.8705 (m) REVERT: F 186 TRP cc_start: 0.7812 (t60) cc_final: 0.7447 (t60) REVERT: F 218 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8243 (ptp-110) REVERT: G 10 VAL cc_start: 0.9041 (t) cc_final: 0.8741 (m) REVERT: G 24 TYR cc_start: 0.8239 (m-80) cc_final: 0.7719 (m-80) REVERT: G 27 LEU cc_start: 0.8232 (tp) cc_final: 0.7862 (tp) REVERT: G 37 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7511 (mp0) REVERT: G 57 SER cc_start: 0.9135 (m) cc_final: 0.8761 (t) REVERT: G 140 THR cc_start: 0.8654 (m) cc_final: 0.8416 (p) REVERT: G 160 LYS cc_start: 0.9165 (pptt) cc_final: 0.8780 (mmtm) REVERT: G 170 PHE cc_start: 0.8006 (t80) cc_final: 0.7667 (t80) REVERT: G 195 MET cc_start: 0.8845 (mpp) cc_final: 0.8633 (mpp) REVERT: G 203 ILE cc_start: 0.9121 (tt) cc_final: 0.8856 (tt) REVERT: G 206 SER cc_start: 0.9665 (m) cc_final: 0.9316 (t) REVERT: G 218 ASP cc_start: 0.7711 (t0) cc_final: 0.7238 (t0) REVERT: G 220 ARG cc_start: 0.8515 (ptp-170) cc_final: 0.8299 (ptp90) REVERT: G 235 GLN cc_start: 0.8753 (pt0) cc_final: 0.8200 (pt0) REVERT: G 324 ARG cc_start: 0.7671 (ptp-170) cc_final: 0.7282 (ptp90) REVERT: G 362 GLN cc_start: 0.8248 (pm20) cc_final: 0.7989 (pm20) REVERT: G 364 ASN cc_start: 0.8952 (t0) cc_final: 0.8602 (t0) REVERT: H 82 LYS cc_start: 0.8609 (mttt) cc_final: 0.7976 (mttm) REVERT: H 117 SER cc_start: 0.8385 (t) cc_final: 0.8152 (p) REVERT: H 139 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6268 (tm-30) REVERT: H 156 ASP cc_start: 0.8289 (t0) cc_final: 0.7928 (t0) REVERT: H 158 LEU cc_start: 0.8790 (mt) cc_final: 0.8462 (mt) REVERT: H 180 LEU cc_start: 0.8832 (mt) cc_final: 0.8616 (mp) REVERT: H 287 LEU cc_start: 0.9119 (mm) cc_final: 0.8754 (mt) REVERT: H 305 ASP cc_start: 0.8511 (t0) cc_final: 0.8298 (t0) REVERT: H 362 ARG cc_start: 0.9099 (mtp180) cc_final: 0.8725 (mmm-85) REVERT: H 395 ASP cc_start: 0.9205 (p0) cc_final: 0.8992 (p0) REVERT: I 152 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7927 (mmtt) REVERT: I 186 TRP cc_start: 0.8211 (t60) cc_final: 0.7691 (t60) REVERT: I 194 GLU cc_start: 0.8414 (tt0) cc_final: 0.7752 (tt0) REVERT: I 212 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.7348 (mmm-85) REVERT: J 9 ASN cc_start: 0.9275 (t0) cc_final: 0.8800 (t0) REVERT: J 15 TYR cc_start: 0.8075 (t80) cc_final: 0.7787 (t80) REVERT: J 37 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7440 (mm-30) REVERT: J 63 CYS cc_start: 0.5532 (t) cc_final: 0.2926 (t) REVERT: J 218 ASP cc_start: 0.8215 (t0) cc_final: 0.7742 (t0) REVERT: J 230 HIS cc_start: 0.8748 (t-90) cc_final: 0.8233 (t-90) REVERT: J 257 PHE cc_start: 0.8415 (m-80) cc_final: 0.7834 (m-80) REVERT: J 271 CYS cc_start: 0.6489 (m) cc_final: 0.6204 (m) REVERT: J 307 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8100 (mm) REVERT: J 372 LYS cc_start: 0.8765 (tptt) cc_final: 0.8461 (tppt) REVERT: J 409 TRP cc_start: 0.8505 (m100) cc_final: 0.8234 (m100) REVERT: K 37 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8424 (mt-10) REVERT: K 78 ASP cc_start: 0.8649 (t0) cc_final: 0.8279 (t70) REVERT: K 121 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: K 168 MET cc_start: 0.8260 (mmp) cc_final: 0.7654 (mmp) REVERT: K 272 HIS cc_start: 0.8744 (t70) cc_final: 0.7593 (t70) REVERT: K 279 TRP cc_start: 0.9065 (p-90) cc_final: 0.8686 (p-90) REVERT: K 330 TRP cc_start: 0.9489 (t-100) cc_final: 0.9260 (t-100) REVERT: K 339 TRP cc_start: 0.8955 (m-90) cc_final: 0.7805 (m-90) REVERT: K 341 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: K 366 TYR cc_start: 0.8289 (m-80) cc_final: 0.7824 (m-80) REVERT: L 110 LYS cc_start: 0.8082 (mppt) cc_final: 0.6951 (pttm) REVERT: L 143 ASN cc_start: 0.8290 (t0) cc_final: 0.7414 (m-40) REVERT: L 145 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8136 (tm-30) REVERT: L 168 MET cc_start: 0.9221 (ppp) cc_final: 0.8794 (tmm) REVERT: L 191 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7640 (t) REVERT: W 72 CYS cc_start: 0.5515 (OUTLIER) cc_final: 0.5093 (p) REVERT: W 90 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7598 (tmtt) REVERT: X 77 PHE cc_start: 0.6310 (t80) cc_final: 0.5999 (t80) REVERT: X 96 ASP cc_start: 0.8088 (m-30) cc_final: 0.7883 (m-30) REVERT: Y 83 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.5619 (pm20) outliers start: 162 outliers final: 114 residues processed: 1111 average time/residue: 0.4246 time to fit residues: 768.8752 Evaluate side-chains 1043 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 920 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 200 VAL 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 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 278 LYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS 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 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 75 SER Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 55 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS Y 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124094 restraints weight = 64350.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128001 restraints weight = 31687.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130498 restraints weight = 19638.406| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33733 Z= 0.161 Angle : 0.681 10.026 45942 Z= 0.356 Chirality : 0.046 0.314 5080 Planarity : 0.004 0.046 5924 Dihedral : 6.490 80.705 4619 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 5.26 % Allowed : 20.29 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4240 helix: 0.23 (0.24), residues: 442 sheet: -0.83 (0.14), residues: 1124 loop : -0.39 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 236 HIS 0.012 0.001 HIS H 272 PHE 0.032 0.002 PHE H 51 TYR 0.027 0.002 TYR J 233 ARG 0.008 0.001 ARG L 220 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1197) hydrogen bonds : angle 6.32899 ( 3135) SS BOND : bond 0.00520 ( 73) SS BOND : angle 1.69711 ( 146) covalent geometry : bond 0.00365 (33660) covalent geometry : angle 0.67496 (45796) *********************** 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 1154 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 964 time to evaluate : 3.766 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: A 16 LYS cc_start: 0.8581 (mtmt) cc_final: 0.7868 (mtpt) REVERT: A 24 TYR cc_start: 0.8560 (m-80) cc_final: 0.8008 (m-80) REVERT: A 75 ASP cc_start: 0.7898 (t0) cc_final: 0.6958 (t0) REVERT: A 158 ASP cc_start: 0.8862 (t0) cc_final: 0.8619 (t0) REVERT: A 280 ILE cc_start: 0.9353 (mp) cc_final: 0.9010 (mp) REVERT: A 367 VAL cc_start: 0.9527 (t) cc_final: 0.9285 (m) REVERT: A 395 ASP cc_start: 0.8451 (t0) cc_final: 0.8101 (t0) REVERT: B 32 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7715 (tp30) REVERT: B 33 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7435 (t0) REVERT: B 70 ASP cc_start: 0.7850 (p0) cc_final: 0.7196 (p0) REVERT: B 92 ARG cc_start: 0.2499 (mtt180) cc_final: 0.1744 (mtm180) REVERT: B 114 SER cc_start: 0.9145 (m) cc_final: 0.8709 (p) REVERT: B 122 ASN cc_start: 0.8808 (m110) cc_final: 0.8575 (m-40) REVERT: B 176 TYR cc_start: 0.7314 (m-80) cc_final: 0.6616 (m-80) REVERT: B 257 ILE cc_start: 0.8297 (mt) cc_final: 0.8016 (pt) REVERT: B 278 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9054 (mttm) REVERT: B 305 ASP cc_start: 0.8855 (t0) cc_final: 0.8517 (t0) REVERT: B 330 TRP cc_start: 0.8950 (t-100) cc_final: 0.8674 (t-100) REVERT: B 332 ASN cc_start: 0.9089 (m-40) cc_final: 0.8889 (m110) REVERT: B 402 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7144 (mm) REVERT: C 32 THR cc_start: 0.9138 (m) cc_final: 0.8677 (p) REVERT: C 97 ASP cc_start: 0.8096 (p0) cc_final: 0.7802 (p0) REVERT: C 100 ASN cc_start: 0.8318 (m-40) cc_final: 0.7740 (m-40) REVERT: C 139 ASN cc_start: 0.8315 (t0) cc_final: 0.7906 (m-40) REVERT: C 262 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7665 (pt0) REVERT: C 307 ILE cc_start: 0.6223 (mt) cc_final: 0.5641 (tt) REVERT: C 308 TYR cc_start: 0.8320 (p90) cc_final: 0.8076 (p90) REVERT: C 362 GLN cc_start: 0.7825 (pm20) cc_final: 0.7518 (pm20) REVERT: C 373 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8791 (mttp) REVERT: C 409 TRP cc_start: 0.8274 (m100) cc_final: 0.7479 (m100) REVERT: D 134 PHE cc_start: 0.8971 (p90) cc_final: 0.8527 (p90) REVERT: D 139 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 195 LYS cc_start: 0.9074 (mttt) cc_final: 0.8655 (mttt) REVERT: D 272 HIS cc_start: 0.8257 (t-170) cc_final: 0.8023 (t70) REVERT: D 339 TRP cc_start: 0.8890 (m-90) cc_final: 0.8531 (m-90) REVERT: E 130 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8092 (tpp80) REVERT: E 160 GLU cc_start: 0.6732 (pm20) cc_final: 0.6354 (mp0) REVERT: E 168 MET cc_start: 0.7711 (pmm) cc_final: 0.7510 (pmm) REVERT: E 186 TRP cc_start: 0.7532 (t60) cc_final: 0.6817 (t60) REVERT: E 194 GLU cc_start: 0.8796 (tp30) cc_final: 0.8389 (tp30) REVERT: F 184 TYR cc_start: 0.6976 (m-80) cc_final: 0.6542 (m-80) REVERT: F 220 ARG cc_start: 0.7952 (ptp-170) cc_final: 0.7575 (ptp-170) REVERT: G 10 VAL cc_start: 0.9088 (t) cc_final: 0.8831 (m) REVERT: G 24 TYR cc_start: 0.8159 (m-80) cc_final: 0.7697 (m-80) REVERT: G 27 LEU cc_start: 0.8271 (tp) cc_final: 0.7925 (tp) REVERT: G 37 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7442 (mp0) REVERT: G 160 LYS cc_start: 0.9163 (pptt) cc_final: 0.8803 (mmtm) REVERT: G 170 PHE cc_start: 0.8025 (t80) cc_final: 0.7431 (t80) REVERT: G 203 ILE cc_start: 0.9095 (tt) cc_final: 0.8804 (tt) REVERT: G 206 SER cc_start: 0.9687 (m) cc_final: 0.9291 (t) REVERT: G 212 ASP cc_start: 0.8912 (p0) cc_final: 0.8577 (p0) REVERT: G 218 ASP cc_start: 0.7698 (t0) cc_final: 0.7118 (t0) REVERT: G 220 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8133 (ptp90) REVERT: G 235 GLN cc_start: 0.8777 (pt0) cc_final: 0.8234 (pt0) REVERT: G 257 PHE cc_start: 0.8538 (m-80) cc_final: 0.8176 (m-80) REVERT: G 267 ARG cc_start: 0.7344 (ptt-90) cc_final: 0.7094 (ptt-90) REVERT: G 273 TYR cc_start: 0.8456 (p90) cc_final: 0.7829 (p90) REVERT: G 362 GLN cc_start: 0.8220 (pm20) cc_final: 0.7908 (pm20) REVERT: G 364 ASN cc_start: 0.8956 (t0) cc_final: 0.8576 (t0) REVERT: H 82 LYS cc_start: 0.8554 (mttt) cc_final: 0.8311 (mtmm) REVERT: H 139 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6289 (tm-30) REVERT: H 156 ASP cc_start: 0.8318 (t0) cc_final: 0.7946 (t0) REVERT: H 158 LEU cc_start: 0.8815 (mt) cc_final: 0.8473 (mt) REVERT: H 180 LEU cc_start: 0.8871 (mt) cc_final: 0.8648 (mp) REVERT: H 186 GLU cc_start: 0.8249 (pm20) cc_final: 0.8040 (pm20) REVERT: H 200 GLU cc_start: 0.7570 (tt0) cc_final: 0.7065 (tt0) REVERT: H 305 ASP cc_start: 0.8534 (t0) cc_final: 0.8261 (t0) REVERT: H 362 ARG cc_start: 0.9101 (mtp180) cc_final: 0.8744 (mmm-85) REVERT: H 395 ASP cc_start: 0.9196 (p0) cc_final: 0.8968 (p0) REVERT: I 130 ARG cc_start: 0.7508 (mtt180) cc_final: 0.7075 (mtt180) REVERT: I 152 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7797 (mmtt) REVERT: I 192 GLN cc_start: 0.8962 (tp40) cc_final: 0.8165 (mm110) REVERT: J 9 ASN cc_start: 0.9304 (t0) cc_final: 0.8769 (t0) REVERT: J 15 TYR cc_start: 0.8156 (t80) cc_final: 0.7831 (t80) REVERT: J 37 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7531 (mm-30) REVERT: J 63 CYS cc_start: 0.5490 (t) cc_final: 0.5077 (t) REVERT: J 133 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8385 (mm) REVERT: J 218 ASP cc_start: 0.8223 (t0) cc_final: 0.7816 (t0) REVERT: J 230 HIS cc_start: 0.8749 (t-90) cc_final: 0.8248 (t-90) REVERT: J 257 PHE cc_start: 0.8374 (m-80) cc_final: 0.7969 (m-80) REVERT: J 271 CYS cc_start: 0.6342 (m) cc_final: 0.6003 (m) REVERT: J 307 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8095 (mm) REVERT: J 368 SER cc_start: 0.8627 (t) cc_final: 0.8392 (t) REVERT: J 372 LYS cc_start: 0.8761 (tptt) cc_final: 0.8501 (tppt) REVERT: J 409 TRP cc_start: 0.8506 (m100) cc_final: 0.8199 (m100) REVERT: K 37 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8440 (mt-10) REVERT: K 77 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7734 (mt-10) REVERT: K 217 MET cc_start: 0.8117 (tpp) cc_final: 0.7581 (tpp) REVERT: K 272 HIS cc_start: 0.8684 (t70) cc_final: 0.7617 (t70) REVERT: K 279 TRP cc_start: 0.9059 (p-90) cc_final: 0.8703 (p-90) REVERT: K 339 TRP cc_start: 0.8982 (m-90) cc_final: 0.7922 (m-90) REVERT: K 341 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: K 351 TRP cc_start: 0.8943 (m-10) cc_final: 0.8732 (m-10) REVERT: K 366 TYR cc_start: 0.8356 (m-80) cc_final: 0.7838 (m-80) REVERT: L 110 LYS cc_start: 0.8073 (mppt) cc_final: 0.6962 (pttm) REVERT: L 143 ASN cc_start: 0.8356 (t0) cc_final: 0.7532 (m-40) REVERT: L 145 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8482 (tm-30) REVERT: L 168 MET cc_start: 0.9225 (ppp) cc_final: 0.8805 (tmm) REVERT: W 72 CYS cc_start: 0.5269 (OUTLIER) cc_final: 0.4848 (p) REVERT: W 90 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7567 (tmtt) REVERT: X 77 PHE cc_start: 0.6410 (t80) cc_final: 0.6068 (t80) REVERT: X 96 ASP cc_start: 0.8046 (m-30) cc_final: 0.7841 (m-30) outliers start: 190 outliers final: 135 residues processed: 1060 average time/residue: 0.4236 time to fit residues: 740.9488 Evaluate side-chains 1046 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 904 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 200 VAL 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 47 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 278 LYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 53 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 363 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN C 252 GLN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS L 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117989 restraints weight = 64509.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121695 restraints weight = 32208.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124104 restraints weight = 20225.645| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 33733 Z= 0.298 Angle : 0.746 11.245 45942 Z= 0.392 Chirality : 0.048 0.355 5080 Planarity : 0.005 0.074 5924 Dihedral : 6.520 82.367 4615 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 6.45 % Allowed : 21.07 % Favored : 72.48 % 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: -0.85 (0.13), residues: 4240 helix: 0.61 (0.25), residues: 406 sheet: -0.94 (0.14), residues: 1173 loop : -0.52 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 236 HIS 0.035 0.002 HIS L 187 PHE 0.035 0.003 PHE H 51 TYR 0.026 0.002 TYR J 233 ARG 0.012 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1197) hydrogen bonds : angle 6.34223 ( 3135) SS BOND : bond 0.00438 ( 73) SS BOND : angle 1.81338 ( 146) covalent geometry : bond 0.00656 (33660) covalent geometry : angle 0.74055 (45796) *********************** 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 1140 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 907 time to evaluate : 3.684 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 16 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8489 (mtmt) REVERT: A 24 TYR cc_start: 0.8462 (m-80) cc_final: 0.8029 (m-80) REVERT: A 69 LYS cc_start: 0.9001 (ptmm) cc_final: 0.8737 (ptmt) REVERT: A 75 ASP cc_start: 0.8088 (t0) cc_final: 0.7208 (t0) REVERT: A 158 ASP cc_start: 0.8940 (t0) cc_final: 0.8705 (t0) REVERT: A 298 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: A 367 VAL cc_start: 0.9556 (t) cc_final: 0.9303 (m) REVERT: A 395 ASP cc_start: 0.8494 (t0) cc_final: 0.8163 (t0) REVERT: A 409 TRP cc_start: 0.8528 (t-100) cc_final: 0.8193 (m-90) REVERT: B 33 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7277 (t0) REVERT: B 39 ASP cc_start: 0.7828 (m-30) cc_final: 0.7385 (m-30) REVERT: B 40 ASP cc_start: 0.8415 (p0) cc_final: 0.7891 (p0) REVERT: B 70 ASP cc_start: 0.7732 (p0) cc_final: 0.6996 (p0) REVERT: B 92 ARG cc_start: 0.2929 (mtt180) cc_final: 0.1877 (mtm180) REVERT: B 156 ASP cc_start: 0.8664 (t0) cc_final: 0.8311 (t0) REVERT: B 176 TYR cc_start: 0.7426 (m-80) cc_final: 0.6586 (m-80) REVERT: B 258 PRO cc_start: 0.8996 (Cg_endo) cc_final: 0.8738 (Cg_exo) REVERT: B 278 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9119 (mttm) REVERT: B 287 LEU cc_start: 0.9497 (mt) cc_final: 0.8573 (mt) REVERT: B 305 ASP cc_start: 0.8901 (t0) cc_final: 0.8533 (t0) REVERT: B 330 TRP cc_start: 0.9045 (t-100) cc_final: 0.8452 (t-100) REVERT: B 332 ASN cc_start: 0.9125 (m-40) cc_final: 0.8917 (m110) REVERT: C 32 THR cc_start: 0.9224 (m) cc_final: 0.8772 (p) REVERT: C 97 ASP cc_start: 0.8091 (p0) cc_final: 0.7788 (p0) REVERT: C 100 ASN cc_start: 0.8354 (m-40) cc_final: 0.7779 (m-40) REVERT: C 139 ASN cc_start: 0.8341 (t0) cc_final: 0.7899 (m-40) REVERT: C 262 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7627 (pt0) REVERT: C 307 ILE cc_start: 0.6290 (mt) cc_final: 0.6074 (mt) REVERT: C 308 TYR cc_start: 0.8478 (p90) cc_final: 0.8168 (p90) REVERT: C 362 GLN cc_start: 0.8019 (pm20) cc_final: 0.7703 (pm20) REVERT: C 373 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8729 (mttp) REVERT: C 409 TRP cc_start: 0.8346 (m100) cc_final: 0.7657 (m100) REVERT: D 134 PHE cc_start: 0.9016 (p90) cc_final: 0.8580 (p90) REVERT: D 139 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8008 (mm-30) REVERT: D 242 ASP cc_start: 0.8700 (m-30) cc_final: 0.8444 (m-30) REVERT: D 272 HIS cc_start: 0.8339 (t-170) cc_final: 0.8094 (t70) REVERT: E 130 ARG cc_start: 0.8440 (tpp80) cc_final: 0.8122 (tpp80) REVERT: E 160 GLU cc_start: 0.6533 (pm20) cc_final: 0.6175 (mp0) REVERT: E 194 GLU cc_start: 0.8818 (tp30) cc_final: 0.8556 (mm-30) REVERT: F 184 TYR cc_start: 0.7059 (m-80) cc_final: 0.6748 (m-80) REVERT: F 186 TRP cc_start: 0.7855 (t60) cc_final: 0.7446 (t60) REVERT: F 218 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8028 (ptp-110) REVERT: G 10 VAL cc_start: 0.9034 (t) cc_final: 0.8808 (m) REVERT: G 24 TYR cc_start: 0.8140 (m-80) cc_final: 0.7920 (m-80) REVERT: G 37 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7548 (mp0) REVERT: G 62 CYS cc_start: 0.4456 (m) cc_final: 0.4252 (m) REVERT: G 160 LYS cc_start: 0.9181 (pptt) cc_final: 0.8660 (mmtm) REVERT: G 170 PHE cc_start: 0.8130 (t80) cc_final: 0.7399 (t80) REVERT: G 203 ILE cc_start: 0.9115 (tt) cc_final: 0.8799 (tt) REVERT: G 218 ASP cc_start: 0.7721 (t0) cc_final: 0.7278 (t0) REVERT: G 220 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8217 (ptp90) REVERT: G 257 PHE cc_start: 0.8567 (m-80) cc_final: 0.8125 (m-80) REVERT: G 273 TYR cc_start: 0.8618 (p90) cc_final: 0.7970 (p90) REVERT: G 281 ASP cc_start: 0.8835 (t0) cc_final: 0.8038 (p0) REVERT: G 324 ARG cc_start: 0.7645 (ptp-170) cc_final: 0.7371 (ptp90) REVERT: G 362 GLN cc_start: 0.8399 (pm20) cc_final: 0.8090 (pm20) REVERT: G 364 ASN cc_start: 0.8966 (t0) cc_final: 0.8519 (t0) REVERT: H 82 LYS cc_start: 0.8702 (mttt) cc_final: 0.7973 (mttm) REVERT: H 139 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: H 200 GLU cc_start: 0.7535 (tt0) cc_final: 0.7152 (tt0) REVERT: H 305 ASP cc_start: 0.8680 (t0) cc_final: 0.8403 (t0) REVERT: H 395 ASP cc_start: 0.9205 (p0) cc_final: 0.9003 (p0) REVERT: I 152 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7915 (mmtt) REVERT: J 9 ASN cc_start: 0.9376 (t0) cc_final: 0.8850 (t0) REVERT: J 15 TYR cc_start: 0.8255 (t80) cc_final: 0.7923 (t80) REVERT: J 133 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8392 (mm) REVERT: J 195 MET cc_start: 0.9033 (mpp) cc_final: 0.8676 (mpp) REVERT: J 218 ASP cc_start: 0.8451 (t0) cc_final: 0.7996 (t0) REVERT: J 230 HIS cc_start: 0.8905 (t-90) cc_final: 0.8432 (t-90) REVERT: J 257 PHE cc_start: 0.8576 (m-80) cc_final: 0.7811 (m-80) REVERT: J 271 CYS cc_start: 0.6575 (m) cc_final: 0.6255 (m) REVERT: J 303 VAL cc_start: 0.8287 (p) cc_final: 0.7504 (m) REVERT: J 307 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8243 (mm) REVERT: J 308 TYR cc_start: 0.7924 (p90) cc_final: 0.7620 (p90) REVERT: J 372 LYS cc_start: 0.8817 (tptt) cc_final: 0.8431 (tppt) REVERT: J 385 ASP cc_start: 0.7998 (p0) cc_final: 0.7766 (p0) REVERT: J 390 GLU cc_start: 0.8429 (tp30) cc_final: 0.7423 (tt0) REVERT: J 409 TRP cc_start: 0.8551 (m100) cc_final: 0.8311 (m100) REVERT: K 38 SER cc_start: 0.9368 (t) cc_final: 0.8985 (p) REVERT: K 168 MET cc_start: 0.8649 (mmp) cc_final: 0.8241 (mmm) REVERT: K 279 TRP cc_start: 0.9120 (p-90) cc_final: 0.8690 (p-90) REVERT: K 341 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8177 (mm110) REVERT: K 351 TRP cc_start: 0.9018 (m-10) cc_final: 0.8791 (m-10) REVERT: L 110 LYS cc_start: 0.8133 (mppt) cc_final: 0.7004 (pttm) REVERT: L 143 ASN cc_start: 0.8551 (t0) cc_final: 0.7613 (m-40) REVERT: L 145 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8439 (tm-30) REVERT: L 168 MET cc_start: 0.9275 (ppp) cc_final: 0.8864 (tmm) REVERT: W 72 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4998 (p) REVERT: X 60 ASP cc_start: 0.8704 (t0) cc_final: 0.7553 (p0) REVERT: X 96 ASP cc_start: 0.8094 (m-30) cc_final: 0.7837 (m-30) outliers start: 233 outliers final: 179 residues processed: 1030 average time/residue: 0.4163 time to fit residues: 705.4599 Evaluate side-chains 1042 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 856 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 236 TRP Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 278 LYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 315 THR Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 195 ASN Chi-restraints excluded: chain L residue 217 ASN Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 103 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 345 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 171 optimal weight: 0.0870 chunk 258 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 186 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 HIS I 117 ASN ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS Y 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.159092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123811 restraints weight = 64538.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127732 restraints weight = 31567.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130241 restraints weight = 19534.957| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33733 Z= 0.140 Angle : 0.694 11.093 45942 Z= 0.358 Chirality : 0.047 0.354 5080 Planarity : 0.005 0.055 5924 Dihedral : 6.286 81.714 4614 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 5.01 % Allowed : 23.50 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4240 helix: 0.68 (0.25), residues: 412 sheet: -0.87 (0.14), residues: 1153 loop : -0.47 (0.12), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 89 HIS 0.017 0.001 HIS K 146 PHE 0.030 0.002 PHE I 198 TYR 0.030 0.002 TYR D 238 ARG 0.006 0.001 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1197) hydrogen bonds : angle 6.16274 ( 3135) SS BOND : bond 0.00340 ( 73) SS BOND : angle 1.84614 ( 146) covalent geometry : bond 0.00319 (33660) covalent geometry : angle 0.68684 (45796) *********************** 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 1148 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 967 time to evaluate : 3.442 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 10 VAL cc_start: 0.9460 (t) cc_final: 0.9260 (m) REVERT: A 24 TYR cc_start: 0.8554 (m-80) cc_final: 0.8216 (m-80) REVERT: A 69 LYS cc_start: 0.8939 (ptmm) cc_final: 0.8696 (ptmt) REVERT: A 75 ASP cc_start: 0.7819 (t0) cc_final: 0.6892 (t0) REVERT: A 262 GLU cc_start: 0.8569 (tt0) cc_final: 0.8226 (tt0) REVERT: A 264 GLU cc_start: 0.8359 (mp0) cc_final: 0.8058 (mp0) REVERT: A 395 ASP cc_start: 0.8430 (t0) cc_final: 0.8031 (t0) REVERT: A 409 TRP cc_start: 0.8492 (t-100) cc_final: 0.8199 (m-90) REVERT: B 30 LYS cc_start: 0.9055 (tptt) cc_final: 0.8627 (tptt) REVERT: B 32 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7693 (tp30) REVERT: B 33 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7412 (t0) REVERT: B 70 ASP cc_start: 0.7655 (p0) cc_final: 0.6951 (p0) REVERT: B 92 ARG cc_start: 0.2654 (mtt180) cc_final: 0.1668 (mtm180) REVERT: B 169 HIS cc_start: 0.8227 (m170) cc_final: 0.7978 (m-70) REVERT: B 176 TYR cc_start: 0.7413 (m-80) cc_final: 0.6668 (m-80) REVERT: B 287 LEU cc_start: 0.9410 (mt) cc_final: 0.8839 (mp) REVERT: B 305 ASP cc_start: 0.8866 (t0) cc_final: 0.8503 (t0) REVERT: B 319 PHE cc_start: 0.8197 (m-10) cc_final: 0.7937 (m-10) REVERT: B 329 VAL cc_start: 0.9391 (t) cc_final: 0.9178 (m) REVERT: B 330 TRP cc_start: 0.8951 (t-100) cc_final: 0.8553 (t-100) REVERT: B 332 ASN cc_start: 0.9058 (m-40) cc_final: 0.8855 (m-40) REVERT: C 32 THR cc_start: 0.9169 (m) cc_final: 0.8779 (p) REVERT: C 97 ASP cc_start: 0.8127 (p0) cc_final: 0.7882 (p0) REVERT: C 100 ASN cc_start: 0.8270 (m-40) cc_final: 0.7902 (m-40) REVERT: C 139 ASN cc_start: 0.8291 (t0) cc_final: 0.7851 (m-40) REVERT: C 221 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8861 (mt) REVERT: C 262 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7666 (pt0) REVERT: C 307 ILE cc_start: 0.6304 (mt) cc_final: 0.5642 (tt) REVERT: C 308 TYR cc_start: 0.8383 (p90) cc_final: 0.8104 (p90) REVERT: C 362 GLN cc_start: 0.7777 (pm20) cc_final: 0.7479 (pm20) REVERT: C 373 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8704 (mttp) REVERT: C 409 TRP cc_start: 0.8320 (m100) cc_final: 0.7576 (m100) REVERT: D 18 TYR cc_start: 0.8511 (t80) cc_final: 0.8256 (t80) REVERT: D 134 PHE cc_start: 0.8974 (p90) cc_final: 0.8613 (p90) REVERT: D 137 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8073 (ptp90) REVERT: D 139 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7980 (mm-30) REVERT: D 195 LYS cc_start: 0.9004 (mttt) cc_final: 0.8790 (mttt) REVERT: D 272 HIS cc_start: 0.8211 (t-170) cc_final: 0.7796 (t70) REVERT: D 323 ARG cc_start: 0.9204 (ptm160) cc_final: 0.8992 (ptm160) REVERT: D 339 TRP cc_start: 0.8881 (m-90) cc_final: 0.8622 (m-90) REVERT: E 130 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8114 (tpp80) REVERT: E 132 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7722 (mtp) REVERT: E 186 TRP cc_start: 0.7598 (t60) cc_final: 0.6629 (t60) REVERT: E 194 GLU cc_start: 0.8734 (tp30) cc_final: 0.8477 (tp30) REVERT: E 195 ASN cc_start: 0.8965 (p0) cc_final: 0.8647 (p0) REVERT: F 127 VAL cc_start: 0.8910 (t) cc_final: 0.8663 (m) REVERT: F 186 TRP cc_start: 0.7838 (t60) cc_final: 0.7454 (t60) REVERT: F 214 ILE cc_start: 0.8872 (mm) cc_final: 0.8607 (pt) REVERT: F 218 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8022 (ptp-110) REVERT: F 243 ASN cc_start: 0.8482 (t0) cc_final: 0.8269 (t0) REVERT: G 10 VAL cc_start: 0.9040 (t) cc_final: 0.8764 (m) REVERT: G 24 TYR cc_start: 0.7973 (m-80) cc_final: 0.7678 (m-80) REVERT: G 27 LEU cc_start: 0.8290 (tp) cc_final: 0.7860 (tp) REVERT: G 37 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7484 (mp0) REVERT: G 62 CYS cc_start: 0.4846 (m) cc_final: 0.4430 (m) REVERT: G 160 LYS cc_start: 0.9153 (pptt) cc_final: 0.8648 (mmtm) REVERT: G 162 ILE cc_start: 0.8592 (mt) cc_final: 0.8080 (mm) REVERT: G 170 PHE cc_start: 0.8003 (t80) cc_final: 0.7345 (t80) REVERT: G 203 ILE cc_start: 0.9062 (tt) cc_final: 0.8749 (tt) REVERT: G 218 ASP cc_start: 0.7604 (t0) cc_final: 0.7165 (t0) REVERT: G 220 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8153 (ptp90) REVERT: G 273 TYR cc_start: 0.8638 (p90) cc_final: 0.8053 (p90) REVERT: G 281 ASP cc_start: 0.8783 (t0) cc_final: 0.7959 (p0) REVERT: G 354 LEU cc_start: 0.8628 (tp) cc_final: 0.8365 (tp) REVERT: G 364 ASN cc_start: 0.8892 (t0) cc_final: 0.8447 (t0) REVERT: H 82 LYS cc_start: 0.8588 (mttt) cc_final: 0.7933 (mttm) REVERT: H 139 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6238 (tm-30) REVERT: H 156 ASP cc_start: 0.8400 (t0) cc_final: 0.8039 (t0) REVERT: H 200 GLU cc_start: 0.7596 (tt0) cc_final: 0.7244 (tt0) REVERT: H 305 ASP cc_start: 0.8631 (t0) cc_final: 0.8403 (t0) REVERT: H 361 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7993 (t-90) REVERT: H 395 ASP cc_start: 0.9138 (p0) cc_final: 0.8920 (p0) REVERT: I 115 MET cc_start: 0.6571 (mmp) cc_final: 0.5912 (mmm) REVERT: I 130 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7223 (mtt180) REVERT: I 152 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8008 (mmtt) REVERT: I 212 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.7651 (mmm-85) REVERT: J 9 ASN cc_start: 0.9347 (t0) cc_final: 0.8796 (t0) REVERT: J 15 TYR cc_start: 0.8185 (t80) cc_final: 0.7836 (t80) REVERT: J 133 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8420 (mm) REVERT: J 218 ASP cc_start: 0.8291 (t0) cc_final: 0.7819 (t0) REVERT: J 230 HIS cc_start: 0.8762 (t-90) cc_final: 0.8543 (t70) REVERT: J 257 PHE cc_start: 0.8410 (m-80) cc_final: 0.7811 (m-80) REVERT: J 271 CYS cc_start: 0.6430 (m) cc_final: 0.6040 (m) REVERT: J 307 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8011 (mm) REVERT: J 362 GLN cc_start: 0.8118 (tp40) cc_final: 0.7902 (tp-100) REVERT: J 368 SER cc_start: 0.8621 (t) cc_final: 0.8369 (t) REVERT: J 372 LYS cc_start: 0.8764 (tptt) cc_final: 0.8353 (tppt) REVERT: J 376 CYS cc_start: 0.4838 (t) cc_final: 0.4301 (t) REVERT: J 390 GLU cc_start: 0.8327 (tp30) cc_final: 0.7446 (tt0) REVERT: J 409 TRP cc_start: 0.8452 (m100) cc_final: 0.8126 (m100) REVERT: K 38 SER cc_start: 0.9234 (t) cc_final: 0.8939 (p) REVERT: K 168 MET cc_start: 0.8358 (mmp) cc_final: 0.7992 (mmp) REVERT: K 170 ARG cc_start: 0.8474 (ptp-170) cc_final: 0.8250 (ptp-170) REVERT: K 217 MET cc_start: 0.8140 (tpp) cc_final: 0.7519 (tpp) REVERT: K 279 TRP cc_start: 0.9080 (p-90) cc_final: 0.8729 (p-90) REVERT: K 366 TYR cc_start: 0.8290 (m-80) cc_final: 0.7897 (m-80) REVERT: L 143 ASN cc_start: 0.8538 (t0) cc_final: 0.7748 (m110) REVERT: L 168 MET cc_start: 0.9209 (ppp) cc_final: 0.8914 (tmm) REVERT: L 250 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7289 (mtmt) REVERT: V 99 ASP cc_start: 0.6945 (p0) cc_final: 0.6675 (p0) REVERT: W 72 CYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4853 (p) REVERT: X 77 PHE cc_start: 0.5964 (t80) cc_final: 0.5466 (t80) REVERT: X 96 ASP cc_start: 0.8014 (m-30) cc_final: 0.7780 (m-30) REVERT: Y 83 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5183 (pm20) outliers start: 181 outliers final: 140 residues processed: 1058 average time/residue: 0.4164 time to fit residues: 726.4037 Evaluate side-chains 1039 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 889 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 278 LYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN 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 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 75 SER Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 168 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 0.0170 chunk 14 optimal weight: 0.8980 chunk 284 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 1.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 246 ASN D 33 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS W 37 GLN ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.158869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123464 restraints weight = 64621.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127352 restraints weight = 31917.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129823 restraints weight = 19826.312| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33733 Z= 0.162 Angle : 0.689 11.993 45942 Z= 0.356 Chirality : 0.047 0.246 5080 Planarity : 0.005 0.056 5924 Dihedral : 6.162 81.618 4614 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 5.32 % Allowed : 23.03 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4240 helix: 0.96 (0.26), residues: 386 sheet: -0.85 (0.14), residues: 1158 loop : -0.42 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 330 HIS 0.009 0.001 HIS D 73 PHE 0.041 0.002 PHE B 100 TYR 0.033 0.002 TYR C 185 ARG 0.007 0.001 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1197) hydrogen bonds : angle 6.05108 ( 3135) SS BOND : bond 0.00386 ( 73) SS BOND : angle 1.67294 ( 146) covalent geometry : bond 0.00368 (33660) covalent geometry : angle 0.68396 (45796) *********************** 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 1094 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 902 time to evaluate : 3.543 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: A 10 VAL cc_start: 0.9478 (t) cc_final: 0.9250 (m) REVERT: A 16 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8288 (mtmt) REVERT: A 75 ASP cc_start: 0.7842 (t0) cc_final: 0.6919 (t0) REVERT: A 264 GLU cc_start: 0.8433 (mp0) cc_final: 0.8083 (mp0) REVERT: A 395 ASP cc_start: 0.8429 (t0) cc_final: 0.8018 (t0) REVERT: A 409 TRP cc_start: 0.8528 (t-100) cc_final: 0.8249 (t-100) REVERT: B 32 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7821 (tp30) REVERT: B 33 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7394 (t0) REVERT: B 70 ASP cc_start: 0.7682 (p0) cc_final: 0.6958 (p0) REVERT: B 92 ARG cc_start: 0.2815 (mtt180) cc_final: 0.1820 (mtm180) REVERT: B 176 TYR cc_start: 0.7453 (m-80) cc_final: 0.6656 (m-80) REVERT: B 287 LEU cc_start: 0.9433 (mt) cc_final: 0.8850 (mp) REVERT: B 305 ASP cc_start: 0.8867 (t0) cc_final: 0.8508 (t0) REVERT: B 319 PHE cc_start: 0.8166 (m-10) cc_final: 0.7918 (m-10) REVERT: B 329 VAL cc_start: 0.9452 (t) cc_final: 0.9208 (m) REVERT: B 330 TRP cc_start: 0.8950 (t-100) cc_final: 0.8549 (t-100) REVERT: B 342 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8491 (mm-30) REVERT: C 32 THR cc_start: 0.9190 (m) cc_final: 0.8811 (p) REVERT: C 97 ASP cc_start: 0.8161 (p0) cc_final: 0.7826 (p0) REVERT: C 186 ASN cc_start: 0.7505 (p0) cc_final: 0.7287 (p0) REVERT: C 221 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8868 (mt) REVERT: C 262 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7719 (pt0) REVERT: C 307 ILE cc_start: 0.6239 (mt) cc_final: 0.5562 (tt) REVERT: C 308 TYR cc_start: 0.8370 (p90) cc_final: 0.8141 (p90) REVERT: C 331 HIS cc_start: 0.8557 (t-90) cc_final: 0.8336 (t-90) REVERT: C 362 GLN cc_start: 0.7779 (pm20) cc_final: 0.7454 (pm20) REVERT: C 373 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8621 (mttp) REVERT: C 409 TRP cc_start: 0.8315 (m100) cc_final: 0.7558 (m100) REVERT: D 134 PHE cc_start: 0.8962 (p90) cc_final: 0.8511 (p90) REVERT: D 137 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8104 (ptp90) REVERT: D 139 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 195 LYS cc_start: 0.9114 (mttt) cc_final: 0.8844 (mttt) REVERT: D 272 HIS cc_start: 0.8143 (t-170) cc_final: 0.7694 (t70) REVERT: D 323 ARG cc_start: 0.9234 (ptm160) cc_final: 0.9004 (ptm160) REVERT: E 130 ARG cc_start: 0.8598 (tpp80) cc_final: 0.8164 (tpp80) REVERT: E 140 LYS cc_start: 0.7305 (tptp) cc_final: 0.7040 (tptt) REVERT: E 160 GLU cc_start: 0.6239 (mp0) cc_final: 0.5973 (mp0) REVERT: E 194 GLU cc_start: 0.8742 (tp30) cc_final: 0.8462 (mm-30) REVERT: E 195 ASN cc_start: 0.8974 (p0) cc_final: 0.8660 (p0) REVERT: F 127 VAL cc_start: 0.8911 (t) cc_final: 0.8681 (m) REVERT: F 156 MET cc_start: 0.8798 (tmm) cc_final: 0.8009 (pmm) REVERT: F 157 TYR cc_start: 0.7758 (m-80) cc_final: 0.6773 (m-80) REVERT: F 214 ILE cc_start: 0.8952 (mm) cc_final: 0.8709 (pt) REVERT: F 218 ARG cc_start: 0.8571 (mtp85) cc_final: 0.7965 (ptp-110) REVERT: F 243 ASN cc_start: 0.8653 (t0) cc_final: 0.8400 (t0) REVERT: G 10 VAL cc_start: 0.9078 (t) cc_final: 0.8818 (m) REVERT: G 24 TYR cc_start: 0.8021 (m-80) cc_final: 0.7710 (m-80) REVERT: G 37 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7527 (mp0) REVERT: G 62 CYS cc_start: 0.4580 (m) cc_final: 0.4275 (m) REVERT: G 160 LYS cc_start: 0.9138 (pptt) cc_final: 0.8631 (mmtm) REVERT: G 162 ILE cc_start: 0.8535 (mt) cc_final: 0.8044 (mm) REVERT: G 170 PHE cc_start: 0.7896 (t80) cc_final: 0.7463 (t80) REVERT: G 204 GLN cc_start: 0.8014 (mt0) cc_final: 0.7523 (mt0) REVERT: G 218 ASP cc_start: 0.7629 (t0) cc_final: 0.7189 (t0) REVERT: G 220 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.8175 (ptp90) REVERT: G 257 PHE cc_start: 0.8376 (m-80) cc_final: 0.7949 (m-80) REVERT: G 273 TYR cc_start: 0.8587 (p90) cc_final: 0.8266 (p90) REVERT: G 281 ASP cc_start: 0.8745 (t0) cc_final: 0.7946 (p0) REVERT: G 354 LEU cc_start: 0.8648 (tp) cc_final: 0.8384 (tp) REVERT: G 364 ASN cc_start: 0.8899 (t0) cc_final: 0.8429 (t0) REVERT: H 82 LYS cc_start: 0.8516 (mttt) cc_final: 0.8105 (mtmm) REVERT: H 139 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: H 155 TYR cc_start: 0.7709 (m-80) cc_final: 0.7345 (m-80) REVERT: H 156 ASP cc_start: 0.8392 (t0) cc_final: 0.8162 (t0) REVERT: H 270 LEU cc_start: 0.9290 (tp) cc_final: 0.9062 (tp) REVERT: H 305 ASP cc_start: 0.8669 (t0) cc_final: 0.8442 (t0) REVERT: H 395 ASP cc_start: 0.9151 (p0) cc_final: 0.8932 (p0) REVERT: I 130 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7272 (mtt180) REVERT: I 152 LYS cc_start: 0.8469 (ttpt) cc_final: 0.7999 (mmtt) REVERT: I 212 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.7679 (mmm-85) REVERT: J 9 ASN cc_start: 0.9360 (t0) cc_final: 0.8922 (t0) REVERT: J 15 TYR cc_start: 0.8248 (t80) cc_final: 0.7884 (t80) REVERT: J 133 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8481 (mm) REVERT: J 195 MET cc_start: 0.8797 (mpp) cc_final: 0.8193 (mpp) REVERT: J 218 ASP cc_start: 0.8329 (t0) cc_final: 0.7875 (t0) REVERT: J 230 HIS cc_start: 0.8727 (t-90) cc_final: 0.8501 (t70) REVERT: J 257 PHE cc_start: 0.8481 (m-80) cc_final: 0.7881 (m-80) REVERT: J 271 CYS cc_start: 0.6480 (m) cc_final: 0.6085 (m) REVERT: J 307 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7990 (mm) REVERT: J 333 HIS cc_start: 0.7814 (m90) cc_final: 0.7559 (m-70) REVERT: J 368 SER cc_start: 0.8615 (t) cc_final: 0.6737 (p) REVERT: J 372 LYS cc_start: 0.8727 (tptt) cc_final: 0.8304 (tppt) REVERT: J 390 GLU cc_start: 0.8361 (tp30) cc_final: 0.7420 (tt0) REVERT: J 409 TRP cc_start: 0.8414 (m100) cc_final: 0.8199 (m100) REVERT: K 38 SER cc_start: 0.9218 (t) cc_final: 0.8868 (p) REVERT: K 78 ASP cc_start: 0.8627 (t0) cc_final: 0.8359 (t70) REVERT: K 91 CYS cc_start: 0.6961 (m) cc_final: 0.6745 (m) REVERT: K 168 MET cc_start: 0.8491 (mmp) cc_final: 0.7853 (mmp) REVERT: K 279 TRP cc_start: 0.9122 (p-90) cc_final: 0.8726 (p-90) REVERT: K 366 TYR cc_start: 0.8307 (m-80) cc_final: 0.7915 (m-80) REVERT: L 110 LYS cc_start: 0.8031 (mppt) cc_final: 0.6981 (pttm) REVERT: L 143 ASN cc_start: 0.8577 (t0) cc_final: 0.8339 (t0) REVERT: L 168 MET cc_start: 0.9244 (ppp) cc_final: 0.8944 (tmm) REVERT: L 250 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7224 (mtmt) REVERT: V 99 ASP cc_start: 0.6348 (p0) cc_final: 0.5979 (p0) REVERT: W 72 CYS cc_start: 0.5256 (OUTLIER) cc_final: 0.4901 (p) REVERT: W 106 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: X 77 PHE cc_start: 0.6314 (t80) cc_final: 0.5771 (t80) REVERT: X 96 ASP cc_start: 0.8027 (m-30) cc_final: 0.7782 (m-30) REVERT: Y 83 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5133 (pm20) outliers start: 192 outliers final: 152 residues processed: 1002 average time/residue: 0.4141 time to fit residues: 686.0736 Evaluate side-chains 1028 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 867 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 176 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 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 195 ASN Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 236 optimal weight: 30.0000 chunk 375 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 343 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 398 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS G 386 HIS ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 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 = 0.3872 r_free = 0.3872 target = 0.151449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115882 restraints weight = 65131.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119538 restraints weight = 32669.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121890 restraints weight = 20542.282| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 33733 Z= 0.354 Angle : 0.801 12.536 45942 Z= 0.419 Chirality : 0.049 0.247 5080 Planarity : 0.006 0.064 5924 Dihedral : 6.488 82.774 4613 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 5.92 % Allowed : 22.81 % Favored : 71.26 % 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: -1.00 (0.13), residues: 4240 helix: 0.50 (0.25), residues: 423 sheet: -1.03 (0.14), residues: 1164 loop : -0.63 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 310 HIS 0.037 0.002 HIS L 187 PHE 0.029 0.003 PHE B 100 TYR 0.022 0.003 TYR C 308 ARG 0.009 0.001 ARG W 88 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1197) hydrogen bonds : angle 6.26067 ( 3135) SS BOND : bond 0.00520 ( 73) SS BOND : angle 1.83353 ( 146) covalent geometry : bond 0.00785 (33660) covalent geometry : angle 0.79509 (45796) *********************** 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 1062 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 848 time to evaluate : 3.696 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 16 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8333 (mtmt) REVERT: A 75 ASP cc_start: 0.8030 (t0) cc_final: 0.7156 (t0) REVERT: A 158 ASP cc_start: 0.8636 (t0) cc_final: 0.8389 (t0) REVERT: A 264 GLU cc_start: 0.8482 (mp0) cc_final: 0.8244 (mp0) REVERT: A 395 ASP cc_start: 0.8557 (t0) cc_final: 0.8251 (t0) REVERT: A 409 TRP cc_start: 0.8522 (t-100) cc_final: 0.8282 (t-100) REVERT: B 33 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.7150 (t0) REVERT: B 39 ASP cc_start: 0.7883 (m-30) cc_final: 0.7447 (m-30) REVERT: B 40 ASP cc_start: 0.8447 (p0) cc_final: 0.7974 (p0) REVERT: B 70 ASP cc_start: 0.7765 (p0) cc_final: 0.7087 (p0) REVERT: B 92 ARG cc_start: 0.3009 (mtt180) cc_final: 0.1942 (mtm180) REVERT: B 176 TYR cc_start: 0.7526 (m-80) cc_final: 0.6764 (m-80) REVERT: B 287 LEU cc_start: 0.9533 (mt) cc_final: 0.9067 (mp) REVERT: B 305 ASP cc_start: 0.8845 (t0) cc_final: 0.8480 (t0) REVERT: B 330 TRP cc_start: 0.9147 (t-100) cc_final: 0.8722 (t-100) REVERT: C 32 THR cc_start: 0.9226 (m) cc_final: 0.8840 (p) REVERT: C 97 ASP cc_start: 0.8122 (p0) cc_final: 0.7838 (p0) REVERT: C 100 ASN cc_start: 0.8099 (m-40) cc_final: 0.7646 (m-40) REVERT: C 139 ASN cc_start: 0.8384 (t0) cc_final: 0.7991 (m-40) REVERT: C 262 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7637 (pt0) REVERT: C 308 TYR cc_start: 0.8518 (p90) cc_final: 0.8238 (p90) REVERT: C 362 GLN cc_start: 0.8055 (pm20) cc_final: 0.7760 (pm20) REVERT: C 364 ASN cc_start: 0.8809 (t0) cc_final: 0.8552 (t0) REVERT: C 373 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8666 (mttp) REVERT: C 390 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 409 TRP cc_start: 0.8356 (m100) cc_final: 0.7687 (m100) REVERT: D 131 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7921 (ptp-110) REVERT: D 134 PHE cc_start: 0.8948 (p90) cc_final: 0.8537 (p90) REVERT: D 137 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8309 (ptm160) REVERT: D 272 HIS cc_start: 0.8306 (t-170) cc_final: 0.7915 (t70) REVERT: E 132 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: E 160 GLU cc_start: 0.6396 (mp0) cc_final: 0.6059 (mp0) REVERT: E 194 GLU cc_start: 0.8700 (tp30) cc_final: 0.8420 (mm-30) REVERT: F 186 TRP cc_start: 0.7843 (t60) cc_final: 0.7525 (t60) REVERT: F 243 ASN cc_start: 0.8730 (t0) cc_final: 0.8404 (t0) REVERT: G 10 VAL cc_start: 0.9113 (t) cc_final: 0.8848 (m) REVERT: G 24 TYR cc_start: 0.8236 (m-80) cc_final: 0.7996 (m-80) REVERT: G 27 LEU cc_start: 0.8400 (tp) cc_final: 0.8104 (tp) REVERT: G 37 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7549 (mp0) REVERT: G 45 GLU cc_start: 0.8766 (tp30) cc_final: 0.8544 (tp30) REVERT: G 157 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7427 (tmm-80) REVERT: G 160 LYS cc_start: 0.9161 (pptt) cc_final: 0.8626 (mmtm) REVERT: G 170 PHE cc_start: 0.8046 (t80) cc_final: 0.7501 (t80) REVERT: G 204 GLN cc_start: 0.8267 (mt0) cc_final: 0.7678 (mt0) REVERT: G 216 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8038 (ttm-80) REVERT: G 218 ASP cc_start: 0.7757 (t0) cc_final: 0.7379 (t0) REVERT: G 220 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8318 (ptp90) REVERT: G 257 PHE cc_start: 0.8475 (m-80) cc_final: 0.8059 (m-80) REVERT: G 273 TYR cc_start: 0.8673 (p90) cc_final: 0.8236 (p90) REVERT: G 281 ASP cc_start: 0.8800 (t0) cc_final: 0.8037 (p0) REVERT: G 354 LEU cc_start: 0.8685 (tp) cc_final: 0.8417 (tp) REVERT: H 82 LYS cc_start: 0.8688 (mttt) cc_final: 0.8016 (mttm) REVERT: H 139 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: H 272 HIS cc_start: 0.8173 (t70) cc_final: 0.7761 (t70) REVERT: H 395 ASP cc_start: 0.9157 (p0) cc_final: 0.8914 (p0) REVERT: I 130 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7285 (mtt180) REVERT: I 136 HIS cc_start: 0.7513 (p90) cc_final: 0.7258 (p90) REVERT: I 152 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7870 (mmtt) REVERT: I 212 ARG cc_start: 0.8817 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: J 9 ASN cc_start: 0.9402 (t0) cc_final: 0.8850 (t0) REVERT: J 15 TYR cc_start: 0.8298 (t80) cc_final: 0.8000 (t80) REVERT: J 133 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8435 (mm) REVERT: J 218 ASP cc_start: 0.8563 (t0) cc_final: 0.8131 (t0) REVERT: J 307 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (mm) REVERT: J 316 LEU cc_start: 0.8040 (pt) cc_final: 0.7702 (pt) REVERT: J 333 HIS cc_start: 0.7993 (m90) cc_final: 0.7748 (m-70) REVERT: J 372 LYS cc_start: 0.8825 (tptt) cc_final: 0.8533 (tppt) REVERT: J 409 TRP cc_start: 0.8608 (m100) cc_final: 0.8327 (m100) REVERT: K 279 TRP cc_start: 0.9161 (p-90) cc_final: 0.8700 (p-90) REVERT: L 110 LYS cc_start: 0.8104 (mppt) cc_final: 0.7047 (pttm) REVERT: L 156 MET cc_start: 0.8940 (ppp) cc_final: 0.8546 (ppp) REVERT: L 168 MET cc_start: 0.9264 (ppp) cc_final: 0.8896 (tmm) REVERT: L 187 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.7905 (t-170) REVERT: L 212 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6728 (mtp180) REVERT: W 72 CYS cc_start: 0.5537 (OUTLIER) cc_final: 0.5184 (p) REVERT: W 88 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7782 (ttm-80) REVERT: X 60 ASP cc_start: 0.8748 (t0) cc_final: 0.8240 (t0) REVERT: X 77 PHE cc_start: 0.6794 (t80) cc_final: 0.6441 (t80) REVERT: Y 83 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5131 (pm20) outliers start: 214 outliers final: 177 residues processed: 963 average time/residue: 0.4113 time to fit residues: 649.5749 Evaluate side-chains 999 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 811 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 176 THR 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 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 117 ASN Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN 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 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 195 ASN Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 201 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 387 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 395 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 246 ASN C 408 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 HIS ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 332 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.156720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121284 restraints weight = 64284.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125099 restraints weight = 31834.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127546 restraints weight = 19862.442| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33733 Z= 0.174 Angle : 0.734 12.145 45942 Z= 0.377 Chirality : 0.047 0.265 5080 Planarity : 0.005 0.082 5924 Dihedral : 6.309 81.177 4613 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 4.82 % Allowed : 24.39 % Favored : 70.79 % 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: -0.90 (0.13), residues: 4240 helix: 0.63 (0.25), residues: 426 sheet: -1.05 (0.14), residues: 1157 loop : -0.53 (0.13), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 89 HIS 0.009 0.001 HIS L 187 PHE 0.027 0.002 PHE W 38 TYR 0.037 0.002 TYR C 185 ARG 0.006 0.001 ARG W 88 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 1197) hydrogen bonds : angle 6.09238 ( 3135) SS BOND : bond 0.00406 ( 73) SS BOND : angle 1.71536 ( 146) covalent geometry : bond 0.00395 (33660) covalent geometry : angle 0.72868 (45796) *********************** 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 1057 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 883 time to evaluate : 3.532 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: A 10 VAL cc_start: 0.9524 (t) cc_final: 0.9273 (m) REVERT: A 16 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8250 (mtmt) REVERT: A 75 ASP cc_start: 0.7849 (t0) cc_final: 0.6941 (t0) REVERT: A 158 ASP cc_start: 0.8692 (t0) cc_final: 0.8337 (t0) REVERT: A 252 GLN cc_start: 0.8891 (mp10) cc_final: 0.8507 (mm-40) REVERT: A 264 GLU cc_start: 0.8527 (mp0) cc_final: 0.8256 (mp0) REVERT: A 395 ASP cc_start: 0.8511 (t0) cc_final: 0.8152 (t0) REVERT: A 409 TRP cc_start: 0.8495 (t-100) cc_final: 0.8253 (t-100) REVERT: B 30 LYS cc_start: 0.9201 (tptt) cc_final: 0.8067 (tttt) REVERT: B 33 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7280 (t0) REVERT: B 40 ASP cc_start: 0.8495 (p0) cc_final: 0.8158 (p0) REVERT: B 70 ASP cc_start: 0.7698 (p0) cc_final: 0.6939 (p0) REVERT: B 92 ARG cc_start: 0.2728 (mtt180) cc_final: 0.1628 (mtm180) REVERT: B 176 TYR cc_start: 0.7390 (m-80) cc_final: 0.6645 (m-80) REVERT: B 287 LEU cc_start: 0.9445 (mt) cc_final: 0.8998 (mp) REVERT: B 305 ASP cc_start: 0.8840 (t0) cc_final: 0.8447 (t0) REVERT: B 319 PHE cc_start: 0.8242 (m-10) cc_final: 0.8023 (m-10) REVERT: B 330 TRP cc_start: 0.9042 (t-100) cc_final: 0.8606 (t-100) REVERT: C 32 THR cc_start: 0.9204 (m) cc_final: 0.8832 (p) REVERT: C 262 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7661 (pt0) REVERT: C 308 TYR cc_start: 0.8447 (p90) cc_final: 0.8145 (p90) REVERT: C 362 GLN cc_start: 0.7995 (pm20) cc_final: 0.7714 (pm20) REVERT: C 373 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8643 (mttp) REVERT: C 409 TRP cc_start: 0.8343 (m100) cc_final: 0.7635 (m100) REVERT: D 137 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8044 (ptp90) REVERT: D 195 LYS cc_start: 0.9178 (mttt) cc_final: 0.8926 (mttt) REVERT: D 272 HIS cc_start: 0.8139 (t-170) cc_final: 0.7642 (t70) REVERT: D 330 TRP cc_start: 0.9368 (t-100) cc_final: 0.9036 (t-100) REVERT: E 132 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: E 160 GLU cc_start: 0.6350 (mp0) cc_final: 0.5959 (mp0) REVERT: E 194 GLU cc_start: 0.8628 (tp30) cc_final: 0.8310 (mm-30) REVERT: F 156 MET cc_start: 0.8727 (tmm) cc_final: 0.8112 (pmm) REVERT: F 157 TYR cc_start: 0.7790 (m-80) cc_final: 0.6901 (m-80) REVERT: F 168 MET cc_start: 0.8180 (pmm) cc_final: 0.7932 (pmm) REVERT: F 186 TRP cc_start: 0.7875 (t60) cc_final: 0.7541 (t60) REVERT: F 207 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8450 (tmtt) REVERT: F 243 ASN cc_start: 0.8681 (t0) cc_final: 0.8346 (t0) REVERT: G 10 VAL cc_start: 0.9109 (t) cc_final: 0.8840 (m) REVERT: G 24 TYR cc_start: 0.8107 (m-80) cc_final: 0.7776 (m-80) REVERT: G 27 LEU cc_start: 0.8366 (tp) cc_final: 0.8027 (tp) REVERT: G 37 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7610 (mp0) REVERT: G 157 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6982 (tmm-80) REVERT: G 160 LYS cc_start: 0.9132 (pptt) cc_final: 0.8497 (mmtm) REVERT: G 170 PHE cc_start: 0.7987 (t80) cc_final: 0.7471 (t80) REVERT: G 204 GLN cc_start: 0.8178 (mt0) cc_final: 0.7777 (mt0) REVERT: G 216 ARG cc_start: 0.8615 (mtp85) cc_final: 0.7968 (ttm-80) REVERT: G 218 ASP cc_start: 0.7650 (t0) cc_final: 0.5862 (t0) REVERT: G 220 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.7672 (ptp90) REVERT: G 257 PHE cc_start: 0.8407 (m-80) cc_final: 0.7995 (m-80) REVERT: G 273 TYR cc_start: 0.8667 (p90) cc_final: 0.8393 (p90) REVERT: G 281 ASP cc_start: 0.8793 (t0) cc_final: 0.8005 (p0) REVERT: G 354 LEU cc_start: 0.8645 (tp) cc_final: 0.8381 (tp) REVERT: G 372 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8676 (mtmm) REVERT: H 82 LYS cc_start: 0.8667 (mttt) cc_final: 0.8116 (mttm) REVERT: H 155 TYR cc_start: 0.7993 (m-80) cc_final: 0.7629 (m-80) REVERT: H 272 HIS cc_start: 0.8054 (t70) cc_final: 0.7613 (t70) REVERT: H 395 ASP cc_start: 0.9140 (p0) cc_final: 0.8905 (p0) REVERT: I 130 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7326 (mtt180) REVERT: I 152 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7842 (mmtt) REVERT: I 212 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: J 9 ASN cc_start: 0.9372 (t0) cc_final: 0.8891 (t0) REVERT: J 13 ILE cc_start: 0.9514 (mm) cc_final: 0.9279 (mp) REVERT: J 15 TYR cc_start: 0.8195 (t80) cc_final: 0.7894 (t80) REVERT: J 133 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8494 (mm) REVERT: J 218 ASP cc_start: 0.8449 (t0) cc_final: 0.7976 (t0) REVERT: J 230 HIS cc_start: 0.8735 (t-90) cc_final: 0.8535 (t70) REVERT: J 257 PHE cc_start: 0.8599 (m-80) cc_final: 0.8105 (m-80) REVERT: J 307 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7965 (mm) REVERT: J 368 SER cc_start: 0.8615 (t) cc_final: 0.7650 (t) REVERT: J 372 LYS cc_start: 0.8798 (tptt) cc_final: 0.8410 (tppt) REVERT: J 390 GLU cc_start: 0.8399 (tp30) cc_final: 0.7532 (tt0) REVERT: J 409 TRP cc_start: 0.8523 (m100) cc_final: 0.8215 (m100) REVERT: K 38 SER cc_start: 0.9334 (t) cc_final: 0.8886 (p) REVERT: K 78 ASP cc_start: 0.8601 (t0) cc_final: 0.8353 (t70) REVERT: K 168 MET cc_start: 0.8127 (mmp) cc_final: 0.7791 (mmp) REVERT: K 259 PHE cc_start: 0.8740 (m-10) cc_final: 0.8506 (m-80) REVERT: K 279 TRP cc_start: 0.9142 (p-90) cc_final: 0.8753 (p-90) REVERT: K 366 TYR cc_start: 0.8353 (m-80) cc_final: 0.7975 (m-80) REVERT: L 156 MET cc_start: 0.8961 (ppp) cc_final: 0.8651 (ppp) REVERT: L 168 MET cc_start: 0.9246 (ppp) cc_final: 0.8862 (tmm) REVERT: W 90 LYS cc_start: 0.8736 (mtpt) cc_final: 0.7756 (tmtt) REVERT: X 77 PHE cc_start: 0.6780 (t80) cc_final: 0.6397 (t80) REVERT: Y 83 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5216 (pm20) outliers start: 174 outliers final: 136 residues processed: 976 average time/residue: 0.4173 time to fit residues: 673.6177 Evaluate side-chains 984 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 841 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 117 ASN Chi-restraints excluded: chain I residue 121 ASN 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 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 100 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.158829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123459 restraints weight = 64298.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127330 restraints weight = 31875.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129808 restraints weight = 19824.045| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33733 Z= 0.154 Angle : 0.737 11.925 45942 Z= 0.377 Chirality : 0.047 0.324 5080 Planarity : 0.005 0.049 5924 Dihedral : 6.201 80.294 4613 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 4.29 % Allowed : 25.42 % Favored : 70.29 % 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: -0.84 (0.13), residues: 4240 helix: 0.71 (0.25), residues: 426 sheet: -1.03 (0.14), residues: 1175 loop : -0.48 (0.13), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 89 HIS 0.008 0.001 HIS D 73 PHE 0.046 0.002 PHE B 280 TYR 0.024 0.002 TYR I 161 ARG 0.017 0.001 ARG F 220 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1197) hydrogen bonds : angle 6.02978 ( 3135) SS BOND : bond 0.00349 ( 73) SS BOND : angle 1.94809 ( 146) covalent geometry : bond 0.00357 (33660) covalent geometry : angle 0.73018 (45796) ********************** 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 1039 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 884 time to evaluate : 4.169 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: A 10 VAL cc_start: 0.9513 (t) cc_final: 0.9270 (m) REVERT: A 16 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8227 (mtmt) REVERT: A 69 LYS cc_start: 0.8902 (ptmm) cc_final: 0.8671 (ptmt) REVERT: A 75 ASP cc_start: 0.7814 (t0) cc_final: 0.6946 (t0) REVERT: A 252 GLN cc_start: 0.8810 (mp10) cc_final: 0.8524 (mm-40) REVERT: A 264 GLU cc_start: 0.8518 (mp0) cc_final: 0.8237 (mp0) REVERT: A 395 ASP cc_start: 0.8465 (t0) cc_final: 0.8052 (t0) REVERT: A 409 TRP cc_start: 0.8479 (t-100) cc_final: 0.8263 (t-100) REVERT: B 30 LYS cc_start: 0.9171 (tptt) cc_final: 0.8099 (tttt) REVERT: B 33 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.7136 (t0) REVERT: B 70 ASP cc_start: 0.7696 (p0) cc_final: 0.6964 (p0) REVERT: B 92 ARG cc_start: 0.2626 (mtt180) cc_final: 0.1624 (mtm180) REVERT: B 168 MET cc_start: 0.6685 (pmm) cc_final: 0.6443 (pmm) REVERT: B 176 TYR cc_start: 0.7454 (m-80) cc_final: 0.6657 (m-80) REVERT: B 287 LEU cc_start: 0.9423 (mt) cc_final: 0.8833 (mp) REVERT: B 305 ASP cc_start: 0.8811 (t0) cc_final: 0.8345 (t0) REVERT: B 319 PHE cc_start: 0.8136 (m-10) cc_final: 0.7936 (m-10) REVERT: B 330 TRP cc_start: 0.9019 (t-100) cc_final: 0.8508 (t-100) REVERT: C 32 THR cc_start: 0.9187 (m) cc_final: 0.8822 (p) REVERT: C 97 ASP cc_start: 0.8143 (p0) cc_final: 0.7812 (p0) REVERT: C 195 MET cc_start: 0.8834 (mpp) cc_final: 0.8540 (mpp) REVERT: C 204 GLN cc_start: 0.8527 (mt0) cc_final: 0.8007 (mt0) REVERT: C 221 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8842 (mt) REVERT: C 262 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7670 (pt0) REVERT: C 300 SER cc_start: 0.8231 (p) cc_final: 0.7945 (p) REVERT: C 308 TYR cc_start: 0.8387 (p90) cc_final: 0.8124 (p90) REVERT: C 409 TRP cc_start: 0.8337 (m100) cc_final: 0.7641 (m100) REVERT: D 137 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8261 (ptm160) REVERT: D 261 LEU cc_start: 0.9386 (tp) cc_final: 0.9074 (tt) REVERT: D 270 LEU cc_start: 0.9434 (mt) cc_final: 0.9107 (mp) REVERT: D 272 HIS cc_start: 0.8047 (t-170) cc_final: 0.7546 (t70) REVERT: D 330 TRP cc_start: 0.9367 (t-100) cc_final: 0.9017 (t-100) REVERT: D 339 TRP cc_start: 0.8821 (m-90) cc_final: 0.8524 (m-90) REVERT: E 132 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7769 (mtp) REVERT: E 160 GLU cc_start: 0.6356 (mp0) cc_final: 0.5964 (mp0) REVERT: E 194 GLU cc_start: 0.8657 (tp30) cc_final: 0.8380 (mm-30) REVERT: F 156 MET cc_start: 0.8756 (tmm) cc_final: 0.8313 (pmm) REVERT: F 207 LYS cc_start: 0.8961 (tmmt) cc_final: 0.8382 (tmtt) REVERT: F 243 ASN cc_start: 0.8639 (t0) cc_final: 0.8295 (t0) REVERT: G 10 VAL cc_start: 0.9096 (t) cc_final: 0.8847 (m) REVERT: G 24 TYR cc_start: 0.8074 (m-80) cc_final: 0.7716 (m-80) REVERT: G 27 LEU cc_start: 0.8359 (tp) cc_final: 0.8027 (tp) REVERT: G 37 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7605 (mp0) REVERT: G 62 CYS cc_start: 0.4598 (m) cc_final: 0.4383 (m) REVERT: G 157 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (tmm-80) REVERT: G 160 LYS cc_start: 0.9129 (pptt) cc_final: 0.8544 (mmtm) REVERT: G 170 PHE cc_start: 0.7933 (t80) cc_final: 0.7393 (t80) REVERT: G 216 ARG cc_start: 0.8592 (mtp85) cc_final: 0.7956 (ttm-80) REVERT: G 218 ASP cc_start: 0.7623 (t0) cc_final: 0.5773 (t0) REVERT: G 220 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.7668 (ptp90) REVERT: G 257 PHE cc_start: 0.8410 (m-80) cc_final: 0.8017 (m-80) REVERT: G 273 TYR cc_start: 0.8598 (p90) cc_final: 0.8272 (p90) REVERT: G 281 ASP cc_start: 0.8773 (t0) cc_final: 0.8011 (p0) REVERT: G 354 LEU cc_start: 0.8626 (tp) cc_final: 0.8391 (tp) REVERT: G 372 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8429 (mtmm) REVERT: H 82 LYS cc_start: 0.8576 (mttt) cc_final: 0.8072 (mttm) REVERT: H 272 HIS cc_start: 0.7974 (t70) cc_final: 0.7595 (t70) REVERT: H 342 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7891 (mm-30) REVERT: H 395 ASP cc_start: 0.9119 (p0) cc_final: 0.8877 (p0) REVERT: I 130 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6987 (mtt180) REVERT: I 152 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7804 (mmtm) REVERT: I 198 PHE cc_start: 0.8073 (m-80) cc_final: 0.7803 (m-80) REVERT: I 212 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8512 (mmm-85) REVERT: J 9 ASN cc_start: 0.9366 (t0) cc_final: 0.8929 (t0) REVERT: J 13 ILE cc_start: 0.9494 (mm) cc_final: 0.9234 (mp) REVERT: J 15 TYR cc_start: 0.8221 (t80) cc_final: 0.7909 (t80) REVERT: J 133 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (mm) REVERT: J 218 ASP cc_start: 0.8356 (t0) cc_final: 0.7872 (t0) REVERT: J 257 PHE cc_start: 0.8538 (m-80) cc_final: 0.7998 (m-80) REVERT: J 307 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7915 (mm) REVERT: J 368 SER cc_start: 0.8565 (t) cc_final: 0.7327 (p) REVERT: J 372 LYS cc_start: 0.8720 (tptt) cc_final: 0.8271 (tppt) REVERT: J 390 GLU cc_start: 0.8389 (tp30) cc_final: 0.7562 (tt0) REVERT: J 409 TRP cc_start: 0.8398 (m100) cc_final: 0.8121 (m100) REVERT: K 38 SER cc_start: 0.9308 (t) cc_final: 0.8873 (p) REVERT: K 78 ASP cc_start: 0.8542 (t0) cc_final: 0.8288 (t70) REVERT: K 168 MET cc_start: 0.8065 (mmp) cc_final: 0.7692 (mmp) REVERT: K 259 PHE cc_start: 0.8724 (m-10) cc_final: 0.8483 (m-80) REVERT: K 279 TRP cc_start: 0.9145 (p-90) cc_final: 0.8768 (p-90) REVERT: K 366 TYR cc_start: 0.8336 (m-80) cc_final: 0.8003 (m-80) REVERT: K 394 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8122 (ttm-80) REVERT: L 156 MET cc_start: 0.8981 (ppp) cc_final: 0.8738 (ppp) REVERT: L 168 MET cc_start: 0.9278 (ppp) cc_final: 0.8921 (tmm) REVERT: L 212 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6585 (mtp85) REVERT: V 99 ASP cc_start: 0.6956 (p0) cc_final: 0.6130 (p0) REVERT: X 77 PHE cc_start: 0.6824 (t80) cc_final: 0.6459 (t80) REVERT: Y 83 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5252 (pm20) outliers start: 155 outliers final: 134 residues processed: 959 average time/residue: 0.4180 time to fit residues: 658.4249 Evaluate side-chains 982 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 839 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 141 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 42 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 117 ASN Chi-restraints excluded: chain I residue 121 ASN 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 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 33 CYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 403 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 392 optimal weight: 9.9990 chunk 367 optimal weight: 0.9990 chunk 400 optimal weight: 0.0870 chunk 118 optimal weight: 8.9990 chunk 141 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124172 restraints weight = 64553.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128070 restraints weight = 32000.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130550 restraints weight = 19907.580| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33733 Z= 0.154 Angle : 0.729 12.110 45942 Z= 0.373 Chirality : 0.047 0.283 5080 Planarity : 0.005 0.069 5924 Dihedral : 6.113 79.967 4613 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 4.01 % Allowed : 25.97 % Favored : 70.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4240 helix: 1.05 (0.26), residues: 393 sheet: -0.94 (0.14), residues: 1196 loop : -0.46 (0.13), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 89 HIS 0.011 0.001 HIS B 349 PHE 0.028 0.002 PHE W 38 TYR 0.026 0.002 TYR H 155 ARG 0.011 0.001 ARG F 220 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1197) hydrogen bonds : angle 5.97991 ( 3135) SS BOND : bond 0.00338 ( 73) SS BOND : angle 1.90173 ( 146) covalent geometry : bond 0.00356 (33660) covalent geometry : angle 0.72247 (45796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14834.81 seconds wall clock time: 259 minutes 4.84 seconds (15544.84 seconds total)