Starting phenix.real_space_refine on Tue Aug 26 03:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9z_47822/08_2025/9e9z_47822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9z_47822/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e9z_47822/08_2025/9e9z_47822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9z_47822/08_2025/9e9z_47822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e9z_47822/08_2025/9e9z_47822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9z_47822/08_2025/9e9z_47822.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.61, per 1000 atoms: 0.23 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.42 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: 6.97 Time building geometry restraints manager: 4.14 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain '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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.630 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- 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 : 8.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.024 0.003 ARG H 245 TYR 0.049 0.005 TYR E 175 PHE 0.066 0.003 PHE V 38 TRP 0.116 0.005 TRP J 89 HIS 0.009 0.002 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00655 (33660) covalent geometry : angle 1.03349 (45796) SS BOND : bond 0.00589 ( 73) SS BOND : angle 1.51313 ( 146) hydrogen bonds : bond 0.21630 ( 1197) hydrogen bonds : angle 9.27592 ( 3135) *********************** 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 : 1.155 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: 0.9060 (Cg_endo) REVERT: A 20 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 24 TYR cc_start: 0.8917 (m-80) cc_final: 0.8528 (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: 0.7848 (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: 0.7948 (t0) REVERT: A 136 VAL cc_start: 0.8225 (p) cc_final: 0.7882 (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: 0.8371 (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: 0.9127 (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: 0.1754 (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: 0.7254 (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: 0.8888 (m-40) REVERT: B 342 GLU cc_start: 0.8459 (tp30) cc_final: 0.8245 (tp30) REVERT: B 354 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8191 (mt-10) REVERT: B 367 THR cc_start: 0.9069 (m) cc_final: 0.8783 (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 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: 0.7923 (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: 0.5349 (tt) REVERT: C 308 TYR cc_start: 0.8310 (p90) cc_final: 0.7854 (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: 0.8567 (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: 0.8172 (m-10) REVERT: D 33 ASN cc_start: 0.8456 (m-40) cc_final: 0.8086 (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: 0.7765 (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: 0.8282 (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: 0.8774 (m-30) REVERT: D 254 LYS cc_start: 0.4150 (pptt) cc_final: 0.3039 (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: 0.8611 (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: 0.7618 (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 129 LEU cc_start: 0.8188 (tp) cc_final: 0.7912 (tt) REVERT: G 133 LEU cc_start: 0.9265 (mt) cc_final: 0.9027 (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: 0.9306 (t) REVERT: G 218 ASP cc_start: 0.7964 (t0) cc_final: 0.7365 (t0) REVERT: G 220 ARG cc_start: 0.8920 (ptp-170) cc_final: 0.8410 (ptp90) REVERT: G 223 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9347 (ttmm) REVERT: G 230 HIS cc_start: 0.8708 (t-90) cc_final: 0.7692 (t-90) REVERT: G 235 GLN cc_start: 0.9045 (pt0) cc_final: 0.8665 (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: 0.7820 (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: 0.8250 (mm-30) REVERT: H 46 GLN cc_start: 0.7110 (mt0) cc_final: 0.6873 (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: 0.6954 (t0) REVERT: H 139 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6944 (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: 0.8057 (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: 0.7891 (m-90) REVERT: H 272 HIS cc_start: 0.7369 (t70) cc_final: 0.6863 (t70) REVERT: H 303 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8483 (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: 0.8701 (m110) REVERT: H 334 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8795 (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: 0.8943 (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: 0.8392 (tp40) REVERT: I 194 GLU cc_start: 0.8381 (tt0) cc_final: 0.7773 (tt0) REVERT: I 235 THR cc_start: 0.3994 (m) cc_final: 0.3677 (m) REVERT: J 9 ASN cc_start: 0.9007 (t0) cc_final: 0.8401 (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: 0.8488 (m-10) REVERT: J 181 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8635 (ttmt) REVERT: J 256 PRO cc_start: 0.9305 (Cg_exo) cc_final: 0.8809 (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: 0.8123 (mm) REVERT: J 311 ASP cc_start: 0.8293 (t0) cc_final: 0.7940 (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: 0.6988 (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: 0.3933 (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: 0.8050 (mt-10) REVERT: K 229 TYR cc_start: 0.8525 (p90) cc_final: 0.8136 (p90) REVERT: K 272 HIS cc_start: 0.8568 (t70) cc_final: 0.7639 (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: 0.7778 (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: 0.7879 (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: 0.1987 time to fit residues: 469.4107 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 : 0.936 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0030 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 169 HIS C 59 GLN C 100 ASN C 408 ASN D 233 GLN D 361 HIS 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 118 HIS ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN G 345 HIS ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128640 restraints weight = 64711.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132634 restraints weight = 31343.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135154 restraints weight = 19233.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136737 restraints weight = 13943.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137717 restraints weight = 11401.152| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 33733 Z= 0.159 Angle : 0.763 13.427 45942 Z= 0.404 Chirality : 0.049 0.261 5080 Planarity : 0.005 0.067 5924 Dihedral : 6.731 80.500 4630 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 3.90 % Allowed : 14.84 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.13), residues: 4240 helix: 0.02 (0.24), residues: 424 sheet: -0.53 (0.14), residues: 1128 loop : -0.62 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 214 TYR 0.031 0.002 TYR F 157 PHE 0.025 0.002 PHE H 51 TRP 0.025 0.002 TRP J 89 HIS 0.018 0.002 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00360 (33660) covalent geometry : angle 0.75562 (45796) SS BOND : bond 0.00431 ( 73) SS BOND : angle 2.04216 ( 146) hydrogen bonds : bond 0.04692 ( 1197) hydrogen bonds : angle 7.01273 ( 3135) *********************** 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 1304 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1163 time to evaluate : 0.987 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: A 27 LEU cc_start: 0.8652 (tp) cc_final: 0.8370 (tp) REVERT: A 45 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7993 (tp30) REVERT: A 75 ASP cc_start: 0.8035 (t0) cc_final: 0.7197 (t0) REVERT: A 117 ASP cc_start: 0.8340 (t0) cc_final: 0.7898 (t0) REVERT: A 218 ASP cc_start: 0.8801 (t0) cc_final: 0.8450 (t0) REVERT: A 252 GLN cc_start: 0.9044 (mp10) cc_final: 0.8423 (mm-40) REVERT: A 284 ASP cc_start: 0.8837 (m-30) cc_final: 0.8617 (m-30) REVERT: A 311 ASP cc_start: 0.9331 (p0) cc_final: 0.9016 (p0) REVERT: A 354 LEU cc_start: 0.9246 (mt) cc_final: 0.8177 (mt) REVERT: A 395 ASP cc_start: 0.8360 (t0) cc_final: 0.8009 (t0) REVERT: B 32 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7817 (tp30) REVERT: B 33 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7416 (t0) REVERT: B 70 ASP cc_start: 0.7799 (p0) cc_final: 0.7147 (p0) REVERT: B 92 ARG cc_start: 0.2607 (mtt180) cc_final: 0.1942 (mtp180) REVERT: B 114 SER cc_start: 0.9095 (m) cc_final: 0.8719 (p) REVERT: B 122 ASN cc_start: 0.8571 (m110) cc_final: 0.8238 (m110) REVERT: B 131 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7646 (mtm110) REVERT: B 138 GLU cc_start: 0.7552 (tt0) cc_final: 0.7304 (tt0) REVERT: B 156 ASP cc_start: 0.8636 (t0) cc_final: 0.8432 (t0) REVERT: B 176 TYR cc_start: 0.7154 (m-80) cc_final: 0.6662 (m-80) REVERT: B 190 LYS cc_start: 0.4997 (mptt) cc_final: 0.4606 (mmtm) REVERT: B 278 LYS cc_start: 0.9274 (mtmm) cc_final: 0.9046 (mttm) REVERT: B 284 THR cc_start: 0.8811 (m) cc_final: 0.8587 (p) REVERT: B 305 ASP cc_start: 0.8805 (t0) cc_final: 0.8599 (t0) REVERT: B 330 TRP cc_start: 0.9036 (t-100) cc_final: 0.8630 (t-100) REVERT: B 332 ASN cc_start: 0.9199 (m-40) cc_final: 0.8990 (m110) REVERT: B 351 TRP cc_start: 0.8058 (m-90) cc_final: 0.7383 (m-90) REVERT: C 7 VAL cc_start: 0.9417 (t) cc_final: 0.9162 (m) REVERT: C 32 THR cc_start: 0.8979 (m) cc_final: 0.8586 (p) REVERT: C 100 ASN cc_start: 0.8183 (m-40) cc_final: 0.7874 (m-40) REVERT: C 139 ASN cc_start: 0.8160 (t0) cc_final: 0.7938 (m-40) REVERT: C 209 ASP cc_start: 0.8184 (p0) cc_final: 0.7885 (p0) REVERT: C 228 ASN cc_start: 0.9330 (m110) cc_final: 0.9084 (m-40) REVERT: C 307 ILE cc_start: 0.6397 (mt) cc_final: 0.5922 (tt) REVERT: C 373 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8676 (mttp) REVERT: D 33 ASN cc_start: 0.8248 (m-40) cc_final: 0.8024 (m110) REVERT: D 132 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8205 (ttm-80) REVERT: D 134 PHE cc_start: 0.8754 (p90) cc_final: 0.8480 (p90) REVERT: D 169 HIS cc_start: 0.6874 (m90) cc_final: 0.6597 (m-70) REVERT: D 227 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7831 (mm) REVERT: D 254 LYS cc_start: 0.4769 (pptt) cc_final: 0.4543 (pptt) REVERT: D 273 THR cc_start: 0.9278 (m) cc_final: 0.8730 (p) REVERT: D 291 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8497 (mmt180) REVERT: D 305 ASP cc_start: 0.7977 (t0) cc_final: 0.7628 (t70) REVERT: D 339 TRP cc_start: 0.8811 (m-90) cc_final: 0.8584 (m-90) REVERT: E 132 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7581 (mtp) REVERT: E 194 GLU cc_start: 0.8868 (tp30) cc_final: 0.8445 (tp30) REVERT: E 202 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7813 (ptm-80) REVERT: F 207 LYS cc_start: 0.9101 (tmmt) cc_final: 0.8447 (tmtt) REVERT: F 216 ASP cc_start: 0.8118 (t0) cc_final: 0.7711 (t0) REVERT: G 10 VAL cc_start: 0.8981 (t) cc_final: 0.8715 (m) REVERT: G 21 ARG cc_start: 0.8111 (tmm-80) cc_final: 0.7910 (tmm-80) REVERT: G 27 LEU cc_start: 0.8188 (tp) cc_final: 0.7827 (tp) REVERT: G 37 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7456 (mp0) REVERT: G 62 CYS cc_start: 0.4401 (m) cc_final: 0.4059 (m) REVERT: G 140 THR cc_start: 0.8725 (m) cc_final: 0.8486 (p) REVERT: G 170 PHE cc_start: 0.7804 (t80) cc_final: 0.7409 (t80) REVERT: G 203 ILE cc_start: 0.9110 (tt) cc_final: 0.8864 (tt) REVERT: G 206 SER cc_start: 0.9633 (m) cc_final: 0.9308 (t) REVERT: G 218 ASP cc_start: 0.7524 (t0) cc_final: 0.6975 (t0) REVERT: G 220 ARG cc_start: 0.8595 (ptp-170) cc_final: 0.8170 (ptp90) REVERT: G 230 HIS cc_start: 0.8453 (t-90) cc_final: 0.7585 (t70) REVERT: G 235 GLN cc_start: 0.8563 (pt0) cc_final: 0.8237 (pt0) REVERT: G 257 PHE cc_start: 0.8585 (m-80) cc_final: 0.8139 (m-80) REVERT: G 261 ILE cc_start: 0.9340 (mt) cc_final: 0.8973 (mm) REVERT: G 324 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.7351 (ptp90) REVERT: G 364 ASN cc_start: 0.8918 (t0) cc_final: 0.8647 (t0) REVERT: H 46 GLN cc_start: 0.6911 (mt0) cc_final: 0.6562 (mt0) REVERT: H 82 LYS cc_start: 0.8591 (mttt) cc_final: 0.8279 (mtmm) REVERT: H 139 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6297 (tm-30) REVERT: H 200 GLU cc_start: 0.7575 (tt0) cc_final: 0.7144 (tt0) REVERT: H 236 TRP cc_start: 0.8221 (m-90) cc_final: 0.7861 (m-90) REVERT: H 238 TYR cc_start: 0.7092 (m-80) cc_final: 0.5542 (t80) REVERT: H 303 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8321 (ttm-80) REVERT: I 121 ASN cc_start: 0.7109 (p0) cc_final: 0.6889 (p0) REVERT: I 152 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7952 (mmtt) REVERT: I 186 TRP cc_start: 0.8185 (t60) cc_final: 0.7688 (t60) REVERT: I 192 GLN cc_start: 0.8583 (tp40) cc_final: 0.8369 (tp40) REVERT: I 194 GLU cc_start: 0.8507 (tt0) cc_final: 0.7843 (tt0) REVERT: I 212 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.7246 (mmm-85) REVERT: J 9 ASN cc_start: 0.9201 (t0) cc_final: 0.8566 (t0) REVERT: J 15 TYR cc_start: 0.8128 (t80) cc_final: 0.7891 (t80) REVERT: J 133 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8370 (mm) REVERT: J 257 PHE cc_start: 0.8350 (m-80) cc_final: 0.7894 (m-80) REVERT: J 271 CYS cc_start: 0.6394 (m) cc_final: 0.6143 (m) REVERT: J 307 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8076 (mm) REVERT: J 319 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7239 (mm-40) REVERT: J 372 LYS cc_start: 0.8773 (tptt) cc_final: 0.8511 (tppt) REVERT: J 409 TRP cc_start: 0.8535 (m100) cc_final: 0.8247 (m100) REVERT: K 78 ASP cc_start: 0.8155 (t0) cc_final: 0.7917 (t70) REVERT: K 100 PHE cc_start: 0.9032 (m-80) cc_final: 0.8466 (m-10) REVERT: K 121 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: K 146 HIS cc_start: 0.4735 (m-70) cc_final: 0.4084 (m-70) REVERT: K 170 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7995 (ptp-170) REVERT: K 200 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7920 (mt-10) REVERT: K 218 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8055 (p0) REVERT: K 272 HIS cc_start: 0.8653 (t70) cc_final: 0.7484 (t70) REVERT: K 330 TRP cc_start: 0.9432 (t-100) cc_final: 0.9099 (t-100) REVERT: K 339 TRP cc_start: 0.8841 (m-90) cc_final: 0.7820 (m-90) REVERT: K 366 TYR cc_start: 0.8394 (m-80) cc_final: 0.8096 (m-80) REVERT: W 90 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7579 (tmtt) REVERT: X 96 ASP cc_start: 0.7992 (m-30) cc_final: 0.7773 (m-30) REVERT: Y 83 GLN cc_start: 0.5921 (OUTLIER) cc_final: 0.4934 (pm20) outliers start: 141 outliers final: 83 residues processed: 1219 average time/residue: 0.1994 time to fit residues: 400.5050 Evaluate side-chains 1069 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 978 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 GLU 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 152 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 162 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 396 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 96 CYS 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 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 142 PHE 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 315 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 127 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 222 VAL 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 55 ILE Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 218 ASN 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 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 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain K residue 218 ASN Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 195 ASN 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 Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 83 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 268 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 251 optimal weight: 0.3980 chunk 163 optimal weight: 4.9990 chunk 301 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 410 optimal weight: 1.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 50 GLN B 169 HIS C 59 GLN C 93 GLN C 252 GLN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 405 ASN F 187 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS J 102 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 355 HIS ** J 362 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 ** L 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123790 restraints weight = 65106.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127671 restraints weight = 32110.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130154 restraints weight = 19985.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131714 restraints weight = 14582.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132682 restraints weight = 11962.349| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33733 Z= 0.205 Angle : 0.724 10.226 45942 Z= 0.379 Chirality : 0.047 0.260 5080 Planarity : 0.005 0.077 5924 Dihedral : 6.557 80.461 4619 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 4.96 % Allowed : 17.72 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4240 helix: 0.12 (0.24), residues: 424 sheet: -0.81 (0.14), residues: 1152 loop : -0.44 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 245 TYR 0.023 0.002 TYR K 229 PHE 0.029 0.002 PHE X 77 TRP 0.016 0.002 TRP J 89 HIS 0.010 0.001 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.00459 (33660) covalent geometry : angle 0.71820 (45796) SS BOND : bond 0.00613 ( 73) SS BOND : angle 1.81203 ( 146) hydrogen bonds : bond 0.04231 ( 1197) hydrogen bonds : angle 6.60238 ( 3135) *********************** 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 1148 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 969 time to evaluate : 0.940 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 24 TYR cc_start: 0.8335 (m-80) cc_final: 0.7953 (m-80) REVERT: A 75 ASP cc_start: 0.7993 (t0) cc_final: 0.7039 (t0) REVERT: A 158 ASP cc_start: 0.8567 (t0) cc_final: 0.8204 (t0) REVERT: A 160 LYS cc_start: 0.8640 (mptt) cc_final: 0.8305 (mmtm) REVERT: A 219 ILE cc_start: 0.9438 (mt) cc_final: 0.9173 (mt) REVERT: A 231 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9270 (p) REVERT: A 280 ILE cc_start: 0.9409 (mp) cc_final: 0.8816 (mp) REVERT: A 395 ASP cc_start: 0.8443 (t0) cc_final: 0.8090 (t0) REVERT: B 32 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7919 (tp30) REVERT: B 33 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7372 (t0) REVERT: B 70 ASP cc_start: 0.7860 (p0) cc_final: 0.7242 (p0) REVERT: B 92 ARG cc_start: 0.2655 (mtt180) cc_final: 0.1986 (mtp180) REVERT: B 114 SER cc_start: 0.9162 (m) cc_final: 0.8784 (p) REVERT: B 122 ASN cc_start: 0.8715 (m110) cc_final: 0.8469 (m-40) REVERT: B 138 GLU cc_start: 0.7545 (tt0) cc_final: 0.7322 (tt0) REVERT: B 176 TYR cc_start: 0.7328 (m-80) cc_final: 0.6747 (m-80) REVERT: B 278 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9008 (mttm) REVERT: B 305 ASP cc_start: 0.8827 (t0) cc_final: 0.8581 (t0) REVERT: B 330 TRP cc_start: 0.8998 (t-100) cc_final: 0.8700 (t-100) REVERT: B 332 ASN cc_start: 0.9230 (m-40) cc_final: 0.8976 (m110) REVERT: C 32 THR cc_start: 0.9068 (m) cc_final: 0.8675 (p) REVERT: C 97 ASP cc_start: 0.7975 (p0) cc_final: 0.7734 (p0) REVERT: C 100 ASN cc_start: 0.8293 (m-40) cc_final: 0.7938 (m-40) REVERT: C 133 LEU cc_start: 0.9342 (mt) cc_final: 0.9132 (mt) REVERT: C 139 ASN cc_start: 0.8213 (t0) cc_final: 0.7971 (m-40) REVERT: C 195 MET cc_start: 0.8789 (mpp) cc_final: 0.8528 (mpp) REVERT: C 209 ASP cc_start: 0.8263 (p0) cc_final: 0.8045 (p0) REVERT: C 228 ASN cc_start: 0.9276 (m110) cc_final: 0.9055 (m-40) REVERT: C 307 ILE cc_start: 0.6454 (mt) cc_final: 0.5932 (tt) REVERT: C 373 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8741 (mttp) REVERT: C 409 TRP cc_start: 0.8304 (m100) cc_final: 0.7534 (m100) REVERT: D 32 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 45 ILE cc_start: 0.9189 (mm) cc_final: 0.8786 (tp) REVERT: D 169 HIS cc_start: 0.7165 (m90) cc_final: 0.6779 (m-70) REVERT: D 273 THR cc_start: 0.9229 (m) cc_final: 0.8745 (p) REVERT: D 305 ASP cc_start: 0.8028 (t0) cc_final: 0.7797 (t0) REVERT: D 339 TRP cc_start: 0.8935 (m-90) cc_final: 0.8484 (m-90) REVERT: E 112 PHE cc_start: 0.8161 (m-80) cc_final: 0.7605 (m-10) REVERT: E 160 GLU cc_start: 0.8256 (pt0) cc_final: 0.8046 (pm20) REVERT: E 194 GLU cc_start: 0.8780 (tp30) cc_final: 0.8386 (tp30) REVERT: F 127 VAL cc_start: 0.8953 (t) cc_final: 0.8744 (m) REVERT: F 207 LYS cc_start: 0.9080 (tmmt) cc_final: 0.8446 (tmtt) REVERT: G 10 VAL cc_start: 0.9075 (t) cc_final: 0.8771 (m) REVERT: G 27 LEU cc_start: 0.8272 (tp) cc_final: 0.7890 (tp) REVERT: G 37 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7459 (mp0) REVERT: G 46 TYR cc_start: 0.8612 (p90) cc_final: 0.8385 (p90) REVERT: G 62 CYS cc_start: 0.4230 (m) cc_final: 0.3956 (m) REVERT: G 140 THR cc_start: 0.8687 (m) cc_final: 0.8428 (p) REVERT: G 160 LYS cc_start: 0.9116 (pptt) cc_final: 0.8751 (mmtm) REVERT: G 170 PHE cc_start: 0.7992 (t80) cc_final: 0.7596 (t80) REVERT: G 195 MET cc_start: 0.8841 (mpp) cc_final: 0.8589 (mpp) REVERT: G 203 ILE cc_start: 0.9082 (tt) cc_final: 0.8834 (tt) REVERT: G 206 SER cc_start: 0.9662 (m) cc_final: 0.9330 (t) REVERT: G 218 ASP cc_start: 0.7576 (t0) cc_final: 0.6393 (t0) REVERT: G 220 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.7752 (ptp90) REVERT: G 230 HIS cc_start: 0.8528 (t-90) cc_final: 0.7647 (t70) REVERT: G 235 GLN cc_start: 0.8693 (pt0) cc_final: 0.8295 (pt0) REVERT: G 257 PHE cc_start: 0.8565 (m-80) cc_final: 0.8100 (m-80) REVERT: G 324 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.7358 (ptp90) REVERT: G 364 ASN cc_start: 0.8919 (t0) cc_final: 0.8533 (t0) REVERT: H 82 LYS cc_start: 0.8634 (mttt) cc_final: 0.8342 (mtmm) REVERT: H 122 ASN cc_start: 0.7233 (t0) cc_final: 0.6990 (t0) REVERT: H 134 PHE cc_start: 0.9324 (p90) cc_final: 0.8870 (p90) REVERT: H 139 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: H 200 GLU cc_start: 0.7568 (tt0) cc_final: 0.7091 (tt0) REVERT: H 287 LEU cc_start: 0.9117 (mm) cc_final: 0.8742 (mt) REVERT: H 305 ASP cc_start: 0.8479 (t0) cc_final: 0.8262 (t0) REVERT: H 362 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8472 (mmm-85) REVERT: H 395 ASP cc_start: 0.9228 (p0) cc_final: 0.9017 (p0) REVERT: I 115 MET cc_start: 0.7399 (ppp) cc_final: 0.6841 (mmm) REVERT: I 152 LYS cc_start: 0.8497 (ttpt) cc_final: 0.7839 (mmtt) REVERT: I 186 TRP cc_start: 0.8245 (t60) cc_final: 0.7778 (t60) REVERT: I 194 GLU cc_start: 0.8415 (tt0) cc_final: 0.7759 (tt0) REVERT: I 212 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: J 9 ASN cc_start: 0.9265 (t0) cc_final: 0.8685 (t0) REVERT: J 15 TYR cc_start: 0.8146 (t80) cc_final: 0.7842 (t80) REVERT: J 37 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7429 (mm-30) REVERT: J 63 CYS cc_start: 0.5673 (t) cc_final: 0.3151 (t) REVERT: J 117 ASP cc_start: 0.8762 (t0) cc_final: 0.8335 (t0) REVERT: J 218 ASP cc_start: 0.8108 (t0) cc_final: 0.7619 (t0) REVERT: J 230 HIS cc_start: 0.8794 (t-90) cc_final: 0.8212 (t-90) REVERT: J 257 PHE cc_start: 0.8445 (m-80) cc_final: 0.7879 (m-80) REVERT: J 271 CYS cc_start: 0.6456 (m) cc_final: 0.6123 (m) REVERT: J 307 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8128 (mm) REVERT: J 372 LYS cc_start: 0.8744 (tptt) cc_final: 0.8543 (tppt) REVERT: J 409 TRP cc_start: 0.8510 (m100) cc_final: 0.8205 (m100) REVERT: K 37 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8253 (mt-10) REVERT: K 78 ASP cc_start: 0.8427 (t0) cc_final: 0.8182 (t70) REVERT: K 100 PHE cc_start: 0.9205 (m-80) cc_final: 0.8526 (m-10) REVERT: K 121 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: K 146 HIS cc_start: 0.4950 (m-70) cc_final: 0.4203 (m-70) REVERT: K 165 TYR cc_start: 0.8653 (p90) cc_final: 0.8422 (p90) REVERT: K 170 ARG cc_start: 0.8314 (ptp-170) cc_final: 0.8085 (ptp-170) REVERT: K 272 HIS cc_start: 0.8744 (t70) cc_final: 0.7479 (t70) REVERT: K 279 TRP cc_start: 0.9090 (p-90) cc_final: 0.8693 (p-90) REVERT: K 339 TRP cc_start: 0.8967 (m-90) cc_final: 0.7814 (m-90) REVERT: K 341 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: K 351 TRP cc_start: 0.8984 (m-10) cc_final: 0.8751 (m-10) REVERT: K 366 TYR cc_start: 0.8343 (m-80) cc_final: 0.7787 (m-80) REVERT: L 115 MET cc_start: 0.8010 (tpt) cc_final: 0.7548 (tpp) REVERT: L 133 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7910 (ptmm) REVERT: L 168 MET cc_start: 0.9161 (ppp) cc_final: 0.8683 (tmm) REVERT: W 72 CYS cc_start: 0.5333 (OUTLIER) cc_final: 0.4929 (p) REVERT: W 90 LYS cc_start: 0.8457 (mtpt) cc_final: 0.7647 (tmtt) REVERT: X 96 ASP cc_start: 0.8117 (m-30) cc_final: 0.7849 (m-30) outliers start: 179 outliers final: 125 residues processed: 1050 average time/residue: 0.1884 time to fit residues: 323.4691 Evaluate side-chains 1034 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 901 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 57 SER 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 146 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 231 VAL 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 367 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 104 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR 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 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 93 GLN 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 282 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 237 VAL 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 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 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 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 54 VAL 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 152 THR Chi-restraints excluded: chain G residue 155 SER 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 271 CYS 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 410 LEU Chi-restraints excluded: chain H residue 109 ASP 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 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 249 ILE 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 298 GLU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 102 LEU 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 314 THR Chi-restraints excluded: chain K residue 321 VAL 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 133 LYS Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 178 ASP 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 232 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 50 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS C 93 GLN C 408 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN ** G 93 GLN ** 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 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS Y 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122628 restraints weight = 64450.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126458 restraints weight = 31905.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128923 restraints weight = 19891.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130479 restraints weight = 14529.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131426 restraints weight = 11925.900| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3500 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= 0.205 Angle : 0.702 9.902 45942 Z= 0.368 Chirality : 0.047 0.334 5080 Planarity : 0.005 0.047 5924 Dihedral : 6.499 80.896 4619 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 5.68 % Allowed : 18.99 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4240 helix: 0.25 (0.24), residues: 424 sheet: -0.89 (0.14), residues: 1171 loop : -0.42 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 220 TYR 0.026 0.002 TYR C 308 PHE 0.031 0.002 PHE A 51 TRP 0.017 0.002 TRP H 236 HIS 0.010 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00461 (33660) covalent geometry : angle 0.69530 (45796) SS BOND : bond 0.00463 ( 73) SS BOND : angle 1.84311 ( 146) hydrogen bonds : bond 0.03977 ( 1197) hydrogen bonds : angle 6.38956 ( 3135) *********************** 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 1168 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 963 time to evaluate : 0.949 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 24 TYR cc_start: 0.8476 (m-80) cc_final: 0.8017 (m-80) REVERT: A 75 ASP cc_start: 0.7963 (t0) cc_final: 0.6850 (t0) REVERT: A 158 ASP cc_start: 0.8596 (t0) cc_final: 0.8374 (t0) REVERT: A 219 ILE cc_start: 0.9477 (mt) cc_final: 0.9274 (mt) REVERT: A 395 ASP cc_start: 0.8445 (t0) cc_final: 0.8093 (t0) REVERT: A 409 TRP cc_start: 0.8532 (t-100) cc_final: 0.8180 (m-90) REVERT: B 30 LYS cc_start: 0.8985 (tptt) cc_final: 0.8513 (tttp) REVERT: B 32 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8024 (tp30) REVERT: B 33 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7417 (t0) REVERT: B 40 ASP cc_start: 0.8417 (p0) cc_final: 0.7818 (p0) REVERT: B 70 ASP cc_start: 0.7851 (p0) cc_final: 0.7221 (p0) REVERT: B 92 ARG cc_start: 0.2544 (mtt180) cc_final: 0.1721 (mtm180) REVERT: B 122 ASN cc_start: 0.8736 (m110) cc_final: 0.8531 (m-40) REVERT: B 131 ARG cc_start: 0.7523 (mtm180) cc_final: 0.7311 (mtm110) REVERT: B 146 HIS cc_start: 0.5191 (OUTLIER) cc_final: 0.4764 (m170) REVERT: B 156 ASP cc_start: 0.8583 (t0) cc_final: 0.8159 (t0) REVERT: B 169 HIS cc_start: 0.8311 (m170) cc_final: 0.8082 (m170) REVERT: B 176 TYR cc_start: 0.7345 (m-80) cc_final: 0.6669 (m-80) REVERT: B 278 LYS cc_start: 0.9325 (mtmm) cc_final: 0.9055 (mttm) REVERT: B 305 ASP cc_start: 0.8849 (t0) cc_final: 0.8524 (t0) REVERT: B 330 TRP cc_start: 0.8982 (t-100) cc_final: 0.8705 (t-100) REVERT: B 332 ASN cc_start: 0.9115 (m-40) cc_final: 0.8867 (m110) REVERT: B 342 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 32 THR cc_start: 0.9100 (m) cc_final: 0.8705 (p) REVERT: C 97 ASP cc_start: 0.8030 (p0) cc_final: 0.7729 (p0) REVERT: C 100 ASN cc_start: 0.8344 (m-40) cc_final: 0.7986 (m-40) REVERT: C 139 ASN cc_start: 0.8252 (t0) cc_final: 0.8013 (m-40) REVERT: C 195 MET cc_start: 0.8781 (mpp) cc_final: 0.8430 (mpp) REVERT: C 262 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7420 (pt0) REVERT: C 307 ILE cc_start: 0.6531 (mt) cc_final: 0.6012 (tt) REVERT: C 362 GLN cc_start: 0.7950 (pm20) cc_final: 0.7612 (pm20) REVERT: C 373 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8719 (mttp) REVERT: C 409 TRP cc_start: 0.8323 (m100) cc_final: 0.7548 (m100) REVERT: D 137 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8159 (ptp90) REVERT: D 273 THR cc_start: 0.9224 (m) cc_final: 0.8737 (p) REVERT: D 339 TRP cc_start: 0.8946 (m-90) cc_final: 0.8637 (m-90) REVERT: D 355 ILE cc_start: 0.8625 (mm) cc_final: 0.8417 (mm) REVERT: E 130 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8132 (tpp80) REVERT: E 160 GLU cc_start: 0.8202 (pt0) cc_final: 0.7926 (pm20) REVERT: E 194 GLU cc_start: 0.8792 (tp30) cc_final: 0.8393 (tp30) REVERT: E 257 GLU cc_start: 0.7973 (mp0) cc_final: 0.7363 (mp0) REVERT: F 127 VAL cc_start: 0.8955 (t) cc_final: 0.8699 (m) REVERT: F 184 TYR cc_start: 0.7038 (m-80) cc_final: 0.6587 (m-80) REVERT: F 207 LYS cc_start: 0.9094 (tmmt) cc_final: 0.8441 (tmtt) REVERT: F 214 ILE cc_start: 0.8774 (mm) cc_final: 0.8400 (pt) REVERT: G 10 VAL cc_start: 0.9060 (t) cc_final: 0.8776 (m) REVERT: G 27 LEU cc_start: 0.8299 (tp) cc_final: 0.7902 (tp) REVERT: G 37 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7441 (mp0) REVERT: G 62 CYS cc_start: 0.4507 (m) cc_final: 0.4203 (m) REVERT: G 140 THR cc_start: 0.8673 (m) cc_final: 0.8428 (p) REVERT: G 160 LYS cc_start: 0.9157 (pptt) cc_final: 0.8814 (mmtm) REVERT: G 170 PHE cc_start: 0.8063 (t80) cc_final: 0.7667 (t80) REVERT: G 195 MET cc_start: 0.8932 (mpp) cc_final: 0.8599 (mpp) REVERT: G 203 ILE cc_start: 0.9088 (tt) cc_final: 0.8843 (tt) REVERT: G 206 SER cc_start: 0.9665 (m) cc_final: 0.9325 (t) REVERT: G 218 ASP cc_start: 0.7651 (t0) cc_final: 0.7073 (t0) REVERT: G 220 ARG cc_start: 0.8528 (ptp-170) cc_final: 0.8150 (ptp90) REVERT: G 230 HIS cc_start: 0.8578 (t-90) cc_final: 0.7630 (t-90) REVERT: G 235 GLN cc_start: 0.8726 (pt0) cc_final: 0.8425 (pt0) REVERT: G 273 TYR cc_start: 0.8459 (p90) cc_final: 0.8001 (p90) REVERT: G 364 ASN cc_start: 0.8927 (t0) cc_final: 0.8564 (t0) REVERT: H 34 VAL cc_start: 0.9614 (t) cc_final: 0.9410 (m) REVERT: H 46 GLN cc_start: 0.6450 (tt0) cc_final: 0.6116 (tt0) REVERT: H 82 LYS cc_start: 0.8591 (mttt) cc_final: 0.7930 (mttm) REVERT: H 134 PHE cc_start: 0.9291 (p90) cc_final: 0.8901 (p90) REVERT: H 139 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: H 305 ASP cc_start: 0.8531 (t0) cc_final: 0.8261 (t0) REVERT: H 362 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.8371 (mtp-110) REVERT: H 395 ASP cc_start: 0.9207 (p0) cc_final: 0.9005 (p0) REVERT: I 130 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7169 (mtt180) REVERT: I 152 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7739 (mmtt) REVERT: I 192 GLN cc_start: 0.8882 (tp40) cc_final: 0.8069 (mm110) REVERT: I 212 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.7397 (mmm-85) REVERT: J 9 ASN cc_start: 0.9268 (t0) cc_final: 0.8737 (t0) REVERT: J 15 TYR cc_start: 0.8204 (t80) cc_final: 0.7810 (t80) REVERT: J 37 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7498 (mm-30) REVERT: J 63 CYS cc_start: 0.5301 (t) cc_final: 0.4766 (t) REVERT: J 117 ASP cc_start: 0.8757 (t0) cc_final: 0.8363 (t0) REVERT: J 133 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8395 (mm) REVERT: J 218 ASP cc_start: 0.8171 (t0) cc_final: 0.7672 (t0) REVERT: J 230 HIS cc_start: 0.8805 (t-90) cc_final: 0.8247 (t-90) REVERT: J 246 ASN cc_start: 0.8185 (t0) cc_final: 0.7727 (t0) REVERT: J 257 PHE cc_start: 0.8413 (m-80) cc_final: 0.7840 (m-80) REVERT: J 262 GLU cc_start: 0.8067 (mp0) cc_final: 0.7810 (mp0) REVERT: J 271 CYS cc_start: 0.6344 (m) cc_final: 0.6000 (m) REVERT: J 307 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8108 (mm) REVERT: J 372 LYS cc_start: 0.8762 (tptt) cc_final: 0.8453 (tppt) REVERT: J 409 TRP cc_start: 0.8480 (m100) cc_final: 0.8206 (m100) REVERT: K 37 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8363 (mt-10) REVERT: K 78 ASP cc_start: 0.8664 (t0) cc_final: 0.8355 (t70) REVERT: K 100 PHE cc_start: 0.9213 (m-80) cc_final: 0.8539 (m-10) REVERT: K 146 HIS cc_start: 0.4874 (m-70) cc_final: 0.4142 (m-70) REVERT: K 168 MET cc_start: 0.8481 (mmp) cc_final: 0.7790 (mmp) REVERT: K 170 ARG cc_start: 0.8385 (ptp-170) cc_final: 0.8169 (ptp-170) REVERT: K 272 HIS cc_start: 0.8715 (t70) cc_final: 0.7647 (t70) REVERT: K 279 TRP cc_start: 0.9088 (p-90) cc_final: 0.8703 (p-90) REVERT: K 339 TRP cc_start: 0.8987 (m-90) cc_final: 0.7857 (m-90) REVERT: K 341 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: K 366 TYR cc_start: 0.8366 (m-80) cc_final: 0.7851 (m-80) REVERT: L 110 LYS cc_start: 0.7991 (mmtm) cc_final: 0.6725 (pttm) REVERT: L 168 MET cc_start: 0.9240 (ppp) cc_final: 0.8816 (tmm) REVERT: W 72 CYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4778 (p) REVERT: W 90 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7629 (tmtt) REVERT: X 77 PHE cc_start: 0.6252 (t80) cc_final: 0.5962 (t80) REVERT: X 96 ASP cc_start: 0.8075 (m-30) cc_final: 0.7796 (m-30) outliers start: 205 outliers final: 150 residues processed: 1067 average time/residue: 0.1797 time to fit residues: 318.5574 Evaluate side-chains 1045 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 887 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 57 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 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 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 367 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 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 130 ILE 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 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 C residue 13 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 99 GLU 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 177 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 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 296 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 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 ILE 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 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 126 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 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 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 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 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 156 MET Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 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 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 178 ASP 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 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 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 84 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 330 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 405 optimal weight: 4.9990 chunk 406 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 169 HIS ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS H 21 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124225 restraints weight = 64685.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128107 restraints weight = 31946.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130579 restraints weight = 19847.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132127 restraints weight = 14500.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133104 restraints weight = 11937.703| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33733 Z= 0.193 Angle : 0.690 10.522 45942 Z= 0.360 Chirality : 0.047 0.455 5080 Planarity : 0.005 0.068 5924 Dihedral : 6.390 81.588 4616 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 5.70 % Allowed : 20.21 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.13), residues: 4240 helix: 0.48 (0.24), residues: 424 sheet: -0.88 (0.14), residues: 1165 loop : -0.43 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 212 TYR 0.022 0.002 TYR K 229 PHE 0.020 0.002 PHE X 77 TRP 0.017 0.001 TRP K 330 HIS 0.021 0.001 HIS L 187 Details of bonding type rmsd covalent geometry : bond 0.00429 (33660) covalent geometry : angle 0.68497 (45796) SS BOND : bond 0.00381 ( 73) SS BOND : angle 1.63998 ( 146) hydrogen bonds : bond 0.03853 ( 1197) hydrogen bonds : angle 6.22740 ( 3135) *********************** 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 1128 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 922 time to evaluate : 1.193 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 24 TYR cc_start: 0.8465 (m-80) cc_final: 0.8026 (m-80) REVERT: A 30 GLU cc_start: 0.6821 (tp30) cc_final: 0.6609 (tp30) REVERT: A 75 ASP cc_start: 0.7858 (t0) cc_final: 0.6836 (t0) REVERT: A 158 ASP cc_start: 0.8635 (t0) cc_final: 0.8399 (t0) REVERT: A 219 ILE cc_start: 0.9493 (mt) cc_final: 0.9266 (mt) REVERT: A 229 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 252 GLN cc_start: 0.8979 (mp10) cc_final: 0.8551 (mm-40) REVERT: A 395 ASP cc_start: 0.8457 (t0) cc_final: 0.8075 (t0) REVERT: A 409 TRP cc_start: 0.8581 (t-100) cc_final: 0.8312 (t-100) REVERT: B 30 LYS cc_start: 0.8982 (tptt) cc_final: 0.8501 (tttp) REVERT: B 32 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7891 (tp30) REVERT: B 33 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7478 (t0) REVERT: B 40 ASP cc_start: 0.8331 (p0) cc_final: 0.7718 (p0) REVERT: B 50 GLN cc_start: 0.6611 (mt0) cc_final: 0.6395 (mt0) REVERT: B 70 ASP cc_start: 0.7738 (p0) cc_final: 0.7034 (p0) REVERT: B 92 ARG cc_start: 0.2664 (mtt180) cc_final: 0.1776 (mtm180) REVERT: B 122 ASN cc_start: 0.8797 (m110) cc_final: 0.8588 (m-40) REVERT: B 146 HIS cc_start: 0.4977 (OUTLIER) cc_final: 0.4622 (m170) REVERT: B 176 TYR cc_start: 0.7336 (m-80) cc_final: 0.6586 (m-80) REVERT: B 190 LYS cc_start: 0.5030 (mmtt) cc_final: 0.4730 (mmtt) REVERT: B 258 PRO cc_start: 0.8676 (Cg_endo) cc_final: 0.8349 (Cg_exo) REVERT: B 278 LYS cc_start: 0.9336 (mtmm) cc_final: 0.9053 (mttm) REVERT: B 287 LEU cc_start: 0.9439 (mt) cc_final: 0.9141 (mp) REVERT: B 305 ASP cc_start: 0.8858 (t0) cc_final: 0.8548 (t0) REVERT: B 330 TRP cc_start: 0.8969 (t-100) cc_final: 0.8663 (t-100) REVERT: C 32 THR cc_start: 0.9123 (m) cc_final: 0.8781 (p) REVERT: C 97 ASP cc_start: 0.8012 (p0) cc_final: 0.7726 (p0) REVERT: C 100 ASN cc_start: 0.8301 (m-40) cc_final: 0.7870 (m-40) REVERT: C 139 ASN cc_start: 0.8295 (t0) cc_final: 0.7885 (m-40) REVERT: C 195 MET cc_start: 0.8743 (mpp) cc_final: 0.8414 (mpp) REVERT: C 262 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7528 (pt0) REVERT: C 307 ILE cc_start: 0.6947 (mt) cc_final: 0.6407 (tt) REVERT: C 362 GLN cc_start: 0.7930 (pm20) cc_final: 0.7665 (pm20) REVERT: C 373 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8707 (mttp) REVERT: C 409 TRP cc_start: 0.8338 (m100) cc_final: 0.7555 (m100) REVERT: D 18 TYR cc_start: 0.8621 (t80) cc_final: 0.8380 (t80) REVERT: D 137 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8123 (ptp90) REVERT: D 272 HIS cc_start: 0.8223 (t-170) cc_final: 0.7905 (t70) REVERT: D 273 THR cc_start: 0.9200 (m) cc_final: 0.8615 (p) REVERT: D 330 TRP cc_start: 0.9292 (t-100) cc_final: 0.9025 (t-100) REVERT: D 339 TRP cc_start: 0.8946 (m-90) cc_final: 0.8593 (m-90) REVERT: D 355 ILE cc_start: 0.8645 (mm) cc_final: 0.8406 (mm) REVERT: E 160 GLU cc_start: 0.8255 (pt0) cc_final: 0.7944 (pm20) REVERT: E 194 GLU cc_start: 0.8731 (tp30) cc_final: 0.8324 (tp30) REVERT: E 195 ASN cc_start: 0.8925 (p0) cc_final: 0.8699 (p0) REVERT: E 257 GLU cc_start: 0.8031 (mp0) cc_final: 0.7830 (mp0) REVERT: F 127 VAL cc_start: 0.8975 (t) cc_final: 0.8716 (m) REVERT: F 184 TYR cc_start: 0.7010 (m-80) cc_final: 0.6622 (m-80) REVERT: F 186 TRP cc_start: 0.7765 (t60) cc_final: 0.7404 (t60) REVERT: F 207 LYS cc_start: 0.9098 (tmmt) cc_final: 0.8443 (tmtt) REVERT: F 214 ILE cc_start: 0.8829 (mm) cc_final: 0.8418 (pt) REVERT: G 10 VAL cc_start: 0.9078 (t) cc_final: 0.8796 (m) REVERT: G 27 LEU cc_start: 0.8328 (tp) cc_final: 0.7806 (tp) REVERT: G 37 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7462 (mp0) REVERT: G 160 LYS cc_start: 0.9158 (pptt) cc_final: 0.8865 (mmtm) REVERT: G 170 PHE cc_start: 0.7919 (t80) cc_final: 0.7700 (t80) REVERT: G 195 MET cc_start: 0.8927 (mpp) cc_final: 0.8612 (mpp) REVERT: G 203 ILE cc_start: 0.9057 (tt) cc_final: 0.8802 (tt) REVERT: G 206 SER cc_start: 0.9638 (m) cc_final: 0.9271 (t) REVERT: G 218 ASP cc_start: 0.7563 (t0) cc_final: 0.7057 (t0) REVERT: G 220 ARG cc_start: 0.8531 (ptp-170) cc_final: 0.8159 (ptp90) REVERT: G 230 HIS cc_start: 0.8542 (t-90) cc_final: 0.7567 (t-90) REVERT: G 235 GLN cc_start: 0.8790 (pt0) cc_final: 0.8552 (pt0) REVERT: G 263 VAL cc_start: 0.9327 (t) cc_final: 0.9034 (m) REVERT: G 273 TYR cc_start: 0.8535 (p90) cc_final: 0.8221 (p90) REVERT: G 364 ASN cc_start: 0.8931 (t0) cc_final: 0.8553 (t0) REVERT: H 46 GLN cc_start: 0.6587 (tt0) cc_final: 0.5991 (tt0) REVERT: H 82 LYS cc_start: 0.8535 (mttt) cc_final: 0.7970 (mttm) REVERT: H 100 PHE cc_start: 0.8424 (m-80) cc_final: 0.7613 (m-80) REVERT: H 134 PHE cc_start: 0.9271 (p90) cc_final: 0.9005 (p90) REVERT: H 139 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6266 (tm-30) REVERT: H 190 LYS cc_start: 0.8731 (tttt) cc_final: 0.8513 (pttp) REVERT: H 305 ASP cc_start: 0.8561 (t0) cc_final: 0.8268 (t0) REVERT: H 362 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8419 (mtp-110) REVERT: I 115 MET cc_start: 0.6407 (mmp) cc_final: 0.5776 (mmm) REVERT: I 130 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7244 (mtt180) REVERT: I 152 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7647 (mmtt) REVERT: I 212 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.7481 (mmm-85) REVERT: J 9 ASN cc_start: 0.9305 (t0) cc_final: 0.8756 (t0) REVERT: J 15 TYR cc_start: 0.8221 (t80) cc_final: 0.7855 (t80) REVERT: J 37 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7539 (mm-30) REVERT: J 117 ASP cc_start: 0.8727 (t0) cc_final: 0.8410 (t0) REVERT: J 133 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8420 (mm) REVERT: J 195 MET cc_start: 0.8982 (mpp) cc_final: 0.8645 (mpp) REVERT: J 218 ASP cc_start: 0.8224 (t0) cc_final: 0.7791 (t0) REVERT: J 230 HIS cc_start: 0.8836 (t-90) cc_final: 0.8259 (t-90) REVERT: J 246 ASN cc_start: 0.8236 (t0) cc_final: 0.7742 (t0) REVERT: J 257 PHE cc_start: 0.8438 (m-80) cc_final: 0.7962 (m-80) REVERT: J 262 GLU cc_start: 0.7963 (mp0) cc_final: 0.7714 (mp0) REVERT: J 271 CYS cc_start: 0.6330 (m) cc_final: 0.5929 (m) REVERT: J 307 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8094 (mm) REVERT: J 368 SER cc_start: 0.8649 (t) cc_final: 0.8432 (t) REVERT: J 372 LYS cc_start: 0.8777 (tptt) cc_final: 0.8369 (tppt) REVERT: J 409 TRP cc_start: 0.8516 (m100) cc_final: 0.8225 (m100) REVERT: K 15 PHE cc_start: 0.8652 (t80) cc_final: 0.8301 (t80) REVERT: K 37 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8325 (mt-10) REVERT: K 146 HIS cc_start: 0.4692 (m-70) cc_final: 0.3927 (m-70) REVERT: K 217 MET cc_start: 0.8146 (tpp) cc_final: 0.7556 (tpp) REVERT: K 272 HIS cc_start: 0.8709 (t70) cc_final: 0.7679 (t70) REVERT: K 279 TRP cc_start: 0.9106 (p-90) cc_final: 0.8709 (p-90) REVERT: K 341 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: K 366 TYR cc_start: 0.8390 (m-80) cc_final: 0.7877 (m-80) REVERT: L 110 LYS cc_start: 0.8025 (mmtm) cc_final: 0.6833 (pttm) REVERT: L 168 MET cc_start: 0.9258 (ppp) cc_final: 0.8912 (tmm) REVERT: W 72 CYS cc_start: 0.5171 (OUTLIER) cc_final: 0.4832 (p) REVERT: W 90 LYS cc_start: 0.8594 (mtpt) cc_final: 0.7681 (tmtt) REVERT: X 77 PHE cc_start: 0.6402 (t80) cc_final: 0.6059 (t80) REVERT: X 96 ASP cc_start: 0.7990 (m-30) cc_final: 0.7784 (m-30) REVERT: Y 83 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.5602 (pm20) outliers start: 206 outliers final: 154 residues processed: 1028 average time/residue: 0.1834 time to fit residues: 313.0334 Evaluate side-chains 1047 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 883 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 229 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 367 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 408 ASN 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 130 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 99 GLU 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 203 ILE Chi-restraints excluded: chain C residue 221 LEU 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 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 198 THR Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 237 VAL 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 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 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 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 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 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 188 ASP Chi-restraints excluded: chain G residue 226 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 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 167 THR 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 307 THR Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 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 167 ASN Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 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 331 HIS Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 47 VAL 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 159 LEU Chi-restraints excluded: chain L residue 187 HIS Chi-restraints excluded: chain L residue 195 ASN Chi-restraints excluded: chain L residue 217 ASN Chi-restraints excluded: chain L residue 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 359 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 415 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 400 optimal weight: 0.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 252 GLN ** 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 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 J 333 HIS ** 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 K 358 HIS W 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124531 restraints weight = 64488.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128416 restraints weight = 31713.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130905 restraints weight = 19667.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132494 restraints weight = 14360.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133468 restraints weight = 11752.270| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33733 Z= 0.171 Angle : 0.685 10.289 45942 Z= 0.354 Chirality : 0.046 0.381 5080 Planarity : 0.005 0.063 5924 Dihedral : 6.280 82.126 4615 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 5.62 % Allowed : 21.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.13), residues: 4240 helix: 0.58 (0.24), residues: 424 sheet: -0.90 (0.14), residues: 1174 loop : -0.44 (0.12), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 131 TYR 0.031 0.002 TYR I 161 PHE 0.029 0.002 PHE I 198 TRP 0.015 0.001 TRP K 330 HIS 0.011 0.001 HIS L 187 Details of bonding type rmsd covalent geometry : bond 0.00388 (33660) covalent geometry : angle 0.67851 (45796) SS BOND : bond 0.00358 ( 73) SS BOND : angle 1.75057 ( 146) hydrogen bonds : bond 0.03719 ( 1197) hydrogen bonds : angle 6.11990 ( 3135) *********************** 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 1130 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 927 time to evaluate : 1.179 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: 0.8537 (mtmt) cc_final: 0.8198 (mttt) REVERT: A 24 TYR cc_start: 0.8442 (m-80) cc_final: 0.8022 (m-80) REVERT: A 75 ASP cc_start: 0.7770 (t0) cc_final: 0.6714 (t0) REVERT: A 219 ILE cc_start: 0.9460 (mt) cc_final: 0.9244 (mt) REVERT: A 252 GLN cc_start: 0.8893 (mp10) cc_final: 0.8553 (mm-40) REVERT: A 298 GLU cc_start: 0.8309 (pt0) cc_final: 0.8047 (pt0) REVERT: A 395 ASP cc_start: 0.8486 (t0) cc_final: 0.8081 (t0) REVERT: A 409 TRP cc_start: 0.8590 (t-100) cc_final: 0.8349 (t-100) REVERT: B 33 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7517 (t0) REVERT: B 70 ASP cc_start: 0.7635 (p0) cc_final: 0.6884 (p0) REVERT: B 92 ARG cc_start: 0.2626 (mtt180) cc_final: 0.1818 (mtm180) REVERT: B 176 TYR cc_start: 0.7384 (m-80) cc_final: 0.6601 (m-80) REVERT: B 258 PRO cc_start: 0.8626 (Cg_endo) cc_final: 0.8291 (Cg_exo) REVERT: B 278 LYS cc_start: 0.9330 (mtmm) cc_final: 0.9083 (mttm) REVERT: B 305 ASP cc_start: 0.8838 (t0) cc_final: 0.8503 (t0) REVERT: B 330 TRP cc_start: 0.8949 (t-100) cc_final: 0.8489 (t-100) REVERT: B 357 ILE cc_start: 0.9429 (pt) cc_final: 0.9221 (tt) REVERT: C 32 THR cc_start: 0.9116 (m) cc_final: 0.8791 (p) REVERT: C 97 ASP cc_start: 0.8051 (p0) cc_final: 0.7708 (p0) REVERT: C 195 MET cc_start: 0.8719 (mpp) cc_final: 0.8433 (mpp) REVERT: C 262 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7519 (pt0) REVERT: C 307 ILE cc_start: 0.6956 (mt) cc_final: 0.6728 (mt) REVERT: C 362 GLN cc_start: 0.7906 (pm20) cc_final: 0.7574 (pm20) REVERT: C 373 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8693 (mttp) REVERT: C 409 TRP cc_start: 0.8314 (m100) cc_final: 0.7517 (m100) REVERT: D 62 THR cc_start: 0.8763 (t) cc_final: 0.8206 (t) REVERT: D 137 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8246 (ptp90) REVERT: D 272 HIS cc_start: 0.8155 (t-170) cc_final: 0.7720 (t70) REVERT: D 330 TRP cc_start: 0.9324 (t-100) cc_final: 0.8999 (t-100) REVERT: D 339 TRP cc_start: 0.8901 (m-90) cc_final: 0.8619 (m-90) REVERT: D 341 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8493 (mm110) REVERT: D 355 ILE cc_start: 0.8633 (mm) cc_final: 0.8339 (mm) REVERT: E 160 GLU cc_start: 0.8322 (pt0) cc_final: 0.8010 (pm20) REVERT: E 194 GLU cc_start: 0.8749 (tp30) cc_final: 0.8299 (tp30) REVERT: E 195 ASN cc_start: 0.8921 (p0) cc_final: 0.8714 (p0) REVERT: E 257 GLU cc_start: 0.8077 (mp0) cc_final: 0.7851 (mp0) REVERT: F 127 VAL cc_start: 0.8938 (t) cc_final: 0.8701 (m) REVERT: F 184 TYR cc_start: 0.7006 (m-80) cc_final: 0.6652 (m-80) REVERT: F 186 TRP cc_start: 0.7790 (t60) cc_final: 0.7427 (t60) REVERT: F 197 ARG cc_start: 0.8775 (mtt90) cc_final: 0.8349 (ttm170) REVERT: F 207 LYS cc_start: 0.9103 (tmmt) cc_final: 0.8446 (tmtt) REVERT: F 214 ILE cc_start: 0.8820 (mm) cc_final: 0.8411 (pt) REVERT: F 243 ASN cc_start: 0.8494 (t0) cc_final: 0.8292 (t0) REVERT: G 10 VAL cc_start: 0.9027 (t) cc_final: 0.8765 (m) REVERT: G 27 LEU cc_start: 0.8376 (tp) cc_final: 0.7812 (tp) REVERT: G 37 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7508 (mp0) REVERT: G 160 LYS cc_start: 0.9143 (pptt) cc_final: 0.8854 (mmtm) REVERT: G 170 PHE cc_start: 0.7988 (t80) cc_final: 0.7629 (t80) REVERT: G 203 ILE cc_start: 0.9047 (tt) cc_final: 0.8761 (tt) REVERT: G 206 SER cc_start: 0.9643 (m) cc_final: 0.9296 (t) REVERT: G 212 ASP cc_start: 0.8819 (p0) cc_final: 0.8508 (p0) REVERT: G 218 ASP cc_start: 0.7547 (t0) cc_final: 0.6882 (t0) REVERT: G 220 ARG cc_start: 0.8514 (ptp-170) cc_final: 0.7913 (ptp90) REVERT: G 230 HIS cc_start: 0.8555 (t-90) cc_final: 0.7534 (t-90) REVERT: G 235 GLN cc_start: 0.8773 (pt0) cc_final: 0.8542 (pt0) REVERT: G 257 PHE cc_start: 0.8362 (m-80) cc_final: 0.7675 (m-80) REVERT: G 263 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9061 (m) REVERT: G 273 TYR cc_start: 0.8602 (p90) cc_final: 0.8355 (p90) REVERT: G 354 LEU cc_start: 0.8624 (tp) cc_final: 0.8367 (tp) REVERT: G 364 ASN cc_start: 0.8944 (t0) cc_final: 0.8556 (t0) REVERT: H 46 GLN cc_start: 0.6722 (tt0) cc_final: 0.6386 (tt0) REVERT: H 53 TYR cc_start: 0.7132 (m-80) cc_final: 0.5932 (m-10) REVERT: H 82 LYS cc_start: 0.8477 (mttt) cc_final: 0.7872 (mttm) REVERT: H 100 PHE cc_start: 0.8409 (m-80) cc_final: 0.8001 (m-10) REVERT: H 139 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: H 257 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8071 (mm) REVERT: H 305 ASP cc_start: 0.8604 (t0) cc_final: 0.8354 (t0) REVERT: H 362 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8432 (mtp-110) REVERT: I 115 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5679 (mmm) REVERT: I 152 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7584 (mmtt) REVERT: I 186 TRP cc_start: 0.8214 (t60) cc_final: 0.7736 (t60) REVERT: I 212 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: J 9 ASN cc_start: 0.9332 (t0) cc_final: 0.8755 (t0) REVERT: J 15 TYR cc_start: 0.8246 (t80) cc_final: 0.7892 (t80) REVERT: J 117 ASP cc_start: 0.8717 (t0) cc_final: 0.8390 (t0) REVERT: J 133 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8443 (mm) REVERT: J 195 MET cc_start: 0.8972 (mpp) cc_final: 0.8680 (mpp) REVERT: J 218 ASP cc_start: 0.8263 (t0) cc_final: 0.7782 (t0) REVERT: J 230 HIS cc_start: 0.8819 (t-90) cc_final: 0.8582 (t70) REVERT: J 246 ASN cc_start: 0.8145 (t0) cc_final: 0.7684 (t0) REVERT: J 257 PHE cc_start: 0.8416 (m-80) cc_final: 0.7858 (m-80) REVERT: J 262 GLU cc_start: 0.7869 (mp0) cc_final: 0.7638 (mp0) REVERT: J 271 CYS cc_start: 0.6419 (m) cc_final: 0.6039 (m) REVERT: J 307 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8056 (mm) REVERT: J 372 LYS cc_start: 0.8770 (tptt) cc_final: 0.8348 (tppt) REVERT: J 390 GLU cc_start: 0.8321 (tp30) cc_final: 0.7368 (tt0) REVERT: J 409 TRP cc_start: 0.8511 (m100) cc_final: 0.8233 (m100) REVERT: K 15 PHE cc_start: 0.8664 (t80) cc_final: 0.8360 (t80) REVERT: K 37 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8356 (mt-10) REVERT: K 38 SER cc_start: 0.9266 (t) cc_final: 0.8958 (p) REVERT: K 78 ASP cc_start: 0.8627 (t0) cc_final: 0.8368 (t70) REVERT: K 146 HIS cc_start: 0.4650 (m-70) cc_final: 0.3860 (m-70) REVERT: K 168 MET cc_start: 0.8384 (mmp) cc_final: 0.7998 (mmp) REVERT: K 217 MET cc_start: 0.8128 (tpp) cc_final: 0.7535 (tpp) REVERT: K 272 HIS cc_start: 0.8665 (t70) cc_final: 0.7583 (t70) REVERT: K 279 TRP cc_start: 0.9109 (p-90) cc_final: 0.8711 (p-90) REVERT: K 339 TRP cc_start: 0.9104 (m-90) cc_final: 0.7975 (m-90) REVERT: K 341 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: K 366 TYR cc_start: 0.8391 (m-80) cc_final: 0.7896 (m-80) REVERT: L 110 LYS cc_start: 0.8009 (mmtm) cc_final: 0.6763 (pttm) REVERT: L 168 MET cc_start: 0.9205 (ppp) cc_final: 0.8811 (tmm) REVERT: L 179 LYS cc_start: 0.7140 (ttmm) cc_final: 0.6912 (ttmm) REVERT: V 69 LYS cc_start: 0.8012 (tptt) cc_final: 0.7557 (ttmt) REVERT: W 72 CYS cc_start: 0.5099 (OUTLIER) cc_final: 0.4782 (p) REVERT: W 90 LYS cc_start: 0.8707 (mtpt) cc_final: 0.7738 (tmtt) REVERT: W 106 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: X 77 PHE cc_start: 0.6521 (t80) cc_final: 0.6124 (t80) REVERT: X 96 ASP cc_start: 0.8011 (m-30) cc_final: 0.7761 (m-30) REVERT: Y 83 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.4979 (pm20) outliers start: 203 outliers final: 155 residues processed: 1036 average time/residue: 0.1868 time to fit residues: 320.6170 Evaluate side-chains 1047 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 880 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 124 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 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 330 VAL Chi-restraints excluded: chain A residue 367 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 130 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 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 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 177 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 198 THR Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 237 VAL 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 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain 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 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 226 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 236 TRP Chi-restraints excluded: chain H residue 257 ILE 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 326 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 115 MET 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 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 137 TYR 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 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 331 HIS 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 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 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 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 101 SER Chi-restraints excluded: chain W residue 106 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 395 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN ** 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** L 145 GLN L 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.162301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127142 restraints weight = 64387.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131092 restraints weight = 31536.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133612 restraints weight = 19463.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135207 restraints weight = 14160.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136198 restraints weight = 11587.551| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33733 Z= 0.135 Angle : 0.680 10.159 45942 Z= 0.348 Chirality : 0.046 0.374 5080 Planarity : 0.005 0.054 5924 Dihedral : 6.128 81.536 4614 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 4.68 % Allowed : 22.65 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.13), residues: 4240 helix: 0.93 (0.25), residues: 392 sheet: -0.73 (0.15), residues: 1158 loop : -0.38 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 245 TYR 0.032 0.002 TYR I 161 PHE 0.030 0.002 PHE K 100 TRP 0.016 0.001 TRP J 89 HIS 0.012 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00309 (33660) covalent geometry : angle 0.67509 (45796) SS BOND : bond 0.00296 ( 73) SS BOND : angle 1.60393 ( 146) hydrogen bonds : bond 0.03577 ( 1197) hydrogen bonds : angle 5.98150 ( 3135) *********************** 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 1097 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 928 time to evaluate : 1.324 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 10 VAL cc_start: 0.9478 (t) cc_final: 0.9274 (m) REVERT: A 16 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8224 (mtmt) REVERT: A 24 TYR cc_start: 0.8523 (m-80) cc_final: 0.8174 (m-80) REVERT: A 69 LYS cc_start: 0.8783 (ptmm) cc_final: 0.8544 (ptmt) REVERT: A 75 ASP cc_start: 0.7553 (t0) cc_final: 0.6514 (t0) REVERT: A 77 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 88 MET cc_start: 0.6603 (tpp) cc_final: 0.6294 (mmt) REVERT: A 219 ILE cc_start: 0.9448 (mt) cc_final: 0.9185 (mt) REVERT: A 395 ASP cc_start: 0.8435 (t0) cc_final: 0.8071 (t0) REVERT: A 409 TRP cc_start: 0.8560 (t-100) cc_final: 0.8353 (t-100) REVERT: B 30 LYS cc_start: 0.8960 (tptt) cc_final: 0.8425 (tttp) REVERT: B 32 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7967 (tp30) REVERT: B 33 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7516 (t0) REVERT: B 70 ASP cc_start: 0.7596 (p0) cc_final: 0.6834 (p0) REVERT: B 78 ASP cc_start: 0.7697 (t0) cc_final: 0.7335 (t0) REVERT: B 92 ARG cc_start: 0.2958 (mtt180) cc_final: 0.2065 (mtm180) REVERT: B 176 TYR cc_start: 0.7344 (m-80) cc_final: 0.6608 (m-80) REVERT: B 258 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8231 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9205 (mp) cc_final: 0.8788 (mt) REVERT: B 305 ASP cc_start: 0.8848 (t0) cc_final: 0.8492 (t0) REVERT: B 330 TRP cc_start: 0.8908 (t-100) cc_final: 0.8289 (t-100) REVERT: C 32 THR cc_start: 0.9117 (m) cc_final: 0.8811 (p) REVERT: C 97 ASP cc_start: 0.8098 (p0) cc_final: 0.7744 (p0) REVERT: C 195 MET cc_start: 0.8720 (mpp) cc_final: 0.8462 (mpp) REVERT: C 221 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8820 (mt) REVERT: C 262 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7600 (pt0) REVERT: C 362 GLN cc_start: 0.7811 (pm20) cc_final: 0.7525 (pm20) REVERT: C 373 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8684 (mttp) REVERT: C 395 ASP cc_start: 0.8302 (t0) cc_final: 0.8003 (t0) REVERT: C 409 TRP cc_start: 0.8299 (m100) cc_final: 0.7582 (m100) REVERT: D 75 ILE cc_start: 0.8029 (mm) cc_final: 0.7276 (mp) REVERT: D 137 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8231 (ptp90) REVERT: D 239 ASN cc_start: 0.9191 (t0) cc_final: 0.8884 (t0) REVERT: D 261 LEU cc_start: 0.9309 (tp) cc_final: 0.8888 (tt) REVERT: D 272 HIS cc_start: 0.8056 (t-170) cc_final: 0.7605 (t70) REVERT: D 330 TRP cc_start: 0.9303 (t-100) cc_final: 0.8993 (t-100) REVERT: D 339 TRP cc_start: 0.8787 (m-90) cc_final: 0.8547 (m-90) REVERT: D 355 ILE cc_start: 0.8581 (mm) cc_final: 0.8346 (mm) REVERT: E 140 LYS cc_start: 0.7227 (tptp) cc_final: 0.6948 (tptt) REVERT: E 160 GLU cc_start: 0.8259 (pt0) cc_final: 0.7867 (pm20) REVERT: E 194 GLU cc_start: 0.8648 (tp30) cc_final: 0.8360 (mm-30) REVERT: E 257 GLU cc_start: 0.8049 (mp0) cc_final: 0.7426 (mp0) REVERT: F 127 VAL cc_start: 0.8915 (t) cc_final: 0.8663 (m) REVERT: F 152 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8294 (mtmt) REVERT: F 156 MET cc_start: 0.8676 (tmm) cc_final: 0.8290 (pmm) REVERT: F 157 TYR cc_start: 0.7623 (m-80) cc_final: 0.6637 (m-80) REVERT: F 184 TYR cc_start: 0.7037 (m-80) cc_final: 0.6714 (m-80) REVERT: F 197 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8329 (ttm170) REVERT: F 207 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8376 (tmtt) REVERT: F 214 ILE cc_start: 0.8831 (mm) cc_final: 0.8491 (pt) REVERT: F 243 ASN cc_start: 0.8598 (t0) cc_final: 0.8346 (t0) REVERT: G 10 VAL cc_start: 0.9009 (t) cc_final: 0.8779 (m) REVERT: G 37 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7566 (mp0) REVERT: G 160 LYS cc_start: 0.9130 (pptt) cc_final: 0.8665 (mmtm) REVERT: G 170 PHE cc_start: 0.7952 (t80) cc_final: 0.7548 (t80) REVERT: G 203 ILE cc_start: 0.9001 (tt) cc_final: 0.8724 (tt) REVERT: G 206 SER cc_start: 0.9642 (m) cc_final: 0.9251 (t) REVERT: G 218 ASP cc_start: 0.7504 (t0) cc_final: 0.5764 (t0) REVERT: G 220 ARG cc_start: 0.8457 (ptp-170) cc_final: 0.7512 (ptp90) REVERT: G 230 HIS cc_start: 0.8487 (t-90) cc_final: 0.8269 (t70) REVERT: G 235 GLN cc_start: 0.8711 (pt0) cc_final: 0.8470 (pt0) REVERT: G 257 PHE cc_start: 0.8340 (m-80) cc_final: 0.7622 (m-80) REVERT: G 263 VAL cc_start: 0.9321 (t) cc_final: 0.9075 (m) REVERT: G 273 TYR cc_start: 0.8673 (p90) cc_final: 0.8412 (p90) REVERT: G 281 ASP cc_start: 0.8817 (t0) cc_final: 0.7962 (p0) REVERT: G 354 LEU cc_start: 0.8600 (tp) cc_final: 0.8333 (tp) REVERT: G 364 ASN cc_start: 0.8913 (t0) cc_final: 0.8488 (t0) REVERT: H 46 GLN cc_start: 0.6822 (tt0) cc_final: 0.6243 (tt0) REVERT: H 82 LYS cc_start: 0.8359 (mttt) cc_final: 0.7818 (mttm) REVERT: H 100 PHE cc_start: 0.8354 (m-80) cc_final: 0.7467 (m-80) REVERT: H 138 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: H 139 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: H 155 TYR cc_start: 0.7579 (m-80) cc_final: 0.7315 (m-80) REVERT: H 257 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7902 (mm) REVERT: H 270 LEU cc_start: 0.9271 (tp) cc_final: 0.9028 (tp) REVERT: H 305 ASP cc_start: 0.8581 (t0) cc_final: 0.8367 (t0) REVERT: H 337 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.8651 (mmm-85) REVERT: H 362 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8445 (mtp-110) REVERT: I 152 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7552 (mmtm) REVERT: I 212 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: J 9 ASN cc_start: 0.9317 (t0) cc_final: 0.8884 (t0) REVERT: J 15 TYR cc_start: 0.8213 (t80) cc_final: 0.7837 (t80) REVERT: J 117 ASP cc_start: 0.8690 (t0) cc_final: 0.8442 (t0) REVERT: J 195 MET cc_start: 0.8944 (mpp) cc_final: 0.8734 (mpp) REVERT: J 218 ASP cc_start: 0.8253 (t0) cc_final: 0.7811 (t0) REVERT: J 246 ASN cc_start: 0.8163 (t0) cc_final: 0.7709 (t0) REVERT: J 262 GLU cc_start: 0.7774 (mp0) cc_final: 0.7560 (mp0) REVERT: J 271 CYS cc_start: 0.6246 (m) cc_final: 0.5785 (m) REVERT: J 307 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (mm) REVERT: J 362 GLN cc_start: 0.8012 (tp40) cc_final: 0.7766 (tp-100) REVERT: J 372 LYS cc_start: 0.8699 (tptt) cc_final: 0.8342 (tppt) REVERT: J 390 GLU cc_start: 0.8308 (tp30) cc_final: 0.7444 (tt0) REVERT: J 409 TRP cc_start: 0.8418 (m100) cc_final: 0.8152 (m100) REVERT: K 37 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8258 (mt-10) REVERT: K 38 SER cc_start: 0.9236 (t) cc_final: 0.8919 (p) REVERT: K 78 ASP cc_start: 0.8518 (t0) cc_final: 0.8273 (t70) REVERT: K 165 TYR cc_start: 0.8570 (p90) cc_final: 0.8327 (p90) REVERT: K 168 MET cc_start: 0.8181 (mmp) cc_final: 0.7828 (mmp) REVERT: K 217 MET cc_start: 0.8135 (tpp) cc_final: 0.7580 (tpp) REVERT: K 272 HIS cc_start: 0.8520 (t70) cc_final: 0.7135 (t70) REVERT: K 279 TRP cc_start: 0.9110 (p-90) cc_final: 0.8767 (p-90) REVERT: K 366 TYR cc_start: 0.8371 (m-80) cc_final: 0.7866 (m-80) REVERT: L 110 LYS cc_start: 0.8008 (mmtm) cc_final: 0.6862 (pttm) REVERT: L 143 ASN cc_start: 0.7910 (t0) cc_final: 0.7507 (m-40) REVERT: L 168 MET cc_start: 0.9214 (ppp) cc_final: 0.8839 (tmm) REVERT: L 192 GLN cc_start: 0.8464 (tp40) cc_final: 0.8167 (tp40) REVERT: L 193 TYR cc_start: 0.6726 (t80) cc_final: 0.5910 (t80) REVERT: W 72 CYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4724 (p) REVERT: W 90 LYS cc_start: 0.8620 (mtpt) cc_final: 0.7698 (tmtt) REVERT: W 106 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: X 77 PHE cc_start: 0.6546 (t80) cc_final: 0.6100 (t80) REVERT: X 96 ASP cc_start: 0.8065 (m-30) cc_final: 0.7809 (m-30) REVERT: Y 83 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5135 (pm20) outliers start: 169 outliers final: 120 residues processed: 1011 average time/residue: 0.1954 time to fit residues: 326.5408 Evaluate side-chains 1003 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 872 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 146 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR 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 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 162 SER 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 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 396 CYS 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 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 221 LEU Chi-restraints excluded: chain C residue 339 LEU 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 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 226 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 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 F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 55 ILE 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 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 G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 ILE 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 208 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 331 HIS 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 321 VAL Chi-restraints excluded: chain K residue 324 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 187 HIS 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 72 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 101 SER Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 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 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 136 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 318 optimal weight: 0.0370 chunk 113 optimal weight: 9.9990 chunk 319 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 overall best weight: 1.7262 ------------------------------------------------------------------------------- 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 319 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS G 204 GLN ** G 252 GLN ** 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 HIS ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN V 66 ASN V 83 GLN W 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126350 restraints weight = 64363.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130258 restraints weight = 31691.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132769 restraints weight = 19616.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134359 restraints weight = 14273.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135347 restraints weight = 11672.704| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4426 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= 0.158 Angle : 0.683 10.939 45942 Z= 0.351 Chirality : 0.047 0.331 5080 Planarity : 0.005 0.047 5924 Dihedral : 6.043 81.293 4613 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 4.73 % Allowed : 23.98 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 4240 helix: 1.01 (0.25), residues: 392 sheet: -0.79 (0.15), residues: 1135 loop : -0.38 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 267 TYR 0.026 0.002 TYR I 161 PHE 0.029 0.002 PHE K 100 TRP 0.021 0.001 TRP H 310 HIS 0.014 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00363 (33660) covalent geometry : angle 0.67808 (45796) SS BOND : bond 0.00318 ( 73) SS BOND : angle 1.62173 ( 146) hydrogen bonds : bond 0.03608 ( 1197) hydrogen bonds : angle 5.93116 ( 3135) *********************** 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 1058 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 887 time to evaluate : 1.295 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: 0.9503 (t) cc_final: 0.9292 (m) REVERT: A 16 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8272 (mtmt) REVERT: A 24 TYR cc_start: 0.8527 (m-80) cc_final: 0.8212 (m-80) REVERT: A 69 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8552 (ptmt) REVERT: A 75 ASP cc_start: 0.7573 (t0) cc_final: 0.6519 (t0) REVERT: A 77 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 102 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: A 143 HIS cc_start: 0.8352 (m90) cc_final: 0.7929 (m-70) REVERT: A 219 ILE cc_start: 0.9411 (mt) cc_final: 0.9145 (mt) REVERT: A 264 GLU cc_start: 0.8447 (mp0) cc_final: 0.8061 (mp0) REVERT: A 354 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9123 (mt) REVERT: A 395 ASP cc_start: 0.8411 (t0) cc_final: 0.8033 (t0) REVERT: A 409 TRP cc_start: 0.8596 (t-100) cc_final: 0.8364 (t-100) REVERT: B 30 LYS cc_start: 0.8999 (tptt) cc_final: 0.8218 (tttp) REVERT: B 33 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 70 ASP cc_start: 0.7603 (p0) cc_final: 0.6848 (p0) REVERT: B 92 ARG cc_start: 0.2776 (mtt180) cc_final: 0.1999 (mtm180) REVERT: B 176 TYR cc_start: 0.7350 (m-80) cc_final: 0.6609 (m-80) REVERT: B 258 PRO cc_start: 0.8590 (Cg_endo) cc_final: 0.8267 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9219 (mp) cc_final: 0.8809 (mt) REVERT: B 305 ASP cc_start: 0.8820 (t0) cc_final: 0.8471 (t0) REVERT: B 329 VAL cc_start: 0.9392 (t) cc_final: 0.9165 (m) REVERT: B 330 TRP cc_start: 0.8986 (t-100) cc_final: 0.8277 (t-100) REVERT: B 342 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 32 THR cc_start: 0.9123 (m) cc_final: 0.8818 (p) REVERT: C 97 ASP cc_start: 0.8104 (p0) cc_final: 0.7707 (p0) REVERT: C 195 MET cc_start: 0.8747 (mpp) cc_final: 0.8500 (mpp) REVERT: C 262 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7576 (pt0) REVERT: C 362 GLN cc_start: 0.7860 (pm20) cc_final: 0.7562 (pm20) REVERT: C 373 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8697 (mttp) REVERT: C 395 ASP cc_start: 0.8403 (t0) cc_final: 0.8125 (t0) REVERT: C 409 TRP cc_start: 0.8325 (m100) cc_final: 0.7602 (m100) REVERT: D 137 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8277 (ptp90) REVERT: D 339 TRP cc_start: 0.8822 (m-90) cc_final: 0.8543 (m-90) REVERT: D 355 ILE cc_start: 0.8604 (mm) cc_final: 0.8398 (mm) REVERT: E 140 LYS cc_start: 0.7333 (tptp) cc_final: 0.7022 (tptt) REVERT: E 194 GLU cc_start: 0.8640 (tp30) cc_final: 0.8253 (mm-30) REVERT: E 257 GLU cc_start: 0.8072 (mp0) cc_final: 0.7424 (mp0) REVERT: F 119 GLN cc_start: 0.8418 (pt0) cc_final: 0.7647 (pm20) REVERT: F 127 VAL cc_start: 0.8898 (t) cc_final: 0.8661 (m) REVERT: F 130 ARG cc_start: 0.7757 (ptp-110) cc_final: 0.7263 (ptp90) REVERT: F 152 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8310 (mtmt) REVERT: F 156 MET cc_start: 0.8755 (tmm) cc_final: 0.8243 (pmm) REVERT: F 157 TYR cc_start: 0.7697 (m-80) cc_final: 0.6692 (m-80) REVERT: F 184 TYR cc_start: 0.7009 (m-80) cc_final: 0.6683 (m-80) REVERT: F 197 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8333 (ttm170) REVERT: F 207 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8385 (tmtt) REVERT: F 214 ILE cc_start: 0.8855 (mm) cc_final: 0.8495 (pt) REVERT: F 220 ARG cc_start: 0.7095 (ptt90) cc_final: 0.6826 (ptt90) REVERT: F 243 ASN cc_start: 0.8574 (t0) cc_final: 0.8280 (t0) REVERT: G 10 VAL cc_start: 0.9037 (t) cc_final: 0.8795 (m) REVERT: G 27 LEU cc_start: 0.8555 (tp) cc_final: 0.8155 (tp) REVERT: G 37 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7513 (mp0) REVERT: G 160 LYS cc_start: 0.9118 (pptt) cc_final: 0.8647 (mmtm) REVERT: G 170 PHE cc_start: 0.7966 (t80) cc_final: 0.7545 (t80) REVERT: G 203 ILE cc_start: 0.8924 (tt) cc_final: 0.8655 (tt) REVERT: G 206 SER cc_start: 0.9635 (m) cc_final: 0.9247 (t) REVERT: G 218 ASP cc_start: 0.7536 (t0) cc_final: 0.5845 (t0) REVERT: G 220 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7486 (ptp90) REVERT: G 230 HIS cc_start: 0.8494 (t-90) cc_final: 0.7568 (t-90) REVERT: G 235 GLN cc_start: 0.8780 (pt0) cc_final: 0.8533 (pt0) REVERT: G 241 GLU cc_start: 0.9130 (tp30) cc_final: 0.8863 (tp30) REVERT: G 257 PHE cc_start: 0.8360 (m-80) cc_final: 0.7636 (m-80) REVERT: G 263 VAL cc_start: 0.9311 (t) cc_final: 0.9050 (m) REVERT: G 273 TYR cc_start: 0.8682 (p90) cc_final: 0.8319 (p90) REVERT: G 281 ASP cc_start: 0.8866 (t0) cc_final: 0.8054 (p0) REVERT: G 364 ASN cc_start: 0.8879 (t0) cc_final: 0.8447 (t0) REVERT: H 46 GLN cc_start: 0.6786 (tt0) cc_final: 0.6178 (tt0) REVERT: H 82 LYS cc_start: 0.8342 (mttt) cc_final: 0.7826 (mttm) REVERT: H 100 PHE cc_start: 0.8376 (m-80) cc_final: 0.7448 (m-80) REVERT: H 139 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: H 155 TYR cc_start: 0.7695 (m-80) cc_final: 0.7324 (m-80) REVERT: H 305 ASP cc_start: 0.8631 (t0) cc_final: 0.8426 (t0) REVERT: H 337 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: H 362 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8413 (mtp-110) REVERT: I 130 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6621 (mtm-85) REVERT: I 152 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7562 (mmtm) REVERT: I 197 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7213 (mmt180) REVERT: I 212 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8504 (mmm-85) REVERT: J 9 ASN cc_start: 0.9314 (t0) cc_final: 0.8883 (t0) REVERT: J 15 TYR cc_start: 0.8216 (t80) cc_final: 0.7815 (t80) REVERT: J 117 ASP cc_start: 0.8707 (t0) cc_final: 0.8396 (t0) REVERT: J 218 ASP cc_start: 0.8311 (t0) cc_final: 0.7808 (t0) REVERT: J 246 ASN cc_start: 0.8142 (t0) cc_final: 0.7701 (t0) REVERT: J 257 PHE cc_start: 0.8391 (m-80) cc_final: 0.7820 (m-80) REVERT: J 262 GLU cc_start: 0.7763 (mp0) cc_final: 0.7507 (mp0) REVERT: J 307 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7936 (mm) REVERT: J 362 GLN cc_start: 0.8082 (tp40) cc_final: 0.7854 (tp-100) REVERT: J 372 LYS cc_start: 0.8689 (tptt) cc_final: 0.8341 (tppt) REVERT: J 390 GLU cc_start: 0.8339 (tp30) cc_final: 0.7429 (tt0) REVERT: J 409 TRP cc_start: 0.8416 (m100) cc_final: 0.8154 (m100) REVERT: K 37 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8251 (mt-10) REVERT: K 38 SER cc_start: 0.9239 (t) cc_final: 0.8880 (p) REVERT: K 78 ASP cc_start: 0.8549 (t0) cc_final: 0.8305 (t70) REVERT: K 146 HIS cc_start: 0.4269 (m-70) cc_final: 0.3499 (m-70) REVERT: K 168 MET cc_start: 0.8289 (mmp) cc_final: 0.7933 (mmp) REVERT: K 272 HIS cc_start: 0.8507 (t70) cc_final: 0.7157 (t70) REVERT: K 279 TRP cc_start: 0.9116 (p-90) cc_final: 0.8752 (p-90) REVERT: K 366 TYR cc_start: 0.8351 (m-80) cc_final: 0.7875 (m-80) REVERT: L 110 LYS cc_start: 0.7997 (mmtm) cc_final: 0.6839 (pttm) REVERT: L 143 ASN cc_start: 0.7857 (t0) cc_final: 0.7384 (m-40) REVERT: L 168 MET cc_start: 0.9245 (ppp) cc_final: 0.8877 (tmm) REVERT: L 192 GLN cc_start: 0.8378 (tp40) cc_final: 0.8065 (tp40) REVERT: L 250 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7248 (mtpt) REVERT: V 99 ASP cc_start: 0.6652 (p0) cc_final: 0.5730 (p0) REVERT: W 90 LYS cc_start: 0.8684 (mtpt) cc_final: 0.7747 (tmtt) REVERT: W 106 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: X 77 PHE cc_start: 0.6579 (t80) cc_final: 0.6139 (t80) REVERT: X 96 ASP cc_start: 0.8062 (m-30) cc_final: 0.7819 (m-30) REVERT: Y 83 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.5188 (pm20) outliers start: 171 outliers final: 140 residues processed: 978 average time/residue: 0.1822 time to fit residues: 296.9223 Evaluate side-chains 1008 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 859 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 102 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR 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 354 LEU 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 130 ILE Chi-restraints excluded: chain B residue 162 SER 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 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 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 339 LEU Chi-restraints excluded: chain C residue 403 SER 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 198 THR Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 320 SER 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 120 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 191 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 F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 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 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 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 G residue 352 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 115 MET 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 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 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 331 HIS 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 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 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 145 GLN 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 78 VAL Chi-restraints excluded: chain V residue 81 ASN 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 106 GLU 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 Y residue 33 CYS 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 138 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 344 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 373 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 319 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 HIS K 157 HIS ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125982 restraints weight = 64067.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129869 restraints weight = 31589.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132398 restraints weight = 19654.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133981 restraints weight = 14292.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134968 restraints weight = 11696.933| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33733 Z= 0.145 Angle : 0.684 11.093 45942 Z= 0.350 Chirality : 0.047 0.322 5080 Planarity : 0.005 0.046 5924 Dihedral : 5.967 81.115 4613 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 4.40 % Allowed : 24.28 % Favored : 71.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 4240 helix: 1.15 (0.26), residues: 380 sheet: -0.78 (0.15), residues: 1130 loop : -0.35 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 130 TYR 0.027 0.002 TYR D 238 PHE 0.019 0.002 PHE K 280 TRP 0.020 0.001 TRP D 330 HIS 0.012 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00333 (33660) covalent geometry : angle 0.67962 (45796) SS BOND : bond 0.00306 ( 73) SS BOND : angle 1.58974 ( 146) hydrogen bonds : bond 0.03572 ( 1197) hydrogen bonds : angle 5.88449 ( 3135) *********************** 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 1044 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 885 time to evaluate : 1.132 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: 0.8610 (mtmt) cc_final: 0.8228 (mtmt) REVERT: A 24 TYR cc_start: 0.8531 (m-80) cc_final: 0.8258 (m-80) REVERT: A 69 LYS cc_start: 0.8735 (ptmm) cc_final: 0.8504 (ptmt) REVERT: A 75 ASP cc_start: 0.7614 (t0) cc_final: 0.6539 (t0) REVERT: A 77 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8224 (p) REVERT: A 88 MET cc_start: 0.6340 (tpp) cc_final: 0.6105 (mmt) REVERT: A 102 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: A 143 HIS cc_start: 0.8374 (m90) cc_final: 0.7995 (m-70) REVERT: A 219 ILE cc_start: 0.9408 (mt) cc_final: 0.9143 (mt) REVERT: A 264 GLU cc_start: 0.8452 (mp0) cc_final: 0.8045 (mp0) REVERT: A 319 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: A 354 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9117 (mt) REVERT: A 395 ASP cc_start: 0.8407 (t0) cc_final: 0.8030 (t0) REVERT: A 409 TRP cc_start: 0.8584 (t-100) cc_final: 0.8349 (t-100) REVERT: B 30 LYS cc_start: 0.8985 (tptt) cc_final: 0.8236 (tttp) REVERT: B 33 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 70 ASP cc_start: 0.7602 (p0) cc_final: 0.6863 (p0) REVERT: B 78 ASP cc_start: 0.8125 (t0) cc_final: 0.7802 (t0) REVERT: B 92 ARG cc_start: 0.3220 (mtt180) cc_final: 0.2395 (mtm180) REVERT: B 176 TYR cc_start: 0.7372 (m-80) cc_final: 0.6595 (m-80) REVERT: B 258 PRO cc_start: 0.8540 (Cg_endo) cc_final: 0.8196 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9214 (mp) cc_final: 0.8744 (mt) REVERT: B 305 ASP cc_start: 0.8848 (t0) cc_final: 0.8517 (t0) REVERT: B 329 VAL cc_start: 0.9375 (t) cc_final: 0.9172 (m) REVERT: B 330 TRP cc_start: 0.9000 (t-100) cc_final: 0.8317 (t-100) REVERT: B 341 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8992 (mm-40) REVERT: C 32 THR cc_start: 0.9116 (m) cc_final: 0.8827 (p) REVERT: C 97 ASP cc_start: 0.8213 (p0) cc_final: 0.7831 (p0) REVERT: C 180 ARG cc_start: 0.8560 (ttt90) cc_final: 0.8109 (ptm-80) REVERT: C 195 MET cc_start: 0.8753 (mpp) cc_final: 0.8505 (mpp) REVERT: C 262 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7610 (pt0) REVERT: C 362 GLN cc_start: 0.7845 (pm20) cc_final: 0.7558 (pm20) REVERT: C 373 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8694 (mttp) REVERT: C 409 TRP cc_start: 0.8316 (m100) cc_final: 0.7598 (m100) REVERT: D 55 GLN cc_start: 0.8507 (tt0) cc_final: 0.8229 (tt0) REVERT: D 75 ILE cc_start: 0.8051 (mm) cc_final: 0.7509 (mm) REVERT: D 137 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8263 (ptp90) REVERT: D 339 TRP cc_start: 0.8805 (m-90) cc_final: 0.8526 (m-90) REVERT: D 355 ILE cc_start: 0.8572 (mm) cc_final: 0.8366 (mm) REVERT: E 140 LYS cc_start: 0.7322 (tptp) cc_final: 0.7008 (tptt) REVERT: E 194 GLU cc_start: 0.8599 (tp30) cc_final: 0.8224 (mm-30) REVERT: E 257 GLU cc_start: 0.8080 (mp0) cc_final: 0.7418 (mp0) REVERT: F 119 GLN cc_start: 0.8408 (pt0) cc_final: 0.7651 (pm20) REVERT: F 127 VAL cc_start: 0.8869 (t) cc_final: 0.8627 (m) REVERT: F 152 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8285 (mtmt) REVERT: F 156 MET cc_start: 0.8805 (tmm) cc_final: 0.8352 (pmm) REVERT: F 157 TYR cc_start: 0.7639 (m-80) cc_final: 0.6797 (m-80) REVERT: F 184 TYR cc_start: 0.7025 (m-80) cc_final: 0.6822 (m-80) REVERT: F 197 ARG cc_start: 0.8619 (mtt90) cc_final: 0.8310 (ttm170) REVERT: F 207 LYS cc_start: 0.9078 (tmmt) cc_final: 0.8393 (tmtt) REVERT: F 243 ASN cc_start: 0.8583 (t0) cc_final: 0.8303 (t0) REVERT: G 10 VAL cc_start: 0.9056 (t) cc_final: 0.8821 (m) REVERT: G 27 LEU cc_start: 0.8479 (tp) cc_final: 0.8130 (tp) REVERT: G 37 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7506 (mp0) REVERT: G 160 LYS cc_start: 0.9103 (pptt) cc_final: 0.8612 (mmtm) REVERT: G 162 ILE cc_start: 0.8643 (mt) cc_final: 0.8102 (mm) REVERT: G 170 PHE cc_start: 0.7948 (t80) cc_final: 0.7523 (t80) REVERT: G 206 SER cc_start: 0.9640 (m) cc_final: 0.9231 (t) REVERT: G 218 ASP cc_start: 0.7536 (t0) cc_final: 0.5831 (t0) REVERT: G 220 ARG cc_start: 0.8443 (ptp-170) cc_final: 0.7504 (ptp90) REVERT: G 230 HIS cc_start: 0.8453 (t-90) cc_final: 0.7542 (t-90) REVERT: G 235 GLN cc_start: 0.8764 (pt0) cc_final: 0.8495 (pt0) REVERT: G 241 GLU cc_start: 0.9116 (tp30) cc_final: 0.8834 (tp30) REVERT: G 257 PHE cc_start: 0.8378 (m-80) cc_final: 0.7696 (m-80) REVERT: G 263 VAL cc_start: 0.9286 (t) cc_final: 0.9045 (m) REVERT: G 273 TYR cc_start: 0.8588 (p90) cc_final: 0.8178 (p90) REVERT: G 281 ASP cc_start: 0.8852 (t0) cc_final: 0.8049 (p0) REVERT: G 364 ASN cc_start: 0.8886 (t0) cc_final: 0.8432 (t0) REVERT: H 26 PHE cc_start: 0.8533 (m-80) cc_final: 0.8272 (m-10) REVERT: H 46 GLN cc_start: 0.6797 (tt0) cc_final: 0.6178 (tt0) REVERT: H 82 LYS cc_start: 0.8363 (mttt) cc_final: 0.7892 (mttm) REVERT: H 100 PHE cc_start: 0.8338 (m-80) cc_final: 0.7432 (m-80) REVERT: H 128 LYS cc_start: 0.8621 (tppt) cc_final: 0.8341 (tppt) REVERT: H 155 TYR cc_start: 0.7640 (m-80) cc_final: 0.7152 (m-80) REVERT: H 287 LEU cc_start: 0.8478 (mm) cc_final: 0.8104 (mm) REVERT: H 337 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: I 130 ARG cc_start: 0.6849 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: I 152 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7508 (mmtm) REVERT: I 197 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7202 (mmt180) REVERT: I 212 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8503 (mmm-85) REVERT: J 9 ASN cc_start: 0.9307 (t0) cc_final: 0.8890 (t0) REVERT: J 15 TYR cc_start: 0.8157 (t80) cc_final: 0.7782 (t80) REVERT: J 76 TYR cc_start: 0.8746 (t80) cc_final: 0.8437 (t80) REVERT: J 117 ASP cc_start: 0.8714 (t0) cc_final: 0.8361 (t0) REVERT: J 195 MET cc_start: 0.8860 (mpp) cc_final: 0.8623 (mpp) REVERT: J 218 ASP cc_start: 0.8277 (t0) cc_final: 0.7765 (t0) REVERT: J 262 GLU cc_start: 0.7654 (mp0) cc_final: 0.7388 (mp0) REVERT: J 307 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (mm) REVERT: J 362 GLN cc_start: 0.8096 (tp40) cc_final: 0.7887 (tp-100) REVERT: J 372 LYS cc_start: 0.8681 (tptt) cc_final: 0.8299 (tppt) REVERT: J 390 GLU cc_start: 0.8374 (tp30) cc_final: 0.7464 (tt0) REVERT: J 409 TRP cc_start: 0.8405 (m100) cc_final: 0.8149 (m100) REVERT: K 38 SER cc_start: 0.9238 (t) cc_final: 0.8858 (p) REVERT: K 78 ASP cc_start: 0.8570 (t0) cc_final: 0.8332 (t70) REVERT: K 146 HIS cc_start: 0.4291 (m-70) cc_final: 0.3484 (m-70) REVERT: K 168 MET cc_start: 0.8254 (mmp) cc_final: 0.7917 (mmp) REVERT: K 259 PHE cc_start: 0.8386 (m-80) cc_final: 0.7994 (m-10) REVERT: K 272 HIS cc_start: 0.8459 (t70) cc_final: 0.7077 (t70) REVERT: K 279 TRP cc_start: 0.9111 (p-90) cc_final: 0.8757 (p-90) REVERT: K 366 TYR cc_start: 0.8348 (m-80) cc_final: 0.7894 (m-80) REVERT: L 110 LYS cc_start: 0.8017 (mmtm) cc_final: 0.6935 (pttm) REVERT: L 156 MET cc_start: 0.9005 (ppp) cc_final: 0.8622 (ppp) REVERT: L 168 MET cc_start: 0.9260 (ppp) cc_final: 0.8906 (tmm) REVERT: L 192 GLN cc_start: 0.8315 (tp40) cc_final: 0.8010 (tp40) REVERT: W 90 LYS cc_start: 0.8659 (mtpt) cc_final: 0.7787 (tmtt) REVERT: W 106 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6369 (pm20) REVERT: X 77 PHE cc_start: 0.6660 (t80) cc_final: 0.6240 (t80) REVERT: X 96 ASP cc_start: 0.8096 (m-30) cc_final: 0.7846 (m-30) REVERT: Y 83 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5167 (pm20) outliers start: 159 outliers final: 133 residues processed: 964 average time/residue: 0.1858 time to fit residues: 296.2118 Evaluate side-chains 999 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 857 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 102 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 ASN 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 162 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN 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 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 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 338 VAL Chi-restraints excluded: chain C residue 339 LEU 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 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 201 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 295 LEU 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 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 F residue 125 CYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 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 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 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 G residue 352 ILE Chi-restraints excluded: chain H residue 50 GLN 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 283 ILE Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 361 HIS Chi-restraints excluded: chain I residue 115 MET 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 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 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 331 HIS 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 321 VAL Chi-restraints excluded: chain K residue 324 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 176 THR 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 W residue 106 GLU 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 Y residue 33 CYS 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 359 optimal weight: 0.0170 chunk 267 optimal weight: 0.9990 chunk 392 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 395 optimal weight: 0.6980 chunk 319 optimal weight: 1.9990 chunk 349 optimal weight: 9.9990 chunk 316 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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** A 364 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 169 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** 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 363 HIS ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN W 37 GLN X 80 ASN Y 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128383 restraints weight = 64669.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132365 restraints weight = 31743.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134927 restraints weight = 19646.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136539 restraints weight = 14268.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137563 restraints weight = 11656.143| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4740 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= 0.128 Angle : 0.694 11.542 45942 Z= 0.354 Chirality : 0.047 0.358 5080 Planarity : 0.005 0.044 5924 Dihedral : 5.881 80.567 4613 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.52 % Allowed : 25.75 % Favored : 70.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 4240 helix: 1.22 (0.26), residues: 380 sheet: -0.71 (0.15), residues: 1139 loop : -0.35 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 131 TYR 0.026 0.001 TYR D 238 PHE 0.026 0.002 PHE B 280 TRP 0.020 0.001 TRP H 310 HIS 0.012 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00296 (33660) covalent geometry : angle 0.68911 (45796) SS BOND : bond 0.00316 ( 73) SS BOND : angle 1.67014 ( 146) hydrogen bonds : bond 0.03528 ( 1197) hydrogen bonds : angle 5.85844 ( 3135) ********************** 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 1022 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 895 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8226 (mtmt) REVERT: A 69 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8475 (ptmt) REVERT: A 75 ASP cc_start: 0.7543 (t0) cc_final: 0.6479 (t0) REVERT: A 143 HIS cc_start: 0.8417 (m90) cc_final: 0.8015 (m-70) REVERT: A 219 ILE cc_start: 0.9403 (mt) cc_final: 0.9130 (mt) REVERT: A 264 GLU cc_start: 0.8470 (mp0) cc_final: 0.8063 (mp0) REVERT: A 395 ASP cc_start: 0.8397 (t0) cc_final: 0.8007 (t0) REVERT: A 409 TRP cc_start: 0.8548 (t-100) cc_final: 0.8267 (t-100) REVERT: B 30 LYS cc_start: 0.8958 (tptt) cc_final: 0.8449 (tttp) REVERT: B 32 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7967 (tp30) REVERT: B 33 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 70 ASP cc_start: 0.7625 (p0) cc_final: 0.6888 (p0) REVERT: B 92 ARG cc_start: 0.3257 (mtt180) cc_final: 0.2494 (mtm180) REVERT: B 146 HIS cc_start: 0.4970 (m170) cc_final: 0.4426 (m170) REVERT: B 156 ASP cc_start: 0.8521 (t0) cc_final: 0.8279 (m-30) REVERT: B 176 TYR cc_start: 0.7399 (m-80) cc_final: 0.6582 (m-80) REVERT: B 287 LEU cc_start: 0.9192 (mp) cc_final: 0.8675 (mt) REVERT: B 305 ASP cc_start: 0.8879 (t0) cc_final: 0.8508 (t0) REVERT: B 330 TRP cc_start: 0.8978 (t-100) cc_final: 0.8327 (t-100) REVERT: C 32 THR cc_start: 0.9095 (m) cc_final: 0.8820 (p) REVERT: C 97 ASP cc_start: 0.8192 (p0) cc_final: 0.7877 (p0) REVERT: C 100 ASN cc_start: 0.7833 (m-40) cc_final: 0.7600 (m-40) REVERT: C 174 ASP cc_start: 0.8072 (m-30) cc_final: 0.7565 (m-30) REVERT: C 180 ARG cc_start: 0.8509 (ttt90) cc_final: 0.8030 (ptm-80) REVERT: C 195 MET cc_start: 0.8763 (mpp) cc_final: 0.8528 (mpp) REVERT: C 262 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7653 (pt0) REVERT: C 362 GLN cc_start: 0.7780 (pm20) cc_final: 0.7494 (pm20) REVERT: C 373 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8692 (mttp) REVERT: C 409 TRP cc_start: 0.8278 (m100) cc_final: 0.7573 (m100) REVERT: D 55 GLN cc_start: 0.8523 (tt0) cc_final: 0.8268 (tt0) REVERT: D 75 ILE cc_start: 0.8015 (mm) cc_final: 0.6722 (mp) REVERT: D 137 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8142 (ptp90) REVERT: D 272 HIS cc_start: 0.7565 (t-170) cc_final: 0.7036 (t-170) REVERT: D 339 TRP cc_start: 0.8790 (m-90) cc_final: 0.8487 (m-90) REVERT: D 355 ILE cc_start: 0.8556 (mm) cc_final: 0.8345 (mm) REVERT: E 140 LYS cc_start: 0.7399 (tptp) cc_final: 0.7099 (tptt) REVERT: E 194 GLU cc_start: 0.8599 (tp30) cc_final: 0.8208 (mm-30) REVERT: E 257 GLU cc_start: 0.8082 (mp0) cc_final: 0.7438 (mp0) REVERT: F 119 GLN cc_start: 0.8405 (pt0) cc_final: 0.7633 (pm20) REVERT: F 127 VAL cc_start: 0.8848 (t) cc_final: 0.8607 (m) REVERT: F 156 MET cc_start: 0.8752 (tmm) cc_final: 0.8269 (pmm) REVERT: F 157 TYR cc_start: 0.7488 (m-80) cc_final: 0.7162 (m-80) REVERT: F 184 TYR cc_start: 0.7004 (m-80) cc_final: 0.6685 (m-80) REVERT: F 207 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8360 (tmtt) REVERT: F 214 ILE cc_start: 0.8838 (mm) cc_final: 0.8552 (pt) REVERT: F 243 ASN cc_start: 0.8521 (t0) cc_final: 0.8264 (t0) REVERT: G 10 VAL cc_start: 0.9045 (t) cc_final: 0.8809 (m) REVERT: G 27 LEU cc_start: 0.8462 (tp) cc_final: 0.8106 (tp) REVERT: G 37 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7477 (mp0) REVERT: G 160 LYS cc_start: 0.9090 (pptt) cc_final: 0.8597 (mmtm) REVERT: G 162 ILE cc_start: 0.8592 (mt) cc_final: 0.8055 (mm) REVERT: G 170 PHE cc_start: 0.7882 (t80) cc_final: 0.7436 (t80) REVERT: G 206 SER cc_start: 0.9640 (m) cc_final: 0.9248 (t) REVERT: G 216 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7824 (ttm-80) REVERT: G 218 ASP cc_start: 0.7523 (t0) cc_final: 0.5807 (t0) REVERT: G 220 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.7468 (ptp90) REVERT: G 230 HIS cc_start: 0.8371 (t-90) cc_final: 0.7519 (t-90) REVERT: G 235 GLN cc_start: 0.8695 (pt0) cc_final: 0.8441 (pt0) REVERT: G 241 GLU cc_start: 0.9109 (tp30) cc_final: 0.8844 (tp30) REVERT: G 257 PHE cc_start: 0.8383 (m-80) cc_final: 0.7753 (m-80) REVERT: G 263 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9046 (m) REVERT: G 273 TYR cc_start: 0.8671 (p90) cc_final: 0.8242 (p90) REVERT: G 281 ASP cc_start: 0.8831 (t0) cc_final: 0.8002 (p0) REVERT: G 364 ASN cc_start: 0.8902 (t0) cc_final: 0.8441 (t0) REVERT: H 26 PHE cc_start: 0.8534 (m-80) cc_final: 0.8279 (m-10) REVERT: H 82 LYS cc_start: 0.8265 (mttt) cc_final: 0.7817 (mttm) REVERT: H 100 PHE cc_start: 0.8370 (m-80) cc_final: 0.7623 (m-80) REVERT: H 128 LYS cc_start: 0.8499 (tppt) cc_final: 0.8260 (tppt) REVERT: H 155 TYR cc_start: 0.7472 (m-80) cc_final: 0.7052 (m-80) REVERT: H 238 TYR cc_start: 0.7082 (m-80) cc_final: 0.5713 (t80) REVERT: H 337 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8410 (mmm-85) REVERT: H 362 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8562 (mtt-85) REVERT: I 130 ARG cc_start: 0.6782 (mtm-85) cc_final: 0.6452 (mtm-85) REVERT: I 152 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7479 (mmtm) REVERT: I 197 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7066 (mmt180) REVERT: I 212 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8521 (mmm-85) REVERT: J 9 ASN cc_start: 0.9057 (t0) cc_final: 0.8554 (t0) REVERT: J 15 TYR cc_start: 0.8111 (t80) cc_final: 0.7709 (t80) REVERT: J 37 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7606 (mm-30) REVERT: J 76 TYR cc_start: 0.8713 (t80) cc_final: 0.8438 (t80) REVERT: J 117 ASP cc_start: 0.8659 (t0) cc_final: 0.8449 (t0) REVERT: J 195 MET cc_start: 0.8869 (mpp) cc_final: 0.8510 (mpp) REVERT: J 218 ASP cc_start: 0.8218 (t0) cc_final: 0.7850 (t0) REVERT: J 307 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7871 (mm) REVERT: J 362 GLN cc_start: 0.7989 (tp40) cc_final: 0.7775 (tp-100) REVERT: J 372 LYS cc_start: 0.8674 (tptt) cc_final: 0.8297 (tppt) REVERT: J 390 GLU cc_start: 0.8399 (tp30) cc_final: 0.7527 (tt0) REVERT: J 409 TRP cc_start: 0.8373 (m100) cc_final: 0.8116 (m100) REVERT: K 38 SER cc_start: 0.9187 (t) cc_final: 0.8891 (p) REVERT: K 78 ASP cc_start: 0.8535 (t0) cc_final: 0.8320 (t70) REVERT: K 146 HIS cc_start: 0.4178 (m-70) cc_final: 0.3348 (m-70) REVERT: K 168 MET cc_start: 0.8120 (mmp) cc_final: 0.7777 (mmp) REVERT: K 236 TRP cc_start: 0.8666 (m-10) cc_final: 0.8455 (m-10) REVERT: K 259 PHE cc_start: 0.8229 (m-80) cc_final: 0.7849 (m-10) REVERT: K 272 HIS cc_start: 0.8381 (t70) cc_final: 0.6985 (t70) REVERT: K 279 TRP cc_start: 0.9115 (p-90) cc_final: 0.8776 (p-90) REVERT: K 366 TYR cc_start: 0.8312 (m-80) cc_final: 0.7852 (m-80) REVERT: L 110 LYS cc_start: 0.7958 (mmtm) cc_final: 0.6893 (pttm) REVERT: L 156 MET cc_start: 0.9111 (ppp) cc_final: 0.8798 (ppp) REVERT: L 168 MET cc_start: 0.9267 (ppp) cc_final: 0.8949 (tmm) REVERT: L 192 GLN cc_start: 0.8477 (tp40) cc_final: 0.8142 (tp40) REVERT: V 69 LYS cc_start: 0.7971 (tptt) cc_final: 0.7753 (mttm) REVERT: W 90 LYS cc_start: 0.8654 (mtpt) cc_final: 0.7762 (tmtt) REVERT: W 106 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: X 77 PHE cc_start: 0.6693 (t80) cc_final: 0.6245 (t80) REVERT: X 96 ASP cc_start: 0.8023 (m-30) cc_final: 0.7739 (m-30) REVERT: Y 83 GLN cc_start: 0.5907 (OUTLIER) cc_final: 0.5040 (pm20) outliers start: 127 outliers final: 111 residues processed: 960 average time/residue: 0.1868 time to fit residues: 295.6392 Evaluate side-chains 974 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 857 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 124 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 THR 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 364 ASN Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS 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 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 338 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 403 SER 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 198 THR Chi-restraints excluded: chain D residue 295 LEU 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 120 VAL Chi-restraints excluded: chain E residue 131 LEU 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 F residue 125 CYS 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 152 THR Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 263 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 352 ILE Chi-restraints excluded: chain H residue 50 GLN 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 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 I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 124 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 331 HIS 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 321 VAL Chi-restraints excluded: chain K residue 324 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 145 GLN Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 97 CYS Chi-restraints excluded: chain W residue 106 GLU 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 Y residue 33 CYS 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 149 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 413 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** A 364 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 186 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** 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 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125276 restraints weight = 65025.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129157 restraints weight = 32258.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131641 restraints weight = 20082.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133233 restraints weight = 14684.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134113 restraints weight = 12035.206| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33733 Z= 0.205 Angle : 0.709 10.686 45942 Z= 0.366 Chirality : 0.047 0.281 5080 Planarity : 0.005 0.075 5924 Dihedral : 5.955 80.944 4613 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 3.88 % Allowed : 25.80 % Favored : 70.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.13), residues: 4240 helix: 1.35 (0.26), residues: 374 sheet: -0.87 (0.15), residues: 1169 loop : -0.38 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 323 TYR 0.034 0.002 TYR D 238 PHE 0.033 0.002 PHE K 15 TRP 0.021 0.002 TRP H 310 HIS 0.011 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00467 (33660) covalent geometry : angle 0.70334 (45796) SS BOND : bond 0.00409 ( 73) SS BOND : angle 1.70168 ( 146) hydrogen bonds : bond 0.03652 ( 1197) hydrogen bonds : angle 5.84504 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7519.66 seconds wall clock time: 130 minutes 11.62 seconds (7811.62 seconds total)