Starting phenix.real_space_refine on Sat Jun 28 10:45:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9z_47822/06_2025/9e9z_47822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9z_47822/06_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_47822/06_2025/9e9z_47822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9z_47822/06_2025/9e9z_47822.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9z_47822/06_2025/9e9z_47822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9z_47822/06_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.14, per 1000 atoms: 0.58 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: 8.46 Conformation dependent library (CDL) restraints added in 4.7 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: 5.83 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: 19.70 Time building geometry restraints manager: 10.35 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: 0.04 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: 2.050 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: 0.050 Extract box with map and model: 1.530 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 84.310 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.900 ------------------------------------------------------------------------------- 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 : 4.043 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: 0.4704 time to fit residues: 1111.8283 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 : 3.540 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121665 restraints weight = 64340.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125433 restraints weight = 31709.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127847 restraints weight = 19763.986| |-----------------------------------------------------------------------------| 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 : 3.578 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: 0.8249 (t0) cc_final: 0.7440 (t0) REVERT: A 125 HIS cc_start: 0.7715 (m90) cc_final: 0.7467 (m90) REVERT: A 129 LEU cc_start: 0.8384 (tt) cc_final: 0.8172 (tt) REVERT: A 158 ASP cc_start: 0.8751 (t0) cc_final: 0.8364 (t0) REVERT: A 160 LYS cc_start: 0.8603 (mptt) cc_final: 0.8150 (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: 0.8254 (OUTLIER) cc_final: 0.7377 (t0) REVERT: B 39 ASP cc_start: 0.7809 (m-30) cc_final: 0.7529 (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: 0.7926 (p0) cc_final: 0.7281 (p0) REVERT: B 92 ARG cc_start: 0.2716 (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: 0.7397 (tt0) REVERT: B 156 ASP cc_start: 0.8749 (t0) cc_final: 0.8372 (t0) REVERT: B 176 TYR cc_start: 0.7367 (m-80) cc_final: 0.6737 (m-80) REVERT: B 278 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9016 (mttm) REVERT: B 284 THR cc_start: 0.8945 (m) cc_final: 0.8682 (p) REVERT: B 305 ASP cc_start: 0.8857 (t0) cc_final: 0.8589 (t0) REVERT: B 327 GLU cc_start: 0.7802 (tt0) cc_final: 0.7414 (tt0) REVERT: B 330 TRP cc_start: 0.9099 (t-100) cc_final: 0.8818 (t-100) REVERT: B 332 ASN cc_start: 0.9179 (m-40) cc_final: 0.8951 (m110) REVERT: B 334 GLU cc_start: 0.8669 (tp30) cc_final: 0.8416 (mm-30) REVERT: C 32 THR cc_start: 0.9086 (m) cc_final: 0.8704 (p) REVERT: C 99 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 100 ASN cc_start: 0.8308 (m-40) cc_final: 0.7987 (m-40) REVERT: C 103 LEU cc_start: 0.9232 (tp) cc_final: 0.9024 (tt) REVERT: C 139 ASN cc_start: 0.8235 (t0) cc_final: 0.7961 (m-40) REVERT: C 228 ASN cc_start: 0.9373 (m110) cc_final: 0.9035 (m-40) REVERT: C 231 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9430 (m) REVERT: C 307 ILE cc_start: 0.6261 (mt) cc_final: 0.5648 (tt) REVERT: C 308 TYR cc_start: 0.8426 (p90) cc_final: 0.8130 (p90) REVERT: C 373 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8656 (mttp) REVERT: C 396 GLN cc_start: 0.7596 (tt0) cc_final: 0.7333 (tt0) REVERT: C 409 TRP cc_start: 0.8310 (m100) cc_final: 0.7546 (m100) REVERT: D 18 TYR cc_start: 0.8482 (t80) cc_final: 0.8235 (t80) REVERT: D 33 ASN cc_start: 0.8385 (m-40) cc_final: 0.8147 (m-40) REVERT: D 134 PHE cc_start: 0.8948 (p90) cc_final: 0.8571 (p90) REVERT: D 139 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8245 (mm-30) REVERT: D 193 SER cc_start: 0.8330 (p) cc_final: 0.7901 (p) REVERT: D 195 LYS cc_start: 0.9124 (mttt) cc_final: 0.8745 (mttt) REVERT: D 227 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7835 (mm) REVERT: D 273 THR cc_start: 0.9322 (m) cc_final: 0.8818 (p) REVERT: D 305 ASP cc_start: 0.8156 (t0) cc_final: 0.7937 (t70) REVERT: D 339 TRP cc_start: 0.9026 (m-90) cc_final: 0.8728 (m-90) REVERT: E 132 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7581 (mtp) REVERT: E 186 TRP cc_start: 0.7532 (t60) cc_final: 0.6945 (t60) REVERT: E 194 GLU cc_start: 0.8907 (tp30) cc_final: 0.8475 (tp30) REVERT: F 112 PHE cc_start: 0.8680 (m-80) cc_final: 0.8449 (m-80) REVERT: G 10 VAL cc_start: 0.9071 (t) cc_final: 0.8799 (m) REVERT: G 27 LEU cc_start: 0.8362 (tp) cc_final: 0.7967 (tp) REVERT: G 62 CYS cc_start: 0.4491 (m) cc_final: 0.4139 (m) REVERT: G 140 THR cc_start: 0.8760 (m) cc_final: 0.8509 (p) REVERT: G 170 PHE cc_start: 0.7913 (t80) cc_final: 0.7367 (t80) REVERT: G 203 ILE cc_start: 0.9155 (tt) cc_final: 0.8892 (tt) REVERT: G 206 SER cc_start: 0.9642 (m) cc_final: 0.9321 (t) REVERT: G 218 ASP cc_start: 0.7700 (t0) cc_final: 0.7154 (t0) REVERT: G 220 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8214 (ptp90) REVERT: G 257 PHE cc_start: 0.8598 (m-80) cc_final: 0.8186 (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: 0.7369 (ptp90) REVERT: G 362 GLN cc_start: 0.8106 (pm20) cc_final: 0.7862 (pm20) REVERT: G 364 ASN cc_start: 0.8968 (t0) cc_final: 0.8708 (t0) REVERT: H 51 PHE cc_start: 0.7948 (m-80) cc_final: 0.7681 (m-80) REVERT: H 82 LYS cc_start: 0.8715 (mttt) cc_final: 0.8426 (mtmm) REVERT: H 104 GLN cc_start: 0.8790 (tt0) cc_final: 0.8466 (tt0) REVERT: H 117 SER cc_start: 0.8409 (t) cc_final: 0.8132 (p) REVERT: H 121 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7461 (tm-30) REVERT: H 139 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: H 158 LEU cc_start: 0.8971 (mt) cc_final: 0.8659 (mt) REVERT: H 180 LEU cc_start: 0.9000 (mt) cc_final: 0.8765 (mt) REVERT: H 200 GLU cc_start: 0.7632 (tt0) cc_final: 0.7172 (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: 0.8387 (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: 0.8696 (mmm-85) REVERT: I 115 MET cc_start: 0.6142 (mmp) cc_final: 0.5847 (mmm) REVERT: I 152 LYS cc_start: 0.8533 (ttpt) cc_final: 0.7840 (mmtt) REVERT: I 161 TYR cc_start: 0.9006 (p90) cc_final: 0.8682 (p90) REVERT: I 186 TRP cc_start: 0.8250 (t60) cc_final: 0.7744 (t60) REVERT: I 192 GLN cc_start: 0.8449 (tp40) cc_final: 0.8236 (tp40) REVERT: I 194 GLU cc_start: 0.8362 (tt0) cc_final: 0.7750 (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: 0.8174 (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: 0.7896 (m-80) REVERT: J 271 CYS cc_start: 0.6599 (m) cc_final: 0.6358 (m) REVERT: J 277 PRO cc_start: 0.9225 (Cg_exo) cc_final: 0.9018 (Cg_endo) REVERT: J 307 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8189 (mm) REVERT: J 319 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7319 (mm-40) REVERT: J 372 LYS cc_start: 0.8847 (tptt) cc_final: 0.8601 (tppt) REVERT: J 398 PHE cc_start: 0.9115 (t80) cc_final: 0.8886 (t80) REVERT: J 409 TRP cc_start: 0.8598 (m100) cc_final: 0.8181 (m100) REVERT: K 78 ASP cc_start: 0.8617 (t0) cc_final: 0.8351 (t70) REVERT: K 100 PHE cc_start: 0.9216 (m-80) cc_final: 0.8676 (m-80) REVERT: K 121 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: K 170 ARG cc_start: 0.8263 (ptp-170) cc_final: 0.7960 (ptp-170) REVERT: K 218 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8414 (p0) REVERT: K 279 TRP cc_start: 0.9136 (p-90) cc_final: 0.8691 (p-90) REVERT: K 339 TRP cc_start: 0.8974 (m-90) cc_final: 0.7806 (m-90) REVERT: L 143 ASN cc_start: 0.8298 (t0) cc_final: 0.7379 (m-40) REVERT: W 90 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7532 (tmtt) REVERT: X 96 ASP cc_start: 0.8022 (m-30) cc_final: 0.7820 (m-30) REVERT: Y 83 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5437 (pm20) outliers start: 172 outliers final: 117 residues processed: 1134 average time/residue: 0.4382 time to fit residues: 811.9221 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 : 4.049 ------------------------------------------------------------------------------- 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: 0.9990 chunk 405 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 223 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 392 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** 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 H 33 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS 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 = 0.3971 r_free = 0.3971 target = 0.159592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124291 restraints weight = 64684.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128190 restraints weight = 31725.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130704 restraints weight = 19635.849| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3240 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= 0.163 Angle : 0.711 10.524 45942 Z= 0.373 Chirality : 0.048 0.258 5080 Planarity : 0.005 0.050 5924 Dihedral : 6.664 79.612 4621 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 4.60 % Allowed : 18.49 % Favored : 76.91 % 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: -0.86 (0.13), residues: 4240 helix: 0.21 (0.24), residues: 424 sheet: -0.86 (0.14), residues: 1175 loop : -0.50 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 89 HIS 0.010 0.001 HIS H 272 PHE 0.026 0.002 PHE I 198 TYR 0.026 0.002 TYR J 233 ARG 0.006 0.001 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1197) hydrogen bonds : angle 6.56123 ( 3135) SS BOND : bond 0.00296 ( 73) SS BOND : angle 1.74747 ( 146) covalent geometry : bond 0.00365 (33660) covalent geometry : angle 0.70576 (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 1193 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1027 time to evaluate : 3.820 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: A 24 TYR cc_start: 0.8451 (m-80) cc_final: 0.7949 (m-80) REVERT: A 75 ASP cc_start: 0.7965 (t0) cc_final: 0.6929 (t0) REVERT: A 158 ASP cc_start: 0.8707 (t0) cc_final: 0.8221 (t0) REVERT: A 160 LYS cc_start: 0.8591 (mptt) cc_final: 0.8228 (mmtm) REVERT: A 280 ILE cc_start: 0.9382 (mp) cc_final: 0.8817 (mp) REVERT: A 367 VAL cc_start: 0.9552 (t) cc_final: 0.9352 (p) REVERT: A 395 ASP cc_start: 0.8430 (t0) cc_final: 0.8120 (t0) REVERT: B 32 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7690 (tp30) REVERT: B 33 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7426 (t0) REVERT: B 37 GLU cc_start: 0.8159 (tp30) cc_final: 0.7919 (tp30) REVERT: B 70 ASP cc_start: 0.7885 (p0) cc_final: 0.7232 (p0) REVERT: B 92 ARG cc_start: 0.2613 (mtt180) cc_final: 0.1849 (mtm180) REVERT: B 114 SER cc_start: 0.9121 (m) cc_final: 0.8676 (p) REVERT: B 122 ASN cc_start: 0.8720 (m110) cc_final: 0.8480 (m-40) REVERT: B 131 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7302 (mtm110) REVERT: B 146 HIS cc_start: 0.5179 (OUTLIER) cc_final: 0.4752 (m170) REVERT: B 156 ASP cc_start: 0.8685 (t0) cc_final: 0.8426 (t70) REVERT: B 176 TYR cc_start: 0.7284 (m-80) cc_final: 0.6681 (m-80) REVERT: B 257 ILE cc_start: 0.8326 (mt) cc_final: 0.8063 (pt) REVERT: B 278 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9068 (mttm) REVERT: B 305 ASP cc_start: 0.8849 (t0) cc_final: 0.8545 (t0) REVERT: B 329 VAL cc_start: 0.9414 (t) cc_final: 0.9169 (m) REVERT: B 330 TRP cc_start: 0.8999 (t-100) cc_final: 0.8688 (t-100) REVERT: B 332 ASN cc_start: 0.9141 (m-40) cc_final: 0.8907 (m110) REVERT: C 32 THR cc_start: 0.9093 (m) cc_final: 0.8672 (p) REVERT: C 97 ASP cc_start: 0.8002 (p0) cc_final: 0.7767 (p0) REVERT: C 100 ASN cc_start: 0.8406 (m-40) cc_final: 0.7952 (m-40) REVERT: C 133 LEU cc_start: 0.9331 (mt) cc_final: 0.9118 (mt) REVERT: C 139 ASN cc_start: 0.8182 (t0) cc_final: 0.7908 (m-40) REVERT: C 221 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8853 (mt) REVERT: C 262 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7567 (pt0) REVERT: C 307 ILE cc_start: 0.6219 (mt) cc_final: 0.5646 (tt) REVERT: C 308 TYR cc_start: 0.8324 (p90) cc_final: 0.8056 (p90) REVERT: C 373 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8707 (mttp) REVERT: C 409 TRP cc_start: 0.8277 (m100) cc_final: 0.7479 (m100) REVERT: D 32 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8064 (mm-30) REVERT: D 121 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7199 (tp30) REVERT: D 134 PHE cc_start: 0.8945 (p90) cc_final: 0.8601 (p90) REVERT: D 139 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 193 SER cc_start: 0.8277 (p) cc_final: 0.7896 (p) REVERT: D 195 LYS cc_start: 0.9101 (mttt) cc_final: 0.8743 (mttt) REVERT: D 227 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 273 THR cc_start: 0.9268 (m) cc_final: 0.8777 (p) REVERT: D 327 GLU cc_start: 0.8299 (tt0) cc_final: 0.8077 (tt0) REVERT: D 339 TRP cc_start: 0.8868 (m-90) cc_final: 0.8533 (m-90) REVERT: E 112 PHE cc_start: 0.8140 (m-80) cc_final: 0.7627 (m-10) REVERT: E 119 GLN cc_start: 0.7985 (pt0) cc_final: 0.7763 (pm20) REVERT: E 130 ARG cc_start: 0.8361 (tpp80) cc_final: 0.8017 (tpp80) REVERT: E 160 GLU cc_start: 0.7038 (pm20) cc_final: 0.6525 (mp0) REVERT: E 186 TRP cc_start: 0.7519 (t60) cc_final: 0.6918 (t60) REVERT: E 194 GLU cc_start: 0.8798 (tp30) cc_final: 0.8393 (tp30) REVERT: F 127 VAL cc_start: 0.8947 (t) cc_final: 0.8720 (m) REVERT: F 218 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8242 (ptp-110) REVERT: G 10 VAL cc_start: 0.9047 (t) cc_final: 0.8744 (m) REVERT: G 24 TYR cc_start: 0.8288 (m-80) cc_final: 0.7689 (m-80) REVERT: G 27 LEU cc_start: 0.8233 (tp) cc_final: 0.7862 (tp) REVERT: G 37 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7507 (mp0) REVERT: G 57 SER cc_start: 0.9130 (m) cc_final: 0.8767 (t) REVERT: G 62 CYS cc_start: 0.4421 (m) cc_final: 0.4218 (m) REVERT: G 140 THR cc_start: 0.8692 (m) cc_final: 0.8451 (p) REVERT: G 160 LYS cc_start: 0.9164 (pptt) cc_final: 0.8786 (mmtm) REVERT: G 170 PHE cc_start: 0.8009 (t80) cc_final: 0.7671 (t80) REVERT: G 195 MET cc_start: 0.8858 (mpp) cc_final: 0.8621 (mpp) REVERT: G 203 ILE cc_start: 0.9130 (tt) cc_final: 0.8873 (tt) REVERT: G 206 SER cc_start: 0.9664 (m) cc_final: 0.9315 (t) REVERT: G 218 ASP cc_start: 0.7708 (t0) cc_final: 0.7244 (t0) REVERT: G 220 ARG cc_start: 0.8517 (ptp-170) cc_final: 0.8305 (ptp90) REVERT: G 235 GLN cc_start: 0.8764 (pt0) cc_final: 0.8208 (pt0) REVERT: G 324 ARG cc_start: 0.7676 (ptp-170) cc_final: 0.7290 (ptp90) REVERT: G 362 GLN cc_start: 0.8256 (pm20) cc_final: 0.7995 (pm20) REVERT: G 364 ASN cc_start: 0.8972 (t0) cc_final: 0.8631 (t0) REVERT: H 82 LYS cc_start: 0.8613 (mttt) cc_final: 0.7981 (mttm) REVERT: H 117 SER cc_start: 0.8382 (t) cc_final: 0.8155 (p) REVERT: H 139 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6292 (tm-30) REVERT: H 156 ASP cc_start: 0.8293 (t0) cc_final: 0.7925 (t0) REVERT: H 158 LEU cc_start: 0.8794 (mt) cc_final: 0.8464 (mt) REVERT: H 180 LEU cc_start: 0.8846 (mt) cc_final: 0.8633 (mp) REVERT: H 287 LEU cc_start: 0.9123 (mm) cc_final: 0.8772 (mt) REVERT: H 305 ASP cc_start: 0.8519 (t0) cc_final: 0.8297 (t0) REVERT: H 362 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8728 (mmm-85) REVERT: H 395 ASP cc_start: 0.9209 (p0) cc_final: 0.8997 (p0) REVERT: I 115 MET cc_start: 0.6332 (mmp) cc_final: 0.6123 (mmm) REVERT: I 130 ARG cc_start: 0.7444 (mtt180) cc_final: 0.7214 (mtt180) 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: 0.7692 (t60) REVERT: I 192 GLN cc_start: 0.8549 (tp40) cc_final: 0.8259 (tp-100) REVERT: I 194 GLU cc_start: 0.8409 (tt0) cc_final: 0.7728 (tt0) REVERT: I 212 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.7351 (mmm-85) REVERT: J 9 ASN cc_start: 0.9277 (t0) cc_final: 0.8802 (t0) REVERT: J 15 TYR cc_start: 0.8070 (t80) cc_final: 0.7785 (t80) REVERT: J 37 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7439 (mm-30) REVERT: J 63 CYS cc_start: 0.5568 (t) cc_final: 0.2978 (t) REVERT: J 218 ASP cc_start: 0.8219 (t0) cc_final: 0.7748 (t0) REVERT: J 230 HIS cc_start: 0.8739 (t-90) cc_final: 0.8213 (t-90) REVERT: J 257 PHE cc_start: 0.8418 (m-80) cc_final: 0.7835 (m-80) REVERT: J 262 GLU cc_start: 0.8021 (mp0) cc_final: 0.7815 (mp0) REVERT: J 271 CYS cc_start: 0.6422 (m) cc_final: 0.6135 (m) REVERT: J 307 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8102 (mm) REVERT: J 372 LYS cc_start: 0.8769 (tptt) cc_final: 0.8469 (tppt) REVERT: J 398 PHE cc_start: 0.9107 (t80) cc_final: 0.8851 (t80) REVERT: J 409 TRP cc_start: 0.8507 (m100) cc_final: 0.8236 (m100) REVERT: K 37 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8443 (mt-10) REVERT: K 78 ASP cc_start: 0.8656 (t0) cc_final: 0.8292 (t70) REVERT: K 121 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.5961 (tm-30) REVERT: K 168 MET cc_start: 0.8286 (mmp) cc_final: 0.7679 (mmp) REVERT: K 272 HIS cc_start: 0.8750 (t70) cc_final: 0.7605 (t70) REVERT: K 279 TRP cc_start: 0.9065 (p-90) cc_final: 0.8688 (p-90) REVERT: K 330 TRP cc_start: 0.9490 (t-100) cc_final: 0.9259 (t-100) REVERT: K 339 TRP cc_start: 0.8960 (m-90) cc_final: 0.7814 (m-90) REVERT: K 341 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7809 (mm110) REVERT: K 366 TYR cc_start: 0.8290 (m-80) cc_final: 0.7829 (m-80) REVERT: L 110 LYS cc_start: 0.8085 (mppt) cc_final: 0.6948 (pttm) REVERT: L 143 ASN cc_start: 0.8301 (t0) cc_final: 0.7423 (m-40) REVERT: L 145 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8136 (tm-30) REVERT: L 168 MET cc_start: 0.9202 (ppp) cc_final: 0.8763 (tmm) REVERT: W 72 CYS cc_start: 0.5441 (OUTLIER) cc_final: 0.5105 (p) REVERT: W 90 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7602 (tmtt) REVERT: X 77 PHE cc_start: 0.6334 (t80) cc_final: 0.6041 (t80) REVERT: X 96 ASP cc_start: 0.8106 (m-30) cc_final: 0.7900 (m-30) REVERT: Y 83 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5615 (pm20) outliers start: 166 outliers final: 114 residues processed: 1104 average time/residue: 0.4332 time to fit residues: 785.2213 Evaluate side-chains 1036 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 912 time to evaluate : 3.653 ------------------------------------------------------------------------------- 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 221 LEU 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 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 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 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: 10.0000 chunk 310 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** 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 ** 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 96 HIS ** 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** ** 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** ** K 332 ASN ** 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 = 0.3946 r_free = 0.3946 target = 0.157454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122070 restraints weight = 64361.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125913 restraints weight = 31738.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128407 restraints weight = 19716.702| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33733 Z= 0.192 Angle : 0.691 10.348 45942 Z= 0.363 Chirality : 0.047 0.319 5080 Planarity : 0.005 0.044 5924 Dihedral : 6.561 81.114 4619 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 5.73 % Allowed : 19.77 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4240 helix: 0.29 (0.24), residues: 430 sheet: -0.92 (0.14), residues: 1131 loop : -0.45 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 236 HIS 0.012 0.001 HIS H 272 PHE 0.035 0.002 PHE I 198 TYR 0.026 0.002 TYR J 233 ARG 0.009 0.001 ARG L 220 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1197) hydrogen bonds : angle 6.37278 ( 3135) SS BOND : bond 0.00432 ( 73) SS BOND : angle 1.70808 ( 146) covalent geometry : bond 0.00430 (33660) covalent geometry : angle 0.68526 (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 1158 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 951 time to evaluate : 3.636 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 24 TYR cc_start: 0.8600 (m-80) cc_final: 0.8010 (m-80) REVERT: A 75 ASP cc_start: 0.7963 (t0) cc_final: 0.7029 (t0) REVERT: A 158 ASP cc_start: 0.8853 (t0) cc_final: 0.8623 (t0) REVERT: A 280 ILE cc_start: 0.9291 (mp) cc_final: 0.9059 (mp) REVERT: A 367 VAL cc_start: 0.9538 (t) cc_final: 0.9314 (p) REVERT: A 395 ASP cc_start: 0.8477 (t0) cc_final: 0.8137 (t0) REVERT: B 33 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7445 (t0) REVERT: B 40 ASP cc_start: 0.8441 (p0) cc_final: 0.7932 (p0) REVERT: B 70 ASP cc_start: 0.7872 (p0) cc_final: 0.7204 (p0) REVERT: B 92 ARG cc_start: 0.2574 (mtt180) cc_final: 0.1732 (mtm180) REVERT: B 122 ASN cc_start: 0.8796 (m110) cc_final: 0.8592 (m-40) REVERT: B 176 TYR cc_start: 0.7382 (m-80) cc_final: 0.6662 (m-80) REVERT: B 257 ILE cc_start: 0.8293 (mt) cc_final: 0.8023 (pt) REVERT: B 278 LYS cc_start: 0.9325 (mtmm) cc_final: 0.9061 (mttm) REVERT: B 305 ASP cc_start: 0.8902 (t0) cc_final: 0.8558 (t0) REVERT: B 330 TRP cc_start: 0.9000 (t-100) cc_final: 0.8733 (t-100) REVERT: B 332 ASN cc_start: 0.9114 (m-40) cc_final: 0.8898 (m110) REVERT: B 402 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7060 (mm) REVERT: C 32 THR cc_start: 0.9152 (m) cc_final: 0.8680 (p) REVERT: C 97 ASP cc_start: 0.8118 (p0) cc_final: 0.7837 (p0) REVERT: C 100 ASN cc_start: 0.8332 (m-40) cc_final: 0.7749 (m-40) REVERT: C 139 ASN cc_start: 0.8263 (t0) cc_final: 0.7867 (m-40) REVERT: C 262 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7643 (pt0) REVERT: C 307 ILE cc_start: 0.6278 (mt) cc_final: 0.5674 (tt) REVERT: C 308 TYR cc_start: 0.8397 (p90) cc_final: 0.8144 (p90) REVERT: C 362 GLN cc_start: 0.7878 (pm20) cc_final: 0.7555 (pm20) REVERT: C 373 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8793 (mttp) REVERT: C 409 TRP cc_start: 0.8269 (m100) cc_final: 0.7457 (m100) REVERT: D 134 PHE cc_start: 0.8996 (p90) cc_final: 0.8533 (p90) REVERT: D 139 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8052 (mm-30) REVERT: D 272 HIS cc_start: 0.8291 (t-170) cc_final: 0.8088 (t70) REVERT: D 273 THR cc_start: 0.9273 (m) cc_final: 0.8706 (p) REVERT: D 339 TRP cc_start: 0.8933 (m-90) cc_final: 0.8577 (m-90) REVERT: E 119 GLN cc_start: 0.7922 (pt0) cc_final: 0.7702 (pm20) REVERT: E 130 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8143 (tpp80) REVERT: E 160 GLU cc_start: 0.6526 (pm20) cc_final: 0.6152 (mp0) REVERT: E 194 GLU cc_start: 0.8802 (tp30) cc_final: 0.8390 (tp30) REVERT: F 184 TYR cc_start: 0.7017 (m-80) cc_final: 0.6592 (m-80) REVERT: G 10 VAL cc_start: 0.9097 (t) cc_final: 0.8826 (m) REVERT: G 24 TYR cc_start: 0.8238 (m-80) cc_final: 0.7717 (m-80) REVERT: G 27 LEU cc_start: 0.8357 (tp) cc_final: 0.7998 (tp) REVERT: G 37 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7474 (mp0) REVERT: G 57 SER cc_start: 0.9161 (m) cc_final: 0.8846 (t) REVERT: G 62 CYS cc_start: 0.4759 (m) cc_final: 0.4407 (m) REVERT: G 160 LYS cc_start: 0.9173 (pptt) cc_final: 0.8808 (mmtm) REVERT: G 170 PHE cc_start: 0.8056 (t80) cc_final: 0.7456 (t80) REVERT: G 203 ILE cc_start: 0.9120 (tt) cc_final: 0.8813 (tt) REVERT: G 206 SER cc_start: 0.9697 (m) cc_final: 0.9293 (t) REVERT: G 218 ASP cc_start: 0.7736 (t0) cc_final: 0.7167 (t0) REVERT: G 220 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8174 (ptp90) REVERT: G 230 HIS cc_start: 0.8607 (t70) cc_final: 0.8357 (t-90) REVERT: G 257 PHE cc_start: 0.8539 (m-80) cc_final: 0.8189 (m-80) REVERT: G 267 ARG cc_start: 0.7296 (ptt-90) cc_final: 0.7045 (ptt-90) REVERT: G 273 TYR cc_start: 0.8466 (p90) cc_final: 0.7843 (p90) REVERT: G 324 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7379 (ptp90) REVERT: G 354 LEU cc_start: 0.8553 (tp) cc_final: 0.8289 (tp) REVERT: G 362 GLN cc_start: 0.8302 (pm20) cc_final: 0.8062 (pm20) REVERT: G 364 ASN cc_start: 0.8954 (t0) cc_final: 0.8555 (t0) REVERT: H 82 LYS cc_start: 0.8596 (mttt) cc_final: 0.7938 (mttm) REVERT: H 117 SER cc_start: 0.8204 (t) cc_final: 0.7979 (p) REVERT: H 139 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6274 (tm-30) REVERT: H 186 GLU cc_start: 0.8290 (pm20) cc_final: 0.8059 (pm20) REVERT: H 305 ASP cc_start: 0.8560 (t0) cc_final: 0.8312 (t0) REVERT: H 362 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8775 (mmm-85) REVERT: H 395 ASP cc_start: 0.9197 (p0) cc_final: 0.8971 (p0) REVERT: I 115 MET cc_start: 0.6663 (mmt) cc_final: 0.6130 (mmm) REVERT: I 130 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7279 (mtt90) REVERT: I 152 LYS cc_start: 0.8432 (ttpt) cc_final: 0.7805 (mmtt) REVERT: I 192 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8112 (tp40) REVERT: J 9 ASN cc_start: 0.9286 (t0) cc_final: 0.8759 (t0) REVERT: J 15 TYR cc_start: 0.8174 (t80) cc_final: 0.7832 (t80) REVERT: J 37 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7530 (mm-30) REVERT: J 63 CYS cc_start: 0.5578 (t) cc_final: 0.4898 (t) REVERT: J 133 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8404 (mm) REVERT: J 218 ASP cc_start: 0.8274 (t0) cc_final: 0.7835 (t0) REVERT: J 230 HIS cc_start: 0.8786 (t-90) cc_final: 0.8306 (t-90) REVERT: J 257 PHE cc_start: 0.8436 (m-80) cc_final: 0.7859 (m-80) REVERT: J 271 CYS cc_start: 0.6384 (m) cc_final: 0.6047 (m) REVERT: J 307 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8116 (mm) REVERT: J 368 SER cc_start: 0.8665 (t) cc_final: 0.8439 (t) REVERT: J 372 LYS cc_start: 0.8772 (tptt) cc_final: 0.8514 (tppt) REVERT: J 409 TRP cc_start: 0.8547 (m100) cc_final: 0.8221 (m100) REVERT: K 217 MET cc_start: 0.8176 (tpp) cc_final: 0.7633 (tpp) REVERT: K 279 TRP cc_start: 0.9070 (p-90) cc_final: 0.8680 (p-90) REVERT: K 341 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7680 (mm110) REVERT: K 351 TRP cc_start: 0.8964 (m-10) cc_final: 0.8712 (m-10) REVERT: K 366 TYR cc_start: 0.8307 (m-80) cc_final: 0.7852 (m-80) REVERT: L 110 LYS cc_start: 0.8117 (mppt) cc_final: 0.6994 (pttm) REVERT: L 143 ASN cc_start: 0.8380 (t0) cc_final: 0.7557 (m-40) REVERT: L 145 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8383 (tm-30) REVERT: L 168 MET cc_start: 0.9243 (ppp) cc_final: 0.8827 (tmm) REVERT: W 72 CYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4717 (p) REVERT: W 90 LYS cc_start: 0.8497 (mtpt) cc_final: 0.7577 (tmtt) REVERT: X 77 PHE cc_start: 0.6449 (t80) cc_final: 0.6081 (t80) REVERT: X 96 ASP cc_start: 0.8038 (m-30) cc_final: 0.7736 (m-30) outliers start: 207 outliers final: 152 residues processed: 1054 average time/residue: 0.4436 time to fit residues: 769.8330 Evaluate side-chains 1042 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 884 time to evaluate : 3.894 ------------------------------------------------------------------------------- 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 104 GLN 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 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 166 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 335 THR 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 19 CYS Chi-restraints excluded: chain D residue 40 ASP 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 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 131 LEU 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 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 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 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 55 ILE 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 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 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 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 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 58 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 133 LYS 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 195 ASN Chi-restraints excluded: chain L residue 222 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 85 VAL Chi-restraints excluded: chain W residue 96 ASP 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 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: 0.7980 chunk 363 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 378 optimal weight: 5.9990 chunk 171 optimal weight: 0.0670 chunk 238 optimal weight: 2.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** 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 L 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121015 restraints weight = 64142.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124806 restraints weight = 31768.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127260 restraints weight = 19843.967| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33733 Z= 0.210 Angle : 0.694 10.835 45942 Z= 0.362 Chirality : 0.047 0.371 5080 Planarity : 0.005 0.070 5924 Dihedral : 6.384 81.745 4615 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 6.04 % Allowed : 21.15 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4240 helix: 0.51 (0.25), residues: 418 sheet: -0.95 (0.14), residues: 1173 loop : -0.46 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 407 HIS 0.019 0.001 HIS L 187 PHE 0.040 0.002 PHE H 51 TYR 0.023 0.002 TYR G 46 ARG 0.010 0.001 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 1197) hydrogen bonds : angle 6.24935 ( 3135) SS BOND : bond 0.00440 ( 73) SS BOND : angle 1.72588 ( 146) covalent geometry : bond 0.00469 (33660) covalent geometry : angle 0.68804 (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 1135 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 917 time to evaluate : 4.472 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 16 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8388 (mtmt) REVERT: A 24 TYR cc_start: 0.8539 (m-80) cc_final: 0.8059 (m-80) REVERT: A 69 LYS cc_start: 0.8971 (ptmm) cc_final: 0.8701 (ptmt) REVERT: A 75 ASP cc_start: 0.8000 (t0) cc_final: 0.7075 (t0) REVERT: A 158 ASP cc_start: 0.8922 (t0) cc_final: 0.8697 (t0) REVERT: A 298 GLU cc_start: 0.8257 (pt0) cc_final: 0.8046 (pt0) REVERT: A 367 VAL cc_start: 0.9543 (t) cc_final: 0.9307 (m) REVERT: A 395 ASP cc_start: 0.8477 (t0) cc_final: 0.8124 (t0) REVERT: A 409 TRP cc_start: 0.8491 (t-100) cc_final: 0.8131 (m-90) REVERT: B 32 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7831 (tp30) REVERT: B 33 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7394 (t0) REVERT: B 70 ASP cc_start: 0.7676 (p0) cc_final: 0.6923 (p0) REVERT: B 92 ARG cc_start: 0.2884 (mtt180) cc_final: 0.1953 (mtm180) REVERT: B 169 HIS cc_start: 0.8379 (m-70) cc_final: 0.7918 (m170) REVERT: B 176 TYR cc_start: 0.7413 (m-80) cc_final: 0.6589 (m-80) REVERT: B 181 GLU cc_start: 0.8019 (mp0) cc_final: 0.7774 (mp0) REVERT: B 257 ILE cc_start: 0.8311 (mt) cc_final: 0.7989 (pt) REVERT: B 258 PRO cc_start: 0.8899 (Cg_endo) cc_final: 0.8535 (Cg_exo) REVERT: B 278 LYS cc_start: 0.9341 (mtmm) cc_final: 0.9131 (mttm) REVERT: B 287 LEU cc_start: 0.9448 (mt) cc_final: 0.8815 (mt) REVERT: B 305 ASP cc_start: 0.8876 (t0) cc_final: 0.8513 (t0) REVERT: B 329 VAL cc_start: 0.9427 (t) cc_final: 0.9179 (m) REVERT: B 330 TRP cc_start: 0.9007 (t-100) cc_final: 0.8549 (t-100) REVERT: B 332 ASN cc_start: 0.9114 (m-40) cc_final: 0.8882 (m110) REVERT: B 342 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8697 (mm-30) REVERT: C 32 THR cc_start: 0.9178 (m) cc_final: 0.8754 (p) REVERT: C 97 ASP cc_start: 0.8071 (p0) cc_final: 0.7781 (p0) REVERT: C 100 ASN cc_start: 0.8309 (m-40) cc_final: 0.7749 (m-40) REVERT: C 139 ASN cc_start: 0.8336 (t0) cc_final: 0.7904 (m-40) REVERT: C 262 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7676 (pt0) REVERT: C 307 ILE cc_start: 0.6328 (mt) cc_final: 0.5679 (tt) REVERT: C 308 TYR cc_start: 0.8343 (p90) cc_final: 0.8129 (p90) REVERT: C 362 GLN cc_start: 0.7903 (pm20) cc_final: 0.7614 (pm20) REVERT: C 373 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8723 (mttp) REVERT: C 409 TRP cc_start: 0.8322 (m100) cc_final: 0.7518 (m100) REVERT: D 134 PHE cc_start: 0.8990 (p90) cc_final: 0.8510 (p90) REVERT: D 137 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7952 (ptp90) REVERT: D 139 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 272 HIS cc_start: 0.8297 (t-170) cc_final: 0.8054 (t70) REVERT: D 273 THR cc_start: 0.9278 (m) cc_final: 0.8694 (p) REVERT: E 160 GLU cc_start: 0.6679 (pm20) cc_final: 0.6322 (mp0) REVERT: E 194 GLU cc_start: 0.8755 (tp30) cc_final: 0.8335 (tp30) REVERT: E 195 ASN cc_start: 0.8960 (p0) cc_final: 0.8745 (p0) REVERT: F 184 TYR cc_start: 0.6977 (m-80) cc_final: 0.6680 (m-80) REVERT: F 218 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8051 (ptp-110) REVERT: G 10 VAL cc_start: 0.9019 (t) cc_final: 0.8786 (m) REVERT: G 24 TYR cc_start: 0.8271 (m-80) cc_final: 0.7654 (m-80) REVERT: G 27 LEU cc_start: 0.8341 (tp) cc_final: 0.7842 (tp) REVERT: G 37 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7520 (mp0) REVERT: G 160 LYS cc_start: 0.9178 (pptt) cc_final: 0.8672 (mmtm) REVERT: G 170 PHE cc_start: 0.8066 (t80) cc_final: 0.7390 (t80) REVERT: G 203 ILE cc_start: 0.9075 (tt) cc_final: 0.8765 (tt) REVERT: G 218 ASP cc_start: 0.7650 (t0) cc_final: 0.7200 (t0) REVERT: G 220 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.8182 (ptp90) REVERT: G 235 GLN cc_start: 0.8922 (pt0) cc_final: 0.8686 (pt0) REVERT: G 257 PHE cc_start: 0.8531 (m-80) cc_final: 0.8137 (m-80) REVERT: G 273 TYR cc_start: 0.8607 (p90) cc_final: 0.7989 (p90) REVERT: G 281 ASP cc_start: 0.8829 (t0) cc_final: 0.7978 (p0) REVERT: G 324 ARG cc_start: 0.7663 (ptp-170) cc_final: 0.7388 (ptp90) REVERT: G 362 GLN cc_start: 0.8352 (pm20) cc_final: 0.8042 (pm20) REVERT: G 364 ASN cc_start: 0.8934 (t0) cc_final: 0.8490 (t0) REVERT: H 53 TYR cc_start: 0.7185 (m-80) cc_final: 0.6275 (m-10) REVERT: H 82 LYS cc_start: 0.8600 (mttt) cc_final: 0.7946 (mttm) REVERT: H 139 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: H 156 ASP cc_start: 0.8392 (t0) cc_final: 0.8072 (t0) REVERT: H 305 ASP cc_start: 0.8627 (t0) cc_final: 0.8344 (t0) REVERT: H 395 ASP cc_start: 0.9175 (p0) cc_final: 0.8962 (p0) REVERT: I 115 MET cc_start: 0.6643 (mmt) cc_final: 0.6063 (mmm) REVERT: I 152 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7840 (mmtt) REVERT: J 9 ASN cc_start: 0.9345 (t0) cc_final: 0.8825 (t0) REVERT: J 15 TYR cc_start: 0.8223 (t80) cc_final: 0.7868 (t80) REVERT: J 133 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8416 (mm) REVERT: J 195 MET cc_start: 0.9019 (mpp) cc_final: 0.8668 (mpp) REVERT: J 218 ASP cc_start: 0.8355 (t0) cc_final: 0.7876 (t0) REVERT: J 230 HIS cc_start: 0.8844 (t-90) cc_final: 0.8590 (t70) REVERT: J 257 PHE cc_start: 0.8515 (m-80) cc_final: 0.8016 (m-80) REVERT: J 271 CYS cc_start: 0.6540 (m) cc_final: 0.6211 (m) REVERT: J 303 VAL cc_start: 0.8240 (p) cc_final: 0.7505 (m) REVERT: J 307 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8102 (mm) REVERT: J 368 SER cc_start: 0.8630 (t) cc_final: 0.8419 (t) REVERT: J 372 LYS cc_start: 0.8789 (tptt) cc_final: 0.8382 (tppt) REVERT: J 390 GLU cc_start: 0.8342 (tp30) cc_final: 0.7387 (tt0) REVERT: J 409 TRP cc_start: 0.8543 (m100) cc_final: 0.8301 (m100) REVERT: K 38 SER cc_start: 0.9261 (t) cc_final: 0.8979 (p) REVERT: K 168 MET cc_start: 0.8456 (mmp) cc_final: 0.7829 (mmp) REVERT: K 217 MET cc_start: 0.8232 (tpp) cc_final: 0.7623 (tpp) REVERT: K 279 TRP cc_start: 0.9101 (p-90) cc_final: 0.8708 (p-90) REVERT: K 341 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8088 (mm110) REVERT: K 351 TRP cc_start: 0.8992 (m-10) cc_final: 0.8771 (m-10) REVERT: K 366 TYR cc_start: 0.8329 (m-80) cc_final: 0.7904 (m-80) REVERT: L 110 LYS cc_start: 0.8103 (mppt) cc_final: 0.7016 (pttm) REVERT: L 143 ASN cc_start: 0.8491 (t0) cc_final: 0.7585 (m-40) REVERT: L 145 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8423 (tm-30) REVERT: L 168 MET cc_start: 0.9258 (ppp) cc_final: 0.8932 (tmm) REVERT: W 72 CYS cc_start: 0.5309 (OUTLIER) cc_final: 0.4915 (p) REVERT: X 77 PHE cc_start: 0.6489 (t80) cc_final: 0.6192 (t80) outliers start: 218 outliers final: 165 residues processed: 1027 average time/residue: 0.4777 time to fit residues: 811.6628 Evaluate side-chains 1037 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 865 time to evaluate : 4.022 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL 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 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 129 LYS 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 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 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 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 45 ILE 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 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 295 LEU Chi-restraints excluded: chain D residue 296 THR 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 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 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 200 VAL 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 44 LYS 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 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 103 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 171 optimal weight: 0.0670 chunk 258 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 333 HIS ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS L 187 HIS Y 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121665 restraints weight = 64704.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125496 restraints weight = 31846.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127947 restraints weight = 19835.402| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4114 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= 0.185 Angle : 0.681 11.418 45942 Z= 0.355 Chirality : 0.046 0.332 5080 Planarity : 0.005 0.061 5924 Dihedral : 6.272 82.114 4614 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 5.81 % Allowed : 22.20 % Favored : 71.98 % 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: 0.69 (0.25), residues: 412 sheet: -0.86 (0.14), residues: 1173 loop : -0.46 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 310 HIS 0.021 0.001 HIS L 187 PHE 0.029 0.002 PHE W 38 TYR 0.030 0.002 TYR D 238 ARG 0.005 0.001 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 1197) hydrogen bonds : angle 6.13372 ( 3135) SS BOND : bond 0.00395 ( 73) SS BOND : angle 1.82190 ( 146) covalent geometry : bond 0.00416 (33660) covalent geometry : angle 0.67463 (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 1128 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 918 time to evaluate : 4.120 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: 0.8665 (mtmt) cc_final: 0.8218 (mtmt) REVERT: A 24 TYR cc_start: 0.8636 (m-80) cc_final: 0.8235 (m-80) REVERT: A 69 LYS cc_start: 0.8963 (ptmm) cc_final: 0.8705 (ptmt) REVERT: A 75 ASP cc_start: 0.7986 (t0) cc_final: 0.7104 (t0) REVERT: A 158 ASP cc_start: 0.8947 (t0) cc_final: 0.8715 (t0) REVERT: A 252 GLN cc_start: 0.8982 (mp10) cc_final: 0.8527 (mm-40) REVERT: A 262 GLU cc_start: 0.8514 (tt0) cc_final: 0.8166 (tt0) REVERT: A 395 ASP cc_start: 0.8457 (t0) cc_final: 0.8069 (t0) REVERT: A 409 TRP cc_start: 0.8500 (t-100) cc_final: 0.8199 (t-100) REVERT: B 30 LYS cc_start: 0.9080 (tptt) cc_final: 0.8236 (tttt) REVERT: B 32 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7881 (tp30) REVERT: B 33 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7391 (t0) REVERT: B 70 ASP cc_start: 0.7668 (p0) cc_final: 0.6934 (p0) REVERT: B 92 ARG cc_start: 0.2794 (mtt180) cc_final: 0.1823 (mtm180) REVERT: B 176 TYR cc_start: 0.7421 (m-80) cc_final: 0.6555 (m-80) REVERT: B 287 LEU cc_start: 0.9457 (mt) cc_final: 0.9004 (mp) REVERT: B 305 ASP cc_start: 0.8869 (t0) cc_final: 0.8498 (t0) REVERT: B 329 VAL cc_start: 0.9460 (t) cc_final: 0.9182 (m) REVERT: B 330 TRP cc_start: 0.8968 (t-100) cc_final: 0.8612 (t-100) REVERT: B 332 ASN cc_start: 0.9088 (m-40) cc_final: 0.8854 (m110) REVERT: C 32 THR cc_start: 0.9175 (m) cc_final: 0.8781 (p) REVERT: C 97 ASP cc_start: 0.8088 (p0) cc_final: 0.7832 (p0) REVERT: C 100 ASN cc_start: 0.8200 (m-40) cc_final: 0.7676 (m-40) REVERT: C 139 ASN cc_start: 0.8324 (t0) cc_final: 0.7887 (m-40) REVERT: C 262 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7706 (pt0) REVERT: C 307 ILE cc_start: 0.6278 (mt) cc_final: 0.5618 (tt) REVERT: C 362 GLN cc_start: 0.7852 (pm20) cc_final: 0.7538 (pm20) REVERT: C 373 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8727 (mttp) REVERT: C 409 TRP cc_start: 0.8312 (m100) cc_final: 0.7556 (m100) REVERT: D 134 PHE cc_start: 0.8998 (p90) cc_final: 0.8618 (p90) REVERT: D 137 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8325 (ptm160) REVERT: D 139 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7947 (mm-30) REVERT: D 272 HIS cc_start: 0.8295 (t-170) cc_final: 0.7980 (t70) REVERT: E 112 PHE cc_start: 0.8165 (m-80) cc_final: 0.7798 (m-10) REVERT: E 132 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: E 160 GLU cc_start: 0.6373 (pm20) cc_final: 0.6091 (mp0) REVERT: E 194 GLU cc_start: 0.8684 (tp30) cc_final: 0.8440 (mm-30) REVERT: F 157 TYR cc_start: 0.7816 (m-80) cc_final: 0.7578 (m-80) REVERT: F 218 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8040 (ptp-110) REVERT: F 243 ASN cc_start: 0.8553 (t0) cc_final: 0.8351 (t0) REVERT: G 10 VAL cc_start: 0.9072 (t) cc_final: 0.8815 (m) REVERT: G 24 TYR cc_start: 0.8197 (m-80) cc_final: 0.7626 (m-80) REVERT: G 27 LEU cc_start: 0.8409 (tp) cc_final: 0.7946 (tp) REVERT: G 37 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7558 (mp0) REVERT: G 160 LYS cc_start: 0.9164 (pptt) cc_final: 0.8687 (mmtm) REVERT: G 162 ILE cc_start: 0.8526 (mt) cc_final: 0.8032 (mm) REVERT: G 170 PHE cc_start: 0.8019 (t80) cc_final: 0.7334 (t80) REVERT: G 203 ILE cc_start: 0.9054 (tt) cc_final: 0.8739 (tt) REVERT: G 218 ASP cc_start: 0.7662 (t0) cc_final: 0.7201 (t0) REVERT: G 220 ARG cc_start: 0.8521 (ptp-170) cc_final: 0.8154 (ptp90) REVERT: G 273 TYR cc_start: 0.8655 (p90) cc_final: 0.8076 (p90) REVERT: G 281 ASP cc_start: 0.8827 (t0) cc_final: 0.7982 (p0) REVERT: G 324 ARG cc_start: 0.7611 (ptp-170) cc_final: 0.7360 (ptp90) REVERT: G 364 ASN cc_start: 0.8899 (t0) cc_final: 0.8434 (t0) REVERT: H 53 TYR cc_start: 0.7159 (m-80) cc_final: 0.6051 (m-10) REVERT: H 82 LYS cc_start: 0.8574 (mttt) cc_final: 0.8125 (mtmm) REVERT: H 139 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: H 156 ASP cc_start: 0.8352 (t0) cc_final: 0.8136 (t0) REVERT: H 305 ASP cc_start: 0.8682 (t0) cc_final: 0.8426 (t0) REVERT: H 395 ASP cc_start: 0.9158 (p0) cc_final: 0.8932 (p0) REVERT: I 130 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7165 (mtt180) REVERT: I 152 LYS cc_start: 0.8496 (ttpt) cc_final: 0.7985 (mmtt) REVERT: I 192 GLN cc_start: 0.9015 (tp40) cc_final: 0.8152 (mm110) REVERT: I 212 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: J 9 ASN cc_start: 0.9344 (t0) cc_final: 0.8771 (t0) REVERT: J 15 TYR cc_start: 0.8230 (t80) cc_final: 0.7862 (t80) REVERT: J 133 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8441 (mm) REVERT: J 195 MET cc_start: 0.8994 (mpp) cc_final: 0.8678 (mpp) REVERT: J 218 ASP cc_start: 0.8345 (t0) cc_final: 0.7877 (t0) REVERT: J 230 HIS cc_start: 0.8827 (t-90) cc_final: 0.8596 (t70) REVERT: J 257 PHE cc_start: 0.8483 (m-80) cc_final: 0.7869 (m-80) REVERT: J 271 CYS cc_start: 0.6535 (m) cc_final: 0.6133 (m) REVERT: J 307 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8048 (mm) REVERT: J 372 LYS cc_start: 0.8765 (tptt) cc_final: 0.8358 (tppt) REVERT: J 390 GLU cc_start: 0.8372 (tp30) cc_final: 0.7405 (tt0) REVERT: J 409 TRP cc_start: 0.8553 (m100) cc_final: 0.8222 (m100) REVERT: K 38 SER cc_start: 0.9246 (t) cc_final: 0.8947 (p) REVERT: K 168 MET cc_start: 0.8553 (mmp) cc_final: 0.7908 (mmp) REVERT: K 279 TRP cc_start: 0.9101 (p-90) cc_final: 0.8707 (p-90) REVERT: K 366 TYR cc_start: 0.8312 (m-80) cc_final: 0.7912 (m-80) REVERT: L 143 ASN cc_start: 0.8551 (t0) cc_final: 0.8265 (t0) REVERT: L 168 MET cc_start: 0.9225 (ppp) cc_final: 0.8931 (tmm) REVERT: V 99 ASP cc_start: 0.6902 (p0) cc_final: 0.6635 (p0) REVERT: W 72 CYS cc_start: 0.5306 (OUTLIER) cc_final: 0.4881 (p) REVERT: X 77 PHE cc_start: 0.6551 (t80) cc_final: 0.6347 (t80) REVERT: Y 83 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5009 (pm20) outliers start: 210 outliers final: 166 residues processed: 1020 average time/residue: 0.4391 time to fit residues: 740.8112 Evaluate side-chains 1040 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 866 time to evaluate : 3.820 ------------------------------------------------------------------------------- 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 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 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 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 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 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 113 VAL 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 201 CYS 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 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 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 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 42 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 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 237 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 146 HIS 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 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 167 ASN 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 204 GLN 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 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 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 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 159 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 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 X residue 94 ASP Chi-restraints excluded: chain X residue 96 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: 10.0000 chunk 273 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 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 204 GLN ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 333 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** ** 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 = 0.3899 r_free = 0.3899 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118146 restraints weight = 64892.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121862 restraints weight = 32212.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124267 restraints weight = 20184.900| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 33733 Z= 0.274 Angle : 0.734 12.014 45942 Z= 0.384 Chirality : 0.047 0.244 5080 Planarity : 0.005 0.051 5924 Dihedral : 6.346 83.764 4614 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 6.01 % Allowed : 22.76 % Favored : 71.23 % 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: -0.87 (0.13), residues: 4240 helix: 0.45 (0.24), residues: 434 sheet: -0.87 (0.15), residues: 1148 loop : -0.57 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 186 HIS 0.018 0.002 HIS L 187 PHE 0.028 0.002 PHE K 100 TYR 0.021 0.002 TYR K 229 ARG 0.009 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1197) hydrogen bonds : angle 6.16973 ( 3135) SS BOND : bond 0.00435 ( 73) SS BOND : angle 1.79974 ( 146) covalent geometry : bond 0.00612 (33660) covalent geometry : angle 0.72783 (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 1082 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 865 time to evaluate : 4.937 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: A 16 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8288 (mtmt) REVERT: A 75 ASP cc_start: 0.8085 (t0) cc_final: 0.7138 (t0) REVERT: A 158 ASP cc_start: 0.8964 (t0) cc_final: 0.8660 (t0) REVERT: A 219 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9019 (mp) REVERT: A 262 GLU cc_start: 0.8570 (tt0) cc_final: 0.8223 (tt0) REVERT: A 264 GLU cc_start: 0.8417 (mp0) cc_final: 0.8111 (mp0) REVERT: A 395 ASP cc_start: 0.8512 (t0) cc_final: 0.8171 (t0) REVERT: A 409 TRP cc_start: 0.8539 (t-100) cc_final: 0.8268 (t-100) REVERT: B 33 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7311 (t0) REVERT: B 39 ASP cc_start: 0.7830 (m-30) cc_final: 0.7390 (m-30) REVERT: B 40 ASP cc_start: 0.8519 (p0) cc_final: 0.8115 (p0) REVERT: B 92 ARG cc_start: 0.2957 (mtt180) cc_final: 0.1924 (mtm180) REVERT: B 176 TYR cc_start: 0.7496 (m-80) cc_final: 0.6664 (m-80) REVERT: B 287 LEU cc_start: 0.9486 (mt) cc_final: 0.8981 (mp) REVERT: B 305 ASP cc_start: 0.8883 (t0) cc_final: 0.8522 (t0) REVERT: B 330 TRP cc_start: 0.9032 (t-100) cc_final: 0.8598 (t-100) REVERT: C 32 THR cc_start: 0.9215 (m) cc_final: 0.8804 (p) REVERT: C 97 ASP cc_start: 0.8084 (p0) cc_final: 0.7799 (p0) REVERT: C 100 ASN cc_start: 0.8216 (m-40) cc_final: 0.7716 (m-40) REVERT: C 139 ASN cc_start: 0.8346 (t0) cc_final: 0.7918 (m-40) REVERT: C 209 ASP cc_start: 0.8304 (p0) cc_final: 0.8061 (p0) REVERT: C 262 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7680 (pt0) REVERT: C 307 ILE cc_start: 0.6383 (mt) cc_final: 0.6062 (mt) REVERT: C 362 GLN cc_start: 0.7925 (pm20) cc_final: 0.7662 (pm20) REVERT: C 373 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8725 (mttp) REVERT: C 409 TRP cc_start: 0.8336 (m100) cc_final: 0.7680 (m100) REVERT: D 134 PHE cc_start: 0.8958 (p90) cc_final: 0.8502 (p90) REVERT: D 137 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8443 (ptm160) REVERT: D 139 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 272 HIS cc_start: 0.8284 (t-170) cc_final: 0.7910 (t70) REVERT: E 112 PHE cc_start: 0.8218 (m-80) cc_final: 0.7861 (m-10) REVERT: E 132 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: E 160 GLU cc_start: 0.6454 (pm20) cc_final: 0.6147 (mp0) REVERT: E 194 GLU cc_start: 0.8631 (tp30) cc_final: 0.8345 (mm-30) REVERT: F 157 TYR cc_start: 0.8037 (m-80) cc_final: 0.7726 (m-80) REVERT: F 243 ASN cc_start: 0.8655 (t0) cc_final: 0.8409 (t0) REVERT: G 10 VAL cc_start: 0.9087 (t) cc_final: 0.8821 (m) REVERT: G 24 TYR cc_start: 0.8248 (m-80) cc_final: 0.7738 (m-80) REVERT: G 27 LEU cc_start: 0.8579 (tp) cc_final: 0.8189 (tp) REVERT: G 37 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7580 (mp0) REVERT: G 57 SER cc_start: 0.9106 (m) cc_final: 0.8484 (p) REVERT: G 157 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6946 (tmm-80) REVERT: G 160 LYS cc_start: 0.9162 (pptt) cc_final: 0.8649 (mmtm) REVERT: G 170 PHE cc_start: 0.7967 (t80) cc_final: 0.7446 (t80) REVERT: G 203 ILE cc_start: 0.9060 (tt) cc_final: 0.8795 (tt) REVERT: G 216 ARG cc_start: 0.8622 (mtp85) cc_final: 0.7962 (ttm-80) REVERT: G 218 ASP cc_start: 0.7726 (t0) cc_final: 0.7253 (t0) REVERT: G 220 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8214 (ptp90) REVERT: G 257 PHE cc_start: 0.8411 (m-80) cc_final: 0.8015 (m-80) REVERT: G 273 TYR cc_start: 0.8584 (p90) cc_final: 0.8234 (p90) REVERT: G 281 ASP cc_start: 0.8854 (t0) cc_final: 0.7981 (p0) REVERT: G 324 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7486 (ttp80) REVERT: G 364 ASN cc_start: 0.8954 (t0) cc_final: 0.8454 (t0) REVERT: H 53 TYR cc_start: 0.7056 (m-80) cc_final: 0.6841 (m-10) REVERT: H 82 LYS cc_start: 0.8630 (mttt) cc_final: 0.8192 (mtmm) REVERT: H 139 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: H 305 ASP cc_start: 0.8747 (t0) cc_final: 0.8510 (t0) REVERT: H 395 ASP cc_start: 0.9153 (p0) cc_final: 0.8909 (p0) REVERT: I 130 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7433 (mtt180) REVERT: I 152 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7942 (mmtt) REVERT: I 212 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: J 9 ASN cc_start: 0.9375 (t0) cc_final: 0.8802 (t0) REVERT: J 15 TYR cc_start: 0.8267 (t80) cc_final: 0.7922 (t80) REVERT: J 133 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8369 (mm) REVERT: J 195 MET cc_start: 0.9005 (mpp) cc_final: 0.8689 (mpp) REVERT: J 218 ASP cc_start: 0.8467 (t0) cc_final: 0.8003 (t0) REVERT: J 230 HIS cc_start: 0.8874 (t-90) cc_final: 0.8639 (t70) REVERT: J 307 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8069 (mm) REVERT: J 372 LYS cc_start: 0.8770 (tptt) cc_final: 0.8468 (tppt) REVERT: J 390 GLU cc_start: 0.8492 (tp30) cc_final: 0.7528 (tt0) REVERT: J 409 TRP cc_start: 0.8532 (m100) cc_final: 0.8249 (m100) REVERT: K 38 SER cc_start: 0.9373 (t) cc_final: 0.9000 (p) REVERT: K 279 TRP cc_start: 0.9113 (p-90) cc_final: 0.8674 (p-90) REVERT: K 366 TYR cc_start: 0.8365 (m-80) cc_final: 0.7964 (m-80) REVERT: L 143 ASN cc_start: 0.8605 (t0) cc_final: 0.8307 (t0) REVERT: L 168 MET cc_start: 0.9245 (ppp) cc_final: 0.8952 (tmm) REVERT: L 217 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6587 (p0) REVERT: V 99 ASP cc_start: 0.6238 (p0) cc_final: 0.5861 (p0) REVERT: W 72 CYS cc_start: 0.5400 (OUTLIER) cc_final: 0.4917 (p) REVERT: X 77 PHE cc_start: 0.6868 (t80) cc_final: 0.6500 (t80) REVERT: Y 83 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5044 (pm20) outliers start: 217 outliers final: 178 residues processed: 982 average time/residue: 0.5518 time to fit residues: 902.1663 Evaluate side-chains 1023 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 834 time to evaluate : 7.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 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 195 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 388 ILE 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 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 180 LEU Chi-restraints excluded: chain B residue 187 VAL 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 276 VAL 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 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 246 ASN 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 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 198 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 247 THR 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 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 E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 204 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 141 ILE 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 120 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 157 ARG Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 237 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 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 236 TRP 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 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 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 204 GLN 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 305 ASP Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 339 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 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 302 LEU 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 159 LEU 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 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 X residue 96 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: 20.0000 chunk 375 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 266 optimal weight: 0.0870 chunk 224 optimal weight: 6.9990 chunk 354 optimal weight: 8.9990 chunk 343 optimal weight: 0.9990 chunk 372 optimal weight: 0.0020 chunk 300 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 398 optimal weight: 0.2980 overall best weight: 1.0770 ------------------------------------------------------------------------------- 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 46 GLN ** B 157 HIS ** 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 235 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 HIS ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 333 HIS ** J 396 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 146 HIS 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** L 187 HIS 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 = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123606 restraints weight = 64477.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127464 restraints weight = 31709.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129967 restraints weight = 19700.496| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33733 Z= 0.144 Angle : 0.696 11.717 45942 Z= 0.357 Chirality : 0.046 0.216 5080 Planarity : 0.005 0.070 5924 Dihedral : 6.172 83.487 4613 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 4.93 % Allowed : 24.25 % Favored : 70.82 % 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: -0.73 (0.13), residues: 4240 helix: 0.86 (0.25), residues: 410 sheet: -0.89 (0.14), residues: 1137 loop : -0.45 (0.13), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 89 HIS 0.009 0.001 HIS D 73 PHE 0.037 0.002 PHE I 198 TYR 0.034 0.002 TYR D 238 ARG 0.009 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 1197) hydrogen bonds : angle 6.02805 ( 3135) SS BOND : bond 0.00339 ( 73) SS BOND : angle 1.57108 ( 146) covalent geometry : bond 0.00325 (33660) covalent geometry : angle 0.69106 (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 1079 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 901 time to evaluate : 4.005 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: A 10 VAL cc_start: 0.9515 (t) cc_final: 0.9297 (m) REVERT: A 16 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8240 (mtmt) REVERT: A 24 TYR cc_start: 0.8245 (m-80) cc_final: 0.7862 (m-80) REVERT: A 69 LYS cc_start: 0.8908 (ptmm) cc_final: 0.8586 (ptmt) REVERT: A 75 ASP cc_start: 0.7828 (t0) cc_final: 0.6806 (t0) REVERT: A 158 ASP cc_start: 0.8984 (t0) cc_final: 0.8686 (t0) REVERT: A 219 ILE cc_start: 0.9316 (mt) cc_final: 0.9015 (mp) REVERT: A 264 GLU cc_start: 0.8434 (mp0) cc_final: 0.8115 (mp0) REVERT: A 395 ASP cc_start: 0.8479 (t0) cc_final: 0.8064 (t0) REVERT: A 409 TRP cc_start: 0.8504 (t-100) cc_final: 0.8214 (t-100) REVERT: B 33 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7289 (t0) REVERT: B 70 ASP cc_start: 0.7662 (p0) cc_final: 0.6923 (p0) REVERT: B 78 ASP cc_start: 0.7773 (t0) cc_final: 0.7474 (t0) REVERT: B 92 ARG cc_start: 0.2829 (mtt180) cc_final: 0.1844 (mtm180) REVERT: B 176 TYR cc_start: 0.7403 (m-80) cc_final: 0.6588 (m-80) REVERT: B 278 LYS cc_start: 0.9294 (mttm) cc_final: 0.8978 (mttm) REVERT: B 287 LEU cc_start: 0.9417 (mt) cc_final: 0.8923 (mp) REVERT: B 305 ASP cc_start: 0.8847 (t0) cc_final: 0.8476 (t0) REVERT: B 330 TRP cc_start: 0.8922 (t-100) cc_final: 0.8517 (t-100) REVERT: C 32 THR cc_start: 0.9193 (m) cc_final: 0.8798 (p) REVERT: C 97 ASP cc_start: 0.8136 (p0) cc_final: 0.7784 (p0) REVERT: C 195 MET cc_start: 0.8788 (mpp) cc_final: 0.7180 (mpp) REVERT: C 204 GLN cc_start: 0.8337 (mt0) cc_final: 0.7873 (mt0) REVERT: C 209 ASP cc_start: 0.8290 (p0) cc_final: 0.8052 (p0) REVERT: C 262 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7652 (pt0) REVERT: C 307 ILE cc_start: 0.6614 (mt) cc_final: 0.6000 (tt) REVERT: C 362 GLN cc_start: 0.7864 (pm20) cc_final: 0.7561 (pm20) REVERT: C 373 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8703 (mttp) REVERT: C 409 TRP cc_start: 0.8291 (m100) cc_final: 0.7599 (m100) REVERT: D 62 THR cc_start: 0.8867 (t) cc_final: 0.8658 (t) REVERT: D 134 PHE cc_start: 0.8954 (p90) cc_final: 0.8503 (p90) REVERT: D 137 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8245 (ptm160) REVERT: D 139 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7880 (mm-30) REVERT: D 261 LEU cc_start: 0.9367 (tp) cc_final: 0.9046 (tt) REVERT: D 272 HIS cc_start: 0.8116 (t-170) cc_final: 0.7684 (t70) REVERT: E 112 PHE cc_start: 0.8147 (m-80) cc_final: 0.7820 (m-10) REVERT: E 130 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8423 (mmm-85) REVERT: E 132 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: E 140 LYS cc_start: 0.7290 (tptp) cc_final: 0.7026 (tptt) REVERT: E 194 GLU cc_start: 0.8640 (tp30) cc_final: 0.8298 (tp30) REVERT: F 157 TYR cc_start: 0.7846 (m-80) cc_final: 0.7374 (m-80) REVERT: F 197 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8308 (ttm170) REVERT: F 218 ARG cc_start: 0.8576 (mtp85) cc_final: 0.7984 (ptp-110) REVERT: F 243 ASN cc_start: 0.8669 (t0) cc_final: 0.8346 (t0) REVERT: G 10 VAL cc_start: 0.9078 (t) cc_final: 0.8819 (m) REVERT: G 24 TYR cc_start: 0.8083 (m-80) cc_final: 0.7572 (m-80) REVERT: G 27 LEU cc_start: 0.8508 (tp) cc_final: 0.8156 (tp) REVERT: G 37 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7552 (mp0) REVERT: G 57 SER cc_start: 0.9054 (m) cc_final: 0.8327 (p) REVERT: G 157 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7248 (tpp80) REVERT: G 160 LYS cc_start: 0.9133 (pptt) cc_final: 0.8604 (mmtm) REVERT: G 162 ILE cc_start: 0.8490 (mt) cc_final: 0.7997 (mm) REVERT: G 170 PHE cc_start: 0.7912 (t80) cc_final: 0.7298 (t80) REVERT: G 203 ILE cc_start: 0.8945 (tt) cc_final: 0.8676 (tt) REVERT: G 204 GLN cc_start: 0.8006 (mt0) cc_final: 0.7591 (mt0) REVERT: G 216 ARG cc_start: 0.8610 (mtp85) cc_final: 0.7945 (ttm-80) REVERT: G 218 ASP cc_start: 0.7599 (t0) cc_final: 0.6956 (t0) REVERT: G 220 ARG cc_start: 0.8545 (ptp-170) cc_final: 0.8020 (ptp90) REVERT: G 257 PHE cc_start: 0.8374 (m-80) cc_final: 0.7957 (m-80) REVERT: G 273 TYR cc_start: 0.8658 (p90) cc_final: 0.8299 (p90) REVERT: G 281 ASP cc_start: 0.8851 (t0) cc_final: 0.7966 (p0) REVERT: G 364 ASN cc_start: 0.8926 (t0) cc_final: 0.8431 (t0) REVERT: H 53 TYR cc_start: 0.6919 (m-80) cc_final: 0.5973 (m-10) REVERT: H 82 LYS cc_start: 0.8541 (mttt) cc_final: 0.7983 (mttm) REVERT: H 155 TYR cc_start: 0.7745 (m-80) cc_final: 0.7358 (m-80) REVERT: H 305 ASP cc_start: 0.8697 (t0) cc_final: 0.8473 (t0) REVERT: H 395 ASP cc_start: 0.9134 (p0) cc_final: 0.8890 (p0) REVERT: I 130 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7266 (mtt180) REVERT: I 152 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7822 (mmtt) REVERT: J 9 ASN cc_start: 0.9378 (t0) cc_final: 0.8920 (t0) REVERT: J 15 TYR cc_start: 0.8172 (t80) cc_final: 0.7862 (t80) REVERT: J 133 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8511 (mm) REVERT: J 195 MET cc_start: 0.8964 (mpp) cc_final: 0.8724 (mpp) REVERT: J 218 ASP cc_start: 0.8331 (t0) cc_final: 0.7869 (t0) REVERT: J 230 HIS cc_start: 0.8715 (t-90) cc_final: 0.8507 (t70) REVERT: J 257 PHE cc_start: 0.8560 (m-80) cc_final: 0.8079 (m-80) REVERT: J 307 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7936 (mm) REVERT: J 372 LYS cc_start: 0.8734 (tptt) cc_final: 0.8383 (tppt) REVERT: J 390 GLU cc_start: 0.8452 (tp30) cc_final: 0.7641 (tt0) REVERT: J 409 TRP cc_start: 0.8412 (m100) cc_final: 0.8170 (m100) REVERT: K 38 SER cc_start: 0.9285 (t) cc_final: 0.8937 (p) REVERT: K 78 ASP cc_start: 0.8597 (t0) cc_final: 0.8312 (t70) REVERT: K 93 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8360 (ttp80) REVERT: K 130 ILE cc_start: 0.8880 (mm) cc_final: 0.8577 (tp) REVERT: K 168 MET cc_start: 0.8092 (mmp) cc_final: 0.7739 (mmp) REVERT: K 279 TRP cc_start: 0.9108 (p-90) cc_final: 0.8719 (p-90) REVERT: K 366 TYR cc_start: 0.8301 (m-80) cc_final: 0.7946 (m-80) REVERT: L 156 MET cc_start: 0.8993 (ppp) cc_final: 0.8565 (ppp) REVERT: L 168 MET cc_start: 0.9238 (ppp) cc_final: 0.8940 (tmm) REVERT: V 101 SER cc_start: 0.8757 (m) cc_final: 0.8536 (p) REVERT: W 88 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7717 (ttm-80) REVERT: W 106 GLU cc_start: 0.7430 (pt0) cc_final: 0.7152 (pp20) REVERT: X 77 PHE cc_start: 0.6859 (t80) cc_final: 0.6495 (t80) REVERT: Y 83 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.5271 (pm20) outliers start: 178 outliers final: 142 residues processed: 994 average time/residue: 0.4256 time to fit residues: 691.9050 Evaluate side-chains 996 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 847 time to evaluate : 3.509 ------------------------------------------------------------------------------- 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 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 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 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 187 VAL Chi-restraints excluded: chain B residue 247 THR 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 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 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 186 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 428 LEU 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 295 LEU 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 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 204 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 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 54 VAL Chi-restraints excluded: chain G residue 55 ILE 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 155 SER Chi-restraints excluded: chain G residue 157 ARG 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 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 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 102 GLN Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 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 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 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 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 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 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: 9.9990 chunk 136 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 387 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 395 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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** D 33 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 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** ** K 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS W 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122414 restraints weight = 64391.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126227 restraints weight = 31907.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128677 restraints weight = 19892.492| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33733 Z= 0.180 Angle : 0.715 11.843 45942 Z= 0.368 Chirality : 0.047 0.303 5080 Planarity : 0.005 0.054 5924 Dihedral : 6.154 83.062 4613 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 4.96 % Allowed : 24.67 % Favored : 70.38 % 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: -0.79 (0.13), residues: 4240 helix: 0.87 (0.26), residues: 402 sheet: -0.95 (0.14), residues: 1148 loop : -0.49 (0.13), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 330 HIS 0.015 0.001 HIS L 187 PHE 0.033 0.002 PHE W 38 TYR 0.031 0.002 TYR C 185 ARG 0.009 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1197) hydrogen bonds : angle 5.99168 ( 3135) SS BOND : bond 0.00397 ( 73) SS BOND : angle 2.02709 ( 146) covalent geometry : bond 0.00412 (33660) covalent geometry : angle 0.70677 (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 1036 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 857 time to evaluate : 4.289 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: A 10 VAL cc_start: 0.9489 (t) cc_final: 0.9268 (m) REVERT: A 16 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8235 (mtmt) REVERT: A 75 ASP cc_start: 0.7872 (t0) cc_final: 0.6897 (t0) REVERT: A 158 ASP cc_start: 0.9000 (t0) cc_final: 0.8707 (t0) REVERT: A 219 ILE cc_start: 0.9339 (mt) cc_final: 0.9056 (mp) REVERT: A 264 GLU cc_start: 0.8520 (mp0) cc_final: 0.8272 (mp0) REVERT: A 395 ASP cc_start: 0.8529 (t0) cc_final: 0.8123 (t0) REVERT: A 409 TRP cc_start: 0.8526 (t-100) cc_final: 0.8272 (t-100) REVERT: B 33 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7265 (t0) REVERT: B 70 ASP cc_start: 0.7670 (p0) cc_final: 0.6932 (p0) REVERT: B 92 ARG cc_start: 0.2729 (mtt180) cc_final: 0.1729 (mtm180) REVERT: B 176 TYR cc_start: 0.7471 (m-80) cc_final: 0.6613 (m-80) REVERT: B 287 LEU cc_start: 0.9426 (mt) cc_final: 0.8997 (mp) REVERT: B 305 ASP cc_start: 0.8844 (t0) cc_final: 0.8435 (t0) REVERT: B 330 TRP cc_start: 0.8968 (t-100) cc_final: 0.8555 (t-100) REVERT: B 357 ILE cc_start: 0.9485 (pt) cc_final: 0.9270 (tt) REVERT: C 32 THR cc_start: 0.9195 (m) cc_final: 0.8822 (p) REVERT: C 195 MET cc_start: 0.8834 (mpp) cc_final: 0.7268 (mpp) REVERT: C 204 GLN cc_start: 0.8347 (mt0) cc_final: 0.7903 (mt0) REVERT: C 209 ASP cc_start: 0.8297 (p0) cc_final: 0.8070 (p0) REVERT: C 262 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7684 (pt0) REVERT: C 307 ILE cc_start: 0.6358 (mt) cc_final: 0.6095 (mt) REVERT: C 362 GLN cc_start: 0.7878 (pm20) cc_final: 0.7621 (pm20) REVERT: C 373 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8723 (mttp) REVERT: C 409 TRP cc_start: 0.8342 (m100) cc_final: 0.7635 (m100) REVERT: D 134 PHE cc_start: 0.8948 (p90) cc_final: 0.8478 (p90) REVERT: D 137 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8318 (ptm160) REVERT: D 139 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 261 LEU cc_start: 0.9379 (tp) cc_final: 0.9059 (tt) REVERT: D 272 HIS cc_start: 0.8118 (t-170) cc_final: 0.7623 (t70) REVERT: D 330 TRP cc_start: 0.9332 (t-100) cc_final: 0.8980 (t-100) REVERT: E 112 PHE cc_start: 0.8161 (m-80) cc_final: 0.7837 (m-10) REVERT: E 130 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8412 (mmm-85) REVERT: E 140 LYS cc_start: 0.7443 (tptp) cc_final: 0.7202 (tptt) REVERT: E 160 GLU cc_start: 0.6121 (mp0) cc_final: 0.5888 (mp0) REVERT: E 192 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: E 194 GLU cc_start: 0.8602 (tp30) cc_final: 0.8325 (mm-30) REVERT: F 156 MET cc_start: 0.8876 (tmm) cc_final: 0.8087 (pmm) REVERT: F 157 TYR cc_start: 0.7879 (m-80) cc_final: 0.6912 (m-80) REVERT: F 186 TRP cc_start: 0.7814 (t60) cc_final: 0.7402 (t60) REVERT: F 197 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8301 (ttm170) REVERT: F 218 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7922 (ptp-110) REVERT: F 243 ASN cc_start: 0.8643 (t0) cc_final: 0.8331 (t0) REVERT: G 10 VAL cc_start: 0.9073 (t) cc_final: 0.8811 (m) REVERT: G 24 TYR cc_start: 0.8160 (m-80) cc_final: 0.7631 (m-80) REVERT: G 27 LEU cc_start: 0.8471 (tp) cc_final: 0.8116 (tp) REVERT: G 37 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7569 (mp0) REVERT: G 57 SER cc_start: 0.9219 (m) cc_final: 0.8606 (p) REVERT: G 157 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7187 (tpp80) REVERT: G 160 LYS cc_start: 0.9129 (pptt) cc_final: 0.8625 (mmtm) REVERT: G 170 PHE cc_start: 0.7939 (t80) cc_final: 0.7439 (t80) REVERT: G 204 GLN cc_start: 0.8057 (mt0) cc_final: 0.7673 (mt0) REVERT: G 216 ARG cc_start: 0.8636 (mtp85) cc_final: 0.7964 (ttm-80) REVERT: G 218 ASP cc_start: 0.7639 (t0) cc_final: 0.7034 (t0) REVERT: G 220 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8059 (ptp90) REVERT: G 257 PHE cc_start: 0.8386 (m-80) cc_final: 0.7982 (m-80) REVERT: G 273 TYR cc_start: 0.8695 (p90) cc_final: 0.8321 (p90) REVERT: G 281 ASP cc_start: 0.8844 (t0) cc_final: 0.7991 (p0) REVERT: G 364 ASN cc_start: 0.8935 (t0) cc_final: 0.8425 (t0) REVERT: G 390 GLU cc_start: 0.8843 (tp30) cc_final: 0.8602 (tp30) REVERT: H 53 TYR cc_start: 0.6850 (m-80) cc_final: 0.5833 (m-10) REVERT: H 82 LYS cc_start: 0.8531 (mttt) cc_final: 0.8127 (mtmm) REVERT: H 155 TYR cc_start: 0.8054 (m-80) cc_final: 0.7681 (m-80) REVERT: H 395 ASP cc_start: 0.9128 (p0) cc_final: 0.8890 (p0) REVERT: I 130 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7291 (mtt180) REVERT: I 152 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7794 (mmtm) REVERT: I 212 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.7901 (mmm-85) REVERT: J 9 ASN cc_start: 0.9390 (t0) cc_final: 0.8926 (t0) REVERT: J 15 TYR cc_start: 0.8234 (t80) cc_final: 0.7906 (t80) REVERT: J 133 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8434 (mm) REVERT: J 218 ASP cc_start: 0.8385 (t0) cc_final: 0.7909 (t0) REVERT: J 257 PHE cc_start: 0.8605 (m-80) cc_final: 0.8082 (m-80) REVERT: J 307 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (mm) REVERT: J 372 LYS cc_start: 0.8750 (tptt) cc_final: 0.8403 (tppt) REVERT: J 390 GLU cc_start: 0.8499 (tp30) cc_final: 0.7696 (tt0) REVERT: J 409 TRP cc_start: 0.8418 (m100) cc_final: 0.8170 (m100) REVERT: K 38 SER cc_start: 0.9230 (t) cc_final: 0.8869 (p) REVERT: K 78 ASP cc_start: 0.8695 (t0) cc_final: 0.8427 (t70) REVERT: K 168 MET cc_start: 0.8303 (mmp) cc_final: 0.7770 (mmp) REVERT: K 259 PHE cc_start: 0.8530 (m-80) cc_final: 0.8087 (m-10) REVERT: K 279 TRP cc_start: 0.9128 (p-90) cc_final: 0.8717 (p-90) REVERT: K 366 TYR cc_start: 0.8316 (m-80) cc_final: 0.7967 (m-80) REVERT: L 156 MET cc_start: 0.9037 (ppp) cc_final: 0.8655 (ppp) REVERT: L 168 MET cc_start: 0.9254 (ppp) cc_final: 0.8870 (tmm) REVERT: V 50 TRP cc_start: 0.8291 (m-10) cc_final: 0.7980 (m-10) REVERT: W 106 GLU cc_start: 0.7442 (pt0) cc_final: 0.7118 (pp20) REVERT: X 77 PHE cc_start: 0.6894 (t80) cc_final: 0.6584 (t80) REVERT: Y 83 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5219 (pm20) outliers start: 179 outliers final: 151 residues processed: 948 average time/residue: 0.4343 time to fit residues: 676.3257 Evaluate side-chains 990 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 832 time to evaluate : 4.159 ------------------------------------------------------------------------------- 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 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 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 195 MET Chi-restraints excluded: chain A residue 203 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 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 29 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 83 ILE 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 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 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 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 280 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 428 LEU 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 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 127 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 204 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 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 54 VAL Chi-restraints excluded: chain G residue 55 ILE 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 155 SER Chi-restraints excluded: chain G residue 157 ARG 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 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 314 THR 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 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 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 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 104 GLN 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 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 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 85 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 76 ASP Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 96 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 100 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** 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** ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 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** L 187 HIS ** 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 = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123287 restraints weight = 64547.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127139 restraints weight = 31844.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129595 restraints weight = 19763.297| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33733 Z= 0.167 Angle : 0.716 11.504 45942 Z= 0.367 Chirality : 0.047 0.341 5080 Planarity : 0.005 0.047 5924 Dihedral : 6.143 82.267 4613 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 4.51 % Allowed : 25.08 % Favored : 70.40 % 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: -0.80 (0.13), residues: 4240 helix: 0.92 (0.25), residues: 402 sheet: -1.04 (0.14), residues: 1180 loop : -0.45 (0.13), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 330 HIS 0.010 0.001 HIS D 73 PHE 0.036 0.002 PHE K 15 TYR 0.022 0.002 TYR K 229 ARG 0.009 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1197) hydrogen bonds : angle 5.97100 ( 3135) SS BOND : bond 0.00369 ( 73) SS BOND : angle 1.95020 ( 146) covalent geometry : bond 0.00384 (33660) covalent geometry : angle 0.70857 (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 1031 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 868 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.9517 (t) cc_final: 0.9285 (m) REVERT: A 16 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8263 (mtmt) REVERT: A 75 ASP cc_start: 0.7838 (t0) cc_final: 0.6854 (t0) REVERT: A 158 ASP cc_start: 0.8970 (t0) cc_final: 0.8674 (t0) REVERT: A 219 ILE cc_start: 0.9327 (mt) cc_final: 0.9035 (mp) REVERT: A 395 ASP cc_start: 0.8528 (t0) cc_final: 0.8216 (t0) REVERT: A 409 TRP cc_start: 0.8542 (t-100) cc_final: 0.8264 (t-100) REVERT: B 33 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7235 (t0) REVERT: B 70 ASP cc_start: 0.7692 (p0) cc_final: 0.6913 (p0) REVERT: B 92 ARG cc_start: 0.2661 (mtt180) cc_final: 0.1686 (mtm180) REVERT: B 176 TYR cc_start: 0.7463 (m-80) cc_final: 0.6546 (m-80) REVERT: B 287 LEU cc_start: 0.9406 (mt) cc_final: 0.8960 (mp) REVERT: B 305 ASP cc_start: 0.8797 (t0) cc_final: 0.8376 (t0) REVERT: B 330 TRP cc_start: 0.8978 (t-100) cc_final: 0.8525 (t-100) REVERT: B 357 ILE cc_start: 0.9483 (pt) cc_final: 0.9279 (tt) REVERT: C 32 THR cc_start: 0.9191 (m) cc_final: 0.8823 (p) REVERT: C 97 ASP cc_start: 0.8127 (p0) cc_final: 0.7810 (p0) REVERT: C 195 MET cc_start: 0.8831 (mpp) cc_final: 0.7260 (mpp) REVERT: C 204 GLN cc_start: 0.8303 (mt0) cc_final: 0.7848 (mt0) REVERT: C 209 ASP cc_start: 0.8280 (p0) cc_final: 0.8047 (p0) REVERT: C 262 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7687 (pt0) REVERT: C 307 ILE cc_start: 0.6663 (mt) cc_final: 0.6365 (mt) REVERT: C 362 GLN cc_start: 0.7865 (pm20) cc_final: 0.7583 (pm20) REVERT: C 373 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8694 (mttp) REVERT: C 409 TRP cc_start: 0.8338 (m100) cc_final: 0.7636 (m100) REVERT: D 134 PHE cc_start: 0.8953 (p90) cc_final: 0.8494 (p90) REVERT: D 137 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8128 (ptp90) REVERT: D 139 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7823 (mm-30) REVERT: D 261 LEU cc_start: 0.9379 (tp) cc_final: 0.9058 (tt) REVERT: D 272 HIS cc_start: 0.8047 (t-170) cc_final: 0.7549 (t70) REVERT: D 330 TRP cc_start: 0.9357 (t-100) cc_final: 0.9008 (t-100) REVERT: E 112 PHE cc_start: 0.8136 (m-80) cc_final: 0.7814 (m-10) REVERT: E 130 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8407 (mmm-85) REVERT: E 140 LYS cc_start: 0.7430 (tptp) cc_final: 0.7193 (tptt) REVERT: E 160 GLU cc_start: 0.6167 (mp0) cc_final: 0.5917 (mp0) REVERT: E 194 GLU cc_start: 0.8640 (tp30) cc_final: 0.8351 (mm-30) REVERT: F 156 MET cc_start: 0.8829 (tmm) cc_final: 0.8038 (pmm) REVERT: F 157 TYR cc_start: 0.7876 (m-80) cc_final: 0.7007 (m-80) REVERT: F 186 TRP cc_start: 0.7824 (t60) cc_final: 0.7432 (t60) REVERT: F 218 ARG cc_start: 0.8550 (mtp85) cc_final: 0.7917 (ptp-110) REVERT: F 243 ASN cc_start: 0.8718 (t0) cc_final: 0.8434 (t0) REVERT: G 10 VAL cc_start: 0.9080 (t) cc_final: 0.8836 (m) REVERT: G 24 TYR cc_start: 0.8082 (m-80) cc_final: 0.7581 (m-80) REVERT: G 27 LEU cc_start: 0.8498 (tp) cc_final: 0.8133 (tp) REVERT: G 37 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7557 (mp0) REVERT: G 57 SER cc_start: 0.9207 (m) cc_final: 0.8588 (p) REVERT: G 157 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7208 (tpp80) REVERT: G 160 LYS cc_start: 0.9116 (pptt) cc_final: 0.8531 (mmtm) REVERT: G 170 PHE cc_start: 0.7900 (t80) cc_final: 0.7309 (t80) REVERT: G 216 ARG cc_start: 0.8607 (mtp85) cc_final: 0.7990 (ttm-80) REVERT: G 218 ASP cc_start: 0.7612 (t0) cc_final: 0.7013 (t0) REVERT: G 220 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8043 (ptp90) REVERT: G 257 PHE cc_start: 0.8383 (m-80) cc_final: 0.7991 (m-80) REVERT: G 273 TYR cc_start: 0.8608 (p90) cc_final: 0.8193 (p90) REVERT: G 281 ASP cc_start: 0.8832 (t0) cc_final: 0.7995 (p0) REVERT: G 364 ASN cc_start: 0.8936 (t0) cc_final: 0.8428 (t0) REVERT: H 53 TYR cc_start: 0.6711 (m-80) cc_final: 0.5717 (m-10) REVERT: H 82 LYS cc_start: 0.8555 (mttt) cc_final: 0.8082 (mtmm) REVERT: H 155 TYR cc_start: 0.7903 (m-80) cc_final: 0.7650 (m-80) REVERT: H 395 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8884 (p0) REVERT: I 130 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7149 (mtt180) REVERT: I 152 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7817 (mmtm) REVERT: J 9 ASN cc_start: 0.9383 (t0) cc_final: 0.8919 (t0) REVERT: J 15 TYR cc_start: 0.8219 (t80) cc_final: 0.7902 (t80) REVERT: J 133 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8478 (mm) REVERT: J 218 ASP cc_start: 0.8342 (t0) cc_final: 0.7877 (t0) REVERT: J 257 PHE cc_start: 0.8572 (m-80) cc_final: 0.8062 (m-80) REVERT: J 307 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7935 (mm) REVERT: J 372 LYS cc_start: 0.8758 (tptt) cc_final: 0.8405 (tppt) REVERT: J 390 GLU cc_start: 0.8444 (tp30) cc_final: 0.7710 (tt0) REVERT: J 409 TRP cc_start: 0.8415 (m100) cc_final: 0.8172 (m100) REVERT: K 38 SER cc_start: 0.9238 (t) cc_final: 0.8915 (p) REVERT: K 78 ASP cc_start: 0.8710 (t0) cc_final: 0.8413 (t70) REVERT: K 91 CYS cc_start: 0.7010 (m) cc_final: 0.6787 (m) REVERT: K 168 MET cc_start: 0.8238 (mmp) cc_final: 0.7873 (mmp) REVERT: K 279 TRP cc_start: 0.9120 (p-90) cc_final: 0.8761 (p-90) REVERT: K 366 TYR cc_start: 0.8315 (m-80) cc_final: 0.7974 (m-80) REVERT: L 156 MET cc_start: 0.9046 (ppp) cc_final: 0.8710 (ppp) REVERT: L 168 MET cc_start: 0.9270 (ppp) cc_final: 0.8910 (tmm) REVERT: V 99 ASP cc_start: 0.6871 (p0) cc_final: 0.6504 (p0) REVERT: W 106 GLU cc_start: 0.7453 (pt0) cc_final: 0.7119 (pp20) REVERT: X 77 PHE cc_start: 0.6920 (t80) cc_final: 0.6587 (t80) REVERT: Y 83 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5129 (pm20) outliers start: 163 outliers final: 145 residues processed: 948 average time/residue: 0.4406 time to fit residues: 689.3966 Evaluate side-chains 976 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 824 time to evaluate : 3.660 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 280 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 19 CYS 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 198 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 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 204 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 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 55 ILE 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 155 SER Chi-restraints excluded: chain G residue 157 ARG 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 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 H residue 395 ASP 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 102 GLN 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 234 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 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 104 GLN 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 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 159 LEU 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 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 94 ASP 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: 7.9990 chunk 5 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 392 optimal weight: 0.6980 chunk 367 optimal weight: 0.7980 chunk 400 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 21 HIS D 33 ASN ** 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** H 104 GLN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 204 GLN ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 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** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125430 restraints weight = 64338.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129322 restraints weight = 31594.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131813 restraints weight = 19553.628| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33733 Z= 0.142 Angle : 0.718 11.578 45942 Z= 0.366 Chirality : 0.047 0.374 5080 Planarity : 0.005 0.048 5924 Dihedral : 6.061 81.010 4613 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 4.15 % Allowed : 25.64 % Favored : 70.21 % 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: -0.74 (0.13), residues: 4240 helix: 1.06 (0.26), residues: 396 sheet: -0.97 (0.14), residues: 1187 loop : -0.43 (0.13), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 89 HIS 0.011 0.001 HIS B 349 PHE 0.033 0.002 PHE K 15 TYR 0.019 0.001 TYR K 229 ARG 0.008 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1197) hydrogen bonds : angle 5.91220 ( 3135) SS BOND : bond 0.00330 ( 73) SS BOND : angle 1.79142 ( 146) covalent geometry : bond 0.00330 (33660) covalent geometry : angle 0.71217 (45796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15969.87 seconds wall clock time: 280 minutes 2.89 seconds (16802.89 seconds total)