Starting phenix.real_space_refine on Mon Jul 6 05:00:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9z_47822/07_2026/9e9z_47822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9z_47822/07_2026/9e9z_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_47822/07_2026/9e9z_47822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9z_47822/07_2026/9e9z_47822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e9z_47822/07_2026/9e9z_47822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9z_47822/07_2026/9e9z_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 7.46, 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: 3.41 Conformation dependent library (CDL) restraints added in 1.5 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7872 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 96 sheets defined 15.6% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 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: 8.31 Time building geometry restraints manager: 4.40 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 3.250 nonbonded pdb=" O TRP X 50 " pdb="CA CA X 201 " model vdw 2.135 3.250 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: 0.02 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.690 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 are 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/Z covalent geometry : bond 0.00655 / 0.36 (33660) covalent geometry : angle 1.03349 / 0.63 (45796) SS BOND : bond 0.00589 / 0.41 ( 73) SS BOND : angle 1.51313 / 1.05 ( 146) hydrogen bonds : bond 0.21630 / 14.97 ( 1197) hydrogen bonds : angle 9.27592 / 6.37 ( 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 : 1.366 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: 0.7849 (pm20) REVERT: A 75 ASP cc_start: 0.8504 (t0) cc_final: 0.7339 (t0) REVERT: A 77 THR cc_start: 0.8881 (m) cc_final: 0.8621 (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: 0.8226 (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: 0.9021 (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: 0.7255 (tt0) REVERT: B 156 ASP cc_start: 0.8297 (t0) cc_final: 0.8075 (t0) REVERT: B 168 MET cc_start: 0.7464 (pmm) cc_final: 0.6925 (pmm) REVERT: B 217 MET cc_start: 0.6391 (tpp) cc_final: 0.4978 (tpp) REVERT: B 261 LEU cc_start: 0.9186 (tp) cc_final: 0.8953 (tp) REVERT: B 305 ASP cc_start: 0.8964 (t0) cc_final: 0.8547 (t0) REVERT: B 327 GLU cc_start: 0.7894 (tt0) cc_final: 0.7428 (tt0) REVERT: B 332 ASN cc_start: 0.9182 (m-40) cc_final: 0.8889 (m-40) REVERT: B 342 GLU cc_start: 0.8459 (tp30) cc_final: 0.8247 (tp30) REVERT: B 354 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 367 THR cc_start: 0.9069 (m) cc_final: 0.8784 (p) REVERT: C 7 VAL cc_start: 0.9392 (t) cc_final: 0.8941 (m) REVERT: C 32 THR cc_start: 0.8818 (m) cc_final: 0.8185 (p) REVERT: C 95 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8085 (p90) REVERT: C 99 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8433 (mt-10) REVERT: C 139 ASN cc_start: 0.8356 (t0) cc_final: 0.7855 (m-40) REVERT: C 151 VAL cc_start: 0.8716 (t) cc_final: 0.8452 (p) REVERT: C 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: 0.5447 (tt) REVERT: C 308 TYR cc_start: 0.8310 (p90) cc_final: 0.7853 (p90) REVERT: C 362 GLN cc_start: 0.8251 (pt0) cc_final: 0.7975 (pm20) REVERT: C 373 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8567 (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: 0.8457 (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: 0.8610 (m-90) REVERT: D 355 ILE cc_start: 0.8318 (mm) cc_final: 0.8105 (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: 0.8290 (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: 0.8693 (t) REVERT: G 161 VAL cc_start: 0.9139 (t) cc_final: 0.8916 (m) REVERT: G 203 ILE cc_start: 0.9109 (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: 0.8751 (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: 0.8908 (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: 0.8988 (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: 0.3995 (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: 0.8398 (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: 0.8204 (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: 0.8262 (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: 0.6638 (p0) cc_final: 0.6305 (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: 0.2082 time to fit residues: 493.7479 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 : 1.268 ------------------------------------------------------------------------------- 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: 5.9990 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... ** 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 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 59 GLN C 100 ASN C 408 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 332 ASN ** L 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4024 r_free = 0.4024 target = 0.163844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128843 restraints weight = 64574.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132832 restraints weight = 31255.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135378 restraints weight = 19199.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136938 restraints weight = 13894.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137933 restraints weight = 11381.102| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 33733 Z= 0.157 Angle : 0.763 13.816 45942 Z= 0.403 Chirality : 0.049 0.248 5080 Planarity : 0.005 0.059 5924 Dihedral : 6.778 80.874 4630 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 3.96 % Allowed : 14.67 % Favored : 81.37 % 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 are not related in a simple way. whole: -0.84 (0.12), residues: 4240 helix: 0.09 (0.25), residues: 418 sheet: -0.52 (0.14), residues: 1127 loop : -0.64 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 245 TYR 0.029 0.002 TYR F 157 PHE 0.025 0.002 PHE H 259 TRP 0.022 0.002 TRP J 89 HIS 0.016 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (33660) covalent geometry : angle 0.75579 / 0.40 (45796) SS BOND : bond 0.00433 / 0.30 ( 73) SS BOND : angle 1.98232 / 1.29 ( 146) hydrogen bonds : bond 0.04588 / 3.09 ( 1197) hydrogen bonds : angle 6.95414 / 4.79 ( 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 1313 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1170 time to evaluate : 1.235 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 16 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8166 (mtpt) REVERT: A 27 LEU cc_start: 0.8642 (tp) cc_final: 0.8343 (tp) REVERT: A 45 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7964 (tp30) REVERT: A 75 ASP cc_start: 0.8020 (t0) cc_final: 0.7187 (t0) REVERT: A 117 ASP cc_start: 0.8356 (t0) cc_final: 0.7913 (t0) REVERT: A 218 ASP cc_start: 0.8797 (t0) cc_final: 0.8447 (t0) REVERT: A 252 GLN cc_start: 0.9037 (mp10) cc_final: 0.8451 (mm-40) REVERT: A 284 ASP cc_start: 0.8841 (m-30) cc_final: 0.8625 (m-30) REVERT: A 311 ASP cc_start: 0.9333 (p0) cc_final: 0.9054 (p0) REVERT: A 354 LEU cc_start: 0.9242 (mt) cc_final: 0.8716 (mt) REVERT: A 395 ASP cc_start: 0.8361 (t0) cc_final: 0.8000 (t0) REVERT: A 397 GLU cc_start: 0.7602 (tp30) cc_final: 0.7401 (tp30) REVERT: B 32 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7915 (tp30) REVERT: B 33 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7444 (t0) REVERT: B 70 ASP cc_start: 0.7776 (p0) cc_final: 0.7102 (p0) REVERT: B 92 ARG cc_start: 0.2600 (mtt180) cc_final: 0.1936 (mtp180) REVERT: B 114 SER cc_start: 0.9094 (m) cc_final: 0.8709 (p) REVERT: B 122 ASN cc_start: 0.8571 (m110) cc_final: 0.8255 (m110) REVERT: B 131 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7643 (mtm110) REVERT: B 138 GLU cc_start: 0.7547 (tt0) cc_final: 0.7305 (tt0) REVERT: B 156 ASP cc_start: 0.8631 (t0) cc_final: 0.8428 (t0) REVERT: B 176 TYR cc_start: 0.7189 (m-80) cc_final: 0.6745 (m-80) REVERT: B 190 LYS cc_start: 0.4986 (mptt) cc_final: 0.4615 (mmtm) REVERT: B 278 LYS cc_start: 0.9286 (mtmm) cc_final: 0.9001 (mttm) REVERT: B 284 THR cc_start: 0.8822 (m) cc_final: 0.8577 (p) REVERT: B 305 ASP cc_start: 0.8794 (t0) cc_final: 0.8554 (t0) REVERT: B 330 TRP cc_start: 0.9023 (t-100) cc_final: 0.8635 (t-100) REVERT: B 351 TRP cc_start: 0.8061 (m-90) cc_final: 0.7412 (m-90) REVERT: C 7 VAL cc_start: 0.9415 (t) cc_final: 0.9165 (m) REVERT: C 32 THR cc_start: 0.8979 (m) cc_final: 0.8594 (p) REVERT: C 100 ASN cc_start: 0.8191 (m-40) cc_final: 0.7817 (m-40) REVERT: C 139 ASN cc_start: 0.8153 (t0) cc_final: 0.7929 (m-40) REVERT: C 209 ASP cc_start: 0.8172 (p0) cc_final: 0.7885 (p0) REVERT: C 228 ASN cc_start: 0.9325 (m110) cc_final: 0.9059 (m-40) REVERT: C 231 VAL cc_start: 0.9635 (OUTLIER) cc_final: 0.9408 (m) REVERT: C 307 ILE cc_start: 0.6394 (mt) cc_final: 0.5925 (tt) REVERT: C 308 TYR cc_start: 0.8169 (p90) cc_final: 0.7950 (p90) REVERT: D 33 ASN cc_start: 0.8247 (m-40) cc_final: 0.8003 (m110) REVERT: D 132 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8220 (ttm-80) REVERT: D 134 PHE cc_start: 0.8742 (p90) cc_final: 0.8467 (p90) REVERT: D 169 HIS cc_start: 0.6875 (m90) cc_final: 0.6606 (m-70) REVERT: D 254 LYS cc_start: 0.4772 (pptt) cc_final: 0.4543 (pptt) REVERT: D 273 THR cc_start: 0.9256 (m) cc_final: 0.8712 (p) REVERT: D 339 TRP cc_start: 0.8781 (m-90) cc_final: 0.8565 (m-90) REVERT: D 362 ARG cc_start: 0.9315 (mtp180) cc_final: 0.9103 (mtm180) REVERT: E 132 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7593 (mtp) REVERT: E 186 TRP cc_start: 0.7316 (t60) cc_final: 0.6758 (t60) REVERT: E 194 GLU cc_start: 0.8856 (tp30) cc_final: 0.8415 (tp30) REVERT: E 202 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7793 (ptm-80) REVERT: F 207 LYS cc_start: 0.9098 (tmmt) cc_final: 0.8436 (tmtt) REVERT: F 216 ASP cc_start: 0.8103 (t0) cc_final: 0.7683 (t0) REVERT: G 10 VAL cc_start: 0.9021 (t) cc_final: 0.8757 (m) REVERT: G 21 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7794 (tmm-80) REVERT: G 24 TYR cc_start: 0.8140 (m-80) cc_final: 0.7911 (m-10) REVERT: G 27 LEU cc_start: 0.8193 (tp) cc_final: 0.7829 (tp) REVERT: G 37 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7463 (mp0) REVERT: G 62 CYS cc_start: 0.4365 (m) cc_final: 0.4011 (m) REVERT: G 140 THR cc_start: 0.8684 (m) cc_final: 0.8459 (p) REVERT: G 170 PHE cc_start: 0.7810 (t80) cc_final: 0.7420 (t80) REVERT: G 203 ILE cc_start: 0.9125 (tt) cc_final: 0.8876 (tt) REVERT: G 206 SER cc_start: 0.9631 (m) cc_final: 0.9306 (t) REVERT: G 218 ASP cc_start: 0.7515 (t0) cc_final: 0.6967 (t0) REVERT: G 220 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8159 (ptp90) REVERT: G 230 HIS cc_start: 0.8439 (t-90) cc_final: 0.7638 (t-90) REVERT: G 235 GLN cc_start: 0.8609 (pt0) cc_final: 0.8256 (pt0) REVERT: G 257 PHE cc_start: 0.8573 (m-80) cc_final: 0.8141 (m-80) REVERT: G 261 ILE cc_start: 0.9343 (mt) cc_final: 0.8973 (mm) REVERT: G 324 ARG cc_start: 0.7717 (ptp-170) cc_final: 0.7326 (ptp90) REVERT: G 364 ASN cc_start: 0.8899 (t0) cc_final: 0.8632 (t0) REVERT: H 82 LYS cc_start: 0.8553 (mttt) cc_final: 0.8232 (mtmm) REVERT: H 139 GLU cc_start: 0.6516 (tm-30) cc_final: 0.6292 (tm-30) REVERT: H 200 GLU cc_start: 0.7562 (tt0) cc_final: 0.7116 (tt0) REVERT: H 230 LYS cc_start: 0.8658 (ptmm) cc_final: 0.8448 (ptmm) REVERT: H 236 TRP cc_start: 0.8211 (m-90) cc_final: 0.7859 (m-90) REVERT: H 303 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8320 (ttm-80) REVERT: I 121 ASN cc_start: 0.7094 (p0) cc_final: 0.6877 (p0) REVERT: I 152 LYS cc_start: 0.8523 (ttpt) cc_final: 0.7941 (mmtt) REVERT: I 186 TRP cc_start: 0.8184 (t60) cc_final: 0.7675 (t60) REVERT: I 192 GLN cc_start: 0.8640 (tp40) cc_final: 0.8347 (tp40) REVERT: I 194 GLU cc_start: 0.8506 (tt0) cc_final: 0.7844 (tt0) REVERT: J 9 ASN cc_start: 0.9196 (t0) cc_final: 0.8577 (t0) REVERT: J 133 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8421 (mm) REVERT: J 257 PHE cc_start: 0.8334 (m-80) cc_final: 0.7910 (m-80) REVERT: J 262 GLU cc_start: 0.8148 (mp0) cc_final: 0.7930 (mp0) REVERT: J 271 CYS cc_start: 0.6450 (m) cc_final: 0.6207 (m) REVERT: J 307 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8072 (mm) REVERT: J 319 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7238 (mm-40) REVERT: J 372 LYS cc_start: 0.8791 (tptt) cc_final: 0.8527 (tppt) REVERT: J 409 TRP cc_start: 0.8532 (m100) cc_final: 0.8250 (m100) REVERT: K 78 ASP cc_start: 0.8182 (t0) cc_final: 0.7944 (t70) REVERT: K 100 PHE cc_start: 0.9017 (m-80) cc_final: 0.8449 (m-10) REVERT: K 121 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: K 146 HIS cc_start: 0.4474 (m-70) cc_final: 0.3876 (m-70) REVERT: K 200 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7902 (mt-10) REVERT: K 218 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8003 (p0) REVERT: K 272 HIS cc_start: 0.8653 (t70) cc_final: 0.7484 (t70) REVERT: K 330 TRP cc_start: 0.9433 (t-100) cc_final: 0.9117 (t-100) REVERT: K 339 TRP cc_start: 0.8830 (m-90) cc_final: 0.7814 (m-90) REVERT: K 366 TYR cc_start: 0.8395 (m-80) cc_final: 0.8093 (m-80) REVERT: V 90 LYS cc_start: 0.8842 (tttt) cc_final: 0.8601 (tptp) REVERT: W 90 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7638 (tmtt) REVERT: Y 83 GLN cc_start: 0.5893 (OUTLIER) cc_final: 0.4822 (pm20) REVERT: Y 90 LYS cc_start: 0.6716 (tptm) cc_final: 0.6428 (tptm) outliers start: 143 outliers final: 87 residues processed: 1230 average time/residue: 0.1985 time to fit residues: 403.2815 Evaluate side-chains 1075 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 980 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 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 231 VAL 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 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 J residue 407 TRP Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 218 ASN Chi-restraints excluded: chain K residue 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 V residue 84 CYS Chi-restraints excluded: chain W residue 62 SER 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 75 SER Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 268 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 176 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 410 optimal weight: 8.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN C 59 GLN C 93 GLN C 252 GLN ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN 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 96 HIS ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.158257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122774 restraints weight = 64829.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126653 restraints weight = 31845.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129122 restraints weight = 19746.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130699 restraints weight = 14443.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131659 restraints weight = 11819.944| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33733 Z= 0.217 Angle : 0.728 10.183 45942 Z= 0.382 Chirality : 0.048 0.260 5080 Planarity : 0.005 0.084 5924 Dihedral : 6.619 79.724 4620 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 5.32 % Allowed : 17.88 % Favored : 76.80 % 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 are not related in a simple way. whole: -0.85 (0.13), residues: 4240 helix: 0.15 (0.25), residues: 424 sheet: -0.81 (0.14), residues: 1151 loop : -0.50 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 170 TYR 0.023 0.002 TYR J 233 PHE 0.028 0.002 PHE H 51 TRP 0.015 0.002 TRP J 89 HIS 0.009 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (33660) covalent geometry : angle 0.72095 / 0.38 (45796) SS BOND : bond 0.00527 / 0.34 ( 73) SS BOND : angle 1.92551 / 1.26 ( 146) hydrogen bonds : bond 0.04227 / 2.87 ( 1197) hydrogen bonds : angle 6.56810 / 4.53 ( 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 1175 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 983 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8322 (m-80) cc_final: 0.7913 (m-80) REVERT: A 75 ASP cc_start: 0.7970 (t0) cc_final: 0.7033 (t0) REVERT: A 158 ASP cc_start: 0.8583 (t0) cc_final: 0.8234 (t0) REVERT: A 160 LYS cc_start: 0.8647 (mptt) cc_final: 0.8312 (mmtm) REVERT: A 219 ILE cc_start: 0.9447 (mt) cc_final: 0.9193 (mt) REVERT: A 395 ASP cc_start: 0.8454 (t0) cc_final: 0.8164 (t0) REVERT: B 32 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7944 (tp30) REVERT: B 33 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7362 (t0) REVERT: B 40 ASP cc_start: 0.8396 (p0) cc_final: 0.7812 (p0) REVERT: B 70 ASP cc_start: 0.7882 (p0) cc_final: 0.7270 (p0) REVERT: B 92 ARG cc_start: 0.2544 (mtt180) cc_final: 0.1849 (mtp180) REVERT: B 114 SER cc_start: 0.9083 (m) cc_final: 0.8663 (p) REVERT: B 122 ASN cc_start: 0.8749 (m110) cc_final: 0.8504 (m-40) REVERT: B 176 TYR cc_start: 0.7344 (m-80) cc_final: 0.6738 (m-80) REVERT: B 278 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9026 (mttm) REVERT: B 305 ASP cc_start: 0.8849 (t0) cc_final: 0.8574 (t0) REVERT: B 330 TRP cc_start: 0.9034 (t-100) cc_final: 0.8730 (t-100) REVERT: B 342 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8091 (tp30) REVERT: C 32 THR cc_start: 0.9065 (m) cc_final: 0.8660 (p) REVERT: C 97 ASP cc_start: 0.7997 (p0) cc_final: 0.7735 (p0) REVERT: C 100 ASN cc_start: 0.8313 (m-40) cc_final: 0.7971 (m-40) REVERT: C 133 LEU cc_start: 0.9347 (mt) cc_final: 0.9131 (mt) REVERT: C 139 ASN cc_start: 0.8220 (t0) cc_final: 0.7979 (m-40) REVERT: C 195 MET cc_start: 0.8795 (mpp) cc_final: 0.8536 (mpp) REVERT: C 307 ILE cc_start: 0.6253 (mt) cc_final: 0.5667 (tt) REVERT: C 308 TYR cc_start: 0.8345 (p90) cc_final: 0.7972 (p90) REVERT: C 409 TRP cc_start: 0.8312 (m100) cc_final: 0.7537 (m100) REVERT: D 32 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8052 (mm-30) REVERT: D 33 ASN cc_start: 0.8203 (m-40) cc_final: 0.7990 (m-40) REVERT: D 45 ILE cc_start: 0.9198 (mm) cc_final: 0.8816 (tp) REVERT: D 137 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8104 (ptp90) REVERT: D 169 HIS cc_start: 0.7273 (m90) cc_final: 0.6889 (m-70) REVERT: D 273 THR cc_start: 0.9203 (m) cc_final: 0.8720 (p) REVERT: D 305 ASP cc_start: 0.8087 (t0) cc_final: 0.7836 (t70) REVERT: D 339 TRP cc_start: 0.8955 (m-90) cc_final: 0.8660 (m-90) REVERT: D 362 ARG cc_start: 0.9299 (mtp180) cc_final: 0.9049 (mtm180) REVERT: E 112 PHE cc_start: 0.8172 (m-80) cc_final: 0.7630 (m-10) REVERT: E 160 GLU cc_start: 0.8240 (pt0) cc_final: 0.8029 (mp0) REVERT: E 194 GLU cc_start: 0.8799 (tp30) cc_final: 0.8404 (tp30) REVERT: F 127 VAL cc_start: 0.8961 (t) cc_final: 0.8749 (m) REVERT: F 207 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8448 (tmtt) REVERT: G 10 VAL cc_start: 0.9072 (t) cc_final: 0.8770 (m) REVERT: G 21 ARG cc_start: 0.8236 (tmm-80) cc_final: 0.7845 (tmm-80) REVERT: G 27 LEU cc_start: 0.8328 (tp) cc_final: 0.7927 (tp) REVERT: G 37 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7526 (mp0) REVERT: G 62 CYS cc_start: 0.4324 (m) cc_final: 0.4046 (m) REVERT: G 140 THR cc_start: 0.8645 (m) cc_final: 0.8396 (p) REVERT: G 160 LYS cc_start: 0.9123 (pptt) cc_final: 0.8765 (mmtm) REVERT: G 170 PHE cc_start: 0.8042 (t80) cc_final: 0.7647 (t80) REVERT: G 195 MET cc_start: 0.8793 (mpp) cc_final: 0.8583 (mpp) REVERT: G 203 ILE cc_start: 0.9084 (tt) cc_final: 0.8845 (tt) REVERT: G 206 SER cc_start: 0.9655 (m) cc_final: 0.9355 (t) REVERT: G 218 ASP cc_start: 0.7626 (t0) cc_final: 0.6413 (t0) REVERT: G 220 ARG cc_start: 0.8571 (ptp-170) cc_final: 0.7753 (ptp90) REVERT: G 235 GLN cc_start: 0.8711 (pt0) cc_final: 0.8332 (pt0) REVERT: G 252 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: G 257 PHE cc_start: 0.8555 (m-80) cc_final: 0.8101 (m-80) REVERT: G 324 ARG cc_start: 0.7699 (ptp-170) cc_final: 0.7389 (ptp90) REVERT: G 364 ASN cc_start: 0.8900 (t0) cc_final: 0.8524 (t0) REVERT: H 46 GLN cc_start: 0.6718 (mt0) cc_final: 0.6406 (mt0) REVERT: H 82 LYS cc_start: 0.8632 (mttt) cc_final: 0.8331 (mtmm) REVERT: H 134 PHE cc_start: 0.9327 (p90) cc_final: 0.8937 (p90) REVERT: H 139 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: H 200 GLU cc_start: 0.7588 (tt0) cc_final: 0.7091 (tt0) REVERT: H 238 TYR cc_start: 0.7138 (m-80) cc_final: 0.5727 (t80) REVERT: H 305 ASP cc_start: 0.8462 (t0) cc_final: 0.8227 (t0) REVERT: H 395 ASP cc_start: 0.9228 (p0) cc_final: 0.9015 (p0) REVERT: I 115 MET cc_start: 0.7426 (ppp) cc_final: 0.6827 (mmm) REVERT: I 130 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7295 (mtt180) REVERT: I 136 HIS cc_start: 0.7124 (p90) cc_final: 0.6857 (p90) REVERT: I 152 LYS cc_start: 0.8464 (ttpt) cc_final: 0.7831 (mmtt) REVERT: I 186 TRP cc_start: 0.8253 (t60) cc_final: 0.7779 (t60) REVERT: I 194 GLU cc_start: 0.8387 (tt0) cc_final: 0.7742 (tt0) REVERT: I 212 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.7320 (mmm-85) REVERT: I 226 LEU cc_start: 0.8105 (mm) cc_final: 0.7888 (mm) REVERT: J 9 ASN cc_start: 0.9264 (t0) cc_final: 0.8782 (t0) REVERT: J 15 TYR cc_start: 0.8213 (t80) cc_final: 0.7714 (t80) REVERT: J 37 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7389 (mm-30) REVERT: J 63 CYS cc_start: 0.5451 (t) cc_final: 0.2874 (t) REVERT: J 117 ASP cc_start: 0.8801 (t0) cc_final: 0.8529 (t0) REVERT: J 218 ASP cc_start: 0.8156 (t0) cc_final: 0.7677 (t0) REVERT: J 230 HIS cc_start: 0.8802 (t-90) cc_final: 0.8223 (t-90) REVERT: J 246 ASN cc_start: 0.8204 (t0) cc_final: 0.7755 (t0) REVERT: J 257 PHE cc_start: 0.8462 (m-80) cc_final: 0.7870 (m-80) REVERT: J 271 CYS cc_start: 0.6479 (m) cc_final: 0.6174 (m) REVERT: J 307 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8105 (mm) REVERT: J 372 LYS cc_start: 0.8756 (tptt) cc_final: 0.8481 (tppt) REVERT: J 409 TRP cc_start: 0.8516 (m100) cc_final: 0.8188 (m100) REVERT: K 37 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8488 (mt-10) REVERT: K 43 ILE cc_start: 0.9547 (pp) cc_final: 0.9342 (pt) REVERT: K 78 ASP cc_start: 0.8525 (t0) cc_final: 0.8269 (t70) REVERT: K 100 PHE cc_start: 0.9210 (m-80) cc_final: 0.8560 (m-80) REVERT: K 121 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6131 (tm-30) REVERT: K 165 TYR cc_start: 0.8700 (p90) cc_final: 0.8460 (p90) REVERT: K 272 HIS cc_start: 0.8737 (t70) cc_final: 0.7568 (t70) REVERT: K 279 TRP cc_start: 0.9095 (p-90) cc_final: 0.8673 (p-90) REVERT: K 339 TRP cc_start: 0.8982 (m-90) cc_final: 0.7841 (m-90) REVERT: K 341 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: K 351 TRP cc_start: 0.8991 (m-10) cc_final: 0.8762 (m-10) REVERT: K 366 TYR cc_start: 0.8349 (m-80) cc_final: 0.7800 (m-80) REVERT: L 168 MET cc_start: 0.9198 (ppp) cc_final: 0.8743 (tmm) REVERT: W 72 CYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4735 (p) REVERT: W 90 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7557 (tmtt) REVERT: X 77 PHE cc_start: 0.6421 (t80) cc_final: 0.6198 (t80) outliers start: 192 outliers final: 134 residues processed: 1074 average time/residue: 0.1956 time to fit residues: 346.3938 Evaluate side-chains 1037 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 895 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 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 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 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 141 LEU 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 320 SER 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 84 VAL Chi-restraints excluded: chain C residue 93 GLN 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 370 CYS 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 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 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 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 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 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 252 GLN 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 125 CYS 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 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 321 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 388 CYS Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 247 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 X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 75 SER Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 232 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 310 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 222 optimal weight: 0.0970 chunk 226 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 169 HIS ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS C 93 GLN C 408 ASN ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** 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** H 21 HIS H 73 HIS ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126955 restraints weight = 64084.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130905 restraints weight = 31398.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133440 restraints weight = 19447.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135058 restraints weight = 14137.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136076 restraints weight = 11541.161| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33733 Z= 0.138 Angle : 0.691 9.985 45942 Z= 0.358 Chirality : 0.047 0.266 5080 Planarity : 0.004 0.045 5924 Dihedral : 6.436 80.297 4619 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 4.62 % Allowed : 20.49 % Favored : 74.89 % 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 are not related in a simple way. whole: -0.65 (0.13), residues: 4240 helix: 0.42 (0.25), residues: 412 sheet: -0.73 (0.15), residues: 1130 loop : -0.37 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 220 TYR 0.030 0.002 TYR J 233 PHE 0.037 0.002 PHE H 51 TRP 0.017 0.001 TRP H 236 HIS 0.010 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (33660) covalent geometry : angle 0.68500 / 0.36 (45796) SS BOND : bond 0.00436 / 0.31 ( 73) SS BOND : angle 1.70143 / 1.09 ( 146) hydrogen bonds : bond 0.03840 / 2.59 ( 1197) hydrogen bonds : angle 6.31434 / 4.35 ( 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 1186 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1019 time to evaluate : 1.151 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 24 TYR cc_start: 0.8456 (m-80) cc_final: 0.8027 (m-80) REVERT: A 75 ASP cc_start: 0.7876 (t0) cc_final: 0.6764 (t0) REVERT: A 158 ASP cc_start: 0.8570 (t0) cc_final: 0.8334 (t0) REVERT: A 219 ILE cc_start: 0.9465 (mt) cc_final: 0.9211 (mt) REVERT: A 280 ILE cc_start: 0.9358 (mp) cc_final: 0.8944 (mp) REVERT: A 341 GLU cc_start: 0.8752 (mp0) cc_final: 0.8506 (pm20) REVERT: A 354 LEU cc_start: 0.9483 (mt) cc_final: 0.8844 (mp) REVERT: A 395 ASP cc_start: 0.8388 (t0) cc_final: 0.8017 (t0) REVERT: A 409 TRP cc_start: 0.8437 (t-100) cc_final: 0.8009 (m-90) REVERT: B 32 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8055 (tp30) REVERT: B 33 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 70 ASP cc_start: 0.7801 (p0) cc_final: 0.7164 (p0) REVERT: B 92 ARG cc_start: 0.2513 (mtt180) cc_final: 0.1848 (mtm180) REVERT: B 114 SER cc_start: 0.9113 (m) cc_final: 0.8701 (p) REVERT: B 122 ASN cc_start: 0.8821 (m110) cc_final: 0.8527 (m-40) REVERT: B 131 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7418 (mtm110) REVERT: B 146 HIS cc_start: 0.5094 (OUTLIER) cc_final: 0.4571 (m170) REVERT: B 156 ASP cc_start: 0.8538 (t0) cc_final: 0.8116 (t0) REVERT: B 176 TYR cc_start: 0.7218 (m-80) cc_final: 0.6592 (m-80) REVERT: B 181 GLU cc_start: 0.8258 (mp0) cc_final: 0.7913 (mp0) REVERT: B 190 LYS cc_start: 0.4995 (mmtm) cc_final: 0.4478 (mmtm) REVERT: B 303 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8420 (ptp-110) REVERT: B 305 ASP cc_start: 0.8840 (t0) cc_final: 0.8507 (t0) REVERT: B 330 TRP cc_start: 0.8964 (t-100) cc_final: 0.8236 (t-100) REVERT: B 337 ARG cc_start: 0.8352 (mmt90) cc_final: 0.8057 (mmt90) REVERT: C 32 THR cc_start: 0.9065 (m) cc_final: 0.8668 (p) REVERT: C 97 ASP cc_start: 0.8023 (p0) cc_final: 0.7723 (p0) REVERT: C 100 ASN cc_start: 0.8273 (m-40) cc_final: 0.7935 (m-40) REVERT: C 139 ASN cc_start: 0.8231 (t0) cc_final: 0.8015 (m-40) REVERT: C 195 MET cc_start: 0.8758 (mpp) cc_final: 0.8520 (mpp) REVERT: C 262 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7411 (pt0) REVERT: C 307 ILE cc_start: 0.6199 (mt) cc_final: 0.5661 (tt) REVERT: C 362 GLN cc_start: 0.7705 (pm20) cc_final: 0.7426 (pm20) REVERT: D 32 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 33 ASN cc_start: 0.8127 (m-40) cc_final: 0.7908 (m-40) REVERT: D 169 HIS cc_start: 0.7175 (m90) cc_final: 0.6603 (m-70) REVERT: D 273 THR cc_start: 0.9162 (m) cc_final: 0.8664 (p) REVERT: D 339 TRP cc_start: 0.8805 (m-90) cc_final: 0.8539 (m-90) REVERT: E 112 PHE cc_start: 0.8161 (m-80) cc_final: 0.7612 (m-10) REVERT: E 130 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8090 (tpp80) REVERT: E 160 GLU cc_start: 0.8165 (pt0) cc_final: 0.7849 (pm20) REVERT: E 168 MET cc_start: 0.7250 (ptp) cc_final: 0.7038 (ptm) REVERT: E 186 TRP cc_start: 0.7481 (t60) cc_final: 0.6805 (t60) REVERT: E 194 GLU cc_start: 0.8727 (tp30) cc_final: 0.8297 (tp30) REVERT: E 195 ASN cc_start: 0.8882 (p0) cc_final: 0.8633 (p0) REVERT: E 257 GLU cc_start: 0.7884 (mp0) cc_final: 0.7321 (mp0) REVERT: F 184 TYR cc_start: 0.7067 (m-80) cc_final: 0.6700 (m-80) REVERT: F 207 LYS cc_start: 0.9061 (tmmt) cc_final: 0.8410 (tmtt) REVERT: F 214 ILE cc_start: 0.8740 (mm) cc_final: 0.8454 (pt) REVERT: G 10 VAL cc_start: 0.9042 (t) cc_final: 0.8757 (m) REVERT: G 27 LEU cc_start: 0.8284 (tp) cc_final: 0.7922 (tp) REVERT: G 37 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7496 (mp0) REVERT: G 62 CYS cc_start: 0.4428 (m) cc_final: 0.4036 (m) REVERT: G 140 THR cc_start: 0.8610 (m) cc_final: 0.8373 (p) REVERT: G 160 LYS cc_start: 0.9128 (pptt) cc_final: 0.8794 (mmtm) REVERT: G 170 PHE cc_start: 0.8002 (t80) cc_final: 0.7573 (t80) REVERT: G 195 MET cc_start: 0.8826 (mpp) cc_final: 0.8599 (mpp) REVERT: G 206 SER cc_start: 0.9676 (m) cc_final: 0.9315 (t) REVERT: G 218 ASP cc_start: 0.7598 (t0) cc_final: 0.6979 (t0) REVERT: G 220 ARG cc_start: 0.8493 (ptp-170) cc_final: 0.8097 (ptp90) REVERT: G 235 GLN cc_start: 0.8627 (pt0) cc_final: 0.8275 (pt0) REVERT: G 251 LEU cc_start: 0.9166 (tp) cc_final: 0.8944 (tt) REVERT: G 257 PHE cc_start: 0.8495 (m-80) cc_final: 0.8286 (m-80) REVERT: G 273 TYR cc_start: 0.8536 (p90) cc_final: 0.7998 (p90) REVERT: H 46 GLN cc_start: 0.6930 (mt0) cc_final: 0.6391 (mt0) REVERT: H 82 LYS cc_start: 0.8508 (mttt) cc_final: 0.7862 (mttm) REVERT: H 134 PHE cc_start: 0.9210 (p90) cc_final: 0.9004 (p90) REVERT: H 200 GLU cc_start: 0.7540 (tt0) cc_final: 0.7122 (tt0) REVERT: H 238 TYR cc_start: 0.7086 (m-80) cc_final: 0.5588 (t80) REVERT: H 305 ASP cc_start: 0.8464 (t0) cc_final: 0.8192 (t0) REVERT: H 327 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8095 (pp20) REVERT: H 362 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8392 (mtp-110) REVERT: H 395 ASP cc_start: 0.9180 (p0) cc_final: 0.8977 (p0) REVERT: I 130 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6932 (mtt90) REVERT: I 152 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7747 (mmtt) REVERT: I 186 TRP cc_start: 0.8232 (t60) cc_final: 0.7670 (t60) REVERT: I 192 GLN cc_start: 0.8926 (tp40) cc_final: 0.8101 (mm110) REVERT: I 197 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7151 (mmt180) REVERT: I 212 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.7422 (mmm-85) REVERT: J 9 ASN cc_start: 0.9240 (t0) cc_final: 0.8695 (t0) REVERT: J 15 TYR cc_start: 0.8164 (t80) cc_final: 0.7667 (t80) REVERT: J 63 CYS cc_start: 0.5291 (t) cc_final: 0.4747 (t) REVERT: J 117 ASP cc_start: 0.8689 (t0) cc_final: 0.8317 (t0) REVERT: J 133 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8379 (mm) REVERT: J 218 ASP cc_start: 0.8086 (t0) cc_final: 0.7506 (t0) REVERT: J 230 HIS cc_start: 0.8707 (t-90) cc_final: 0.8128 (t-90) REVERT: J 246 ASN cc_start: 0.8220 (t0) cc_final: 0.7770 (t0) REVERT: J 257 PHE cc_start: 0.8267 (m-80) cc_final: 0.7945 (m-80) REVERT: J 271 CYS cc_start: 0.6455 (m) cc_final: 0.6117 (m) REVERT: J 307 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8032 (mm) REVERT: J 368 SER cc_start: 0.8639 (t) cc_final: 0.8411 (t) REVERT: J 372 LYS cc_start: 0.8762 (tptt) cc_final: 0.8431 (tppt) REVERT: J 390 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8170 (tt0) REVERT: J 409 TRP cc_start: 0.8445 (m100) cc_final: 0.8159 (m100) REVERT: K 15 PHE cc_start: 0.8461 (t80) cc_final: 0.8254 (t80) REVERT: K 37 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8221 (mt-10) REVERT: K 78 ASP cc_start: 0.8471 (t0) cc_final: 0.8183 (t70) REVERT: K 168 MET cc_start: 0.8013 (mmp) cc_final: 0.7684 (mmp) REVERT: K 272 HIS cc_start: 0.8648 (t70) cc_final: 0.7494 (t70) REVERT: K 279 TRP cc_start: 0.9062 (p-90) cc_final: 0.8740 (p-90) REVERT: K 339 TRP cc_start: 0.8914 (m-90) cc_final: 0.7834 (m-90) REVERT: K 341 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: K 366 TYR cc_start: 0.8338 (m-80) cc_final: 0.7807 (m-80) REVERT: L 110 LYS cc_start: 0.8011 (mmtm) cc_final: 0.6755 (pttm) REVERT: L 135 LEU cc_start: 0.8464 (tp) cc_final: 0.8258 (tp) REVERT: L 168 MET cc_start: 0.9249 (ppp) cc_final: 0.8821 (tmm) REVERT: W 72 CYS cc_start: 0.4739 (OUTLIER) cc_final: 0.4484 (p) REVERT: W 90 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7546 (tmtt) REVERT: W 94 ASP cc_start: 0.8880 (p0) cc_final: 0.8611 (p0) REVERT: X 77 PHE cc_start: 0.6346 (t80) cc_final: 0.6142 (t80) REVERT: Y 90 LYS cc_start: 0.6577 (tptt) cc_final: 0.6265 (tptm) REVERT: Y 96 ASP cc_start: 0.6655 (m-30) cc_final: 0.6327 (p0) outliers start: 167 outliers final: 111 residues processed: 1099 average time/residue: 0.1905 time to fit residues: 349.5351 Evaluate side-chains 1017 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 899 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 238 SER 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 B residue 33 ASN 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 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 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 370 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 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 296 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 127 VAL 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 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 54 VAL 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 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 109 ASP 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 160 GLU 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 80 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 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 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 221 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 X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 84 CYS Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 330 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 405 optimal weight: 20.0000 chunk 406 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 267 optimal weight: 0.9980 chunk 138 optimal weight: 0.0060 chunk 350 optimal weight: 8.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 169 HIS C 59 GLN C 408 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS H 46 GLN ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 ASN ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN L 187 HIS L 188 HIS Y 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120881 restraints weight = 64482.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124713 restraints weight = 32016.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127184 restraints weight = 20001.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128751 restraints weight = 14655.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129728 restraints weight = 12016.130| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33733 Z= 0.246 Angle : 0.713 10.919 45942 Z= 0.373 Chirality : 0.048 0.343 5080 Planarity : 0.005 0.050 5924 Dihedral : 6.440 82.092 4616 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 5.79 % Allowed : 20.93 % Favored : 73.28 % 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 are not related in a simple way. whole: -0.77 (0.13), residues: 4240 helix: 0.57 (0.25), residues: 416 sheet: -0.85 (0.15), residues: 1115 loop : -0.48 (0.12), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 212 TYR 0.026 0.002 TYR C 308 PHE 0.024 0.002 PHE H 51 TRP 0.014 0.002 TRP H 236 HIS 0.027 0.002 HIS L 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (33660) covalent geometry : angle 0.70692 / 0.37 (45796) SS BOND : bond 0.00376 / 0.26 ( 73) SS BOND : angle 1.77303 / 1.15 ( 146) hydrogen bonds : bond 0.03955 / 2.66 ( 1197) hydrogen bonds : angle 6.22324 / 4.28 ( 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 1116 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 907 time to evaluate : 1.303 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 24 TYR cc_start: 0.8498 (m-80) cc_final: 0.8037 (m-80) REVERT: A 30 GLU cc_start: 0.6675 (tp30) cc_final: 0.6243 (tp30) REVERT: A 75 ASP cc_start: 0.7904 (t0) cc_final: 0.6863 (t0) REVERT: A 160 LYS cc_start: 0.8614 (mptt) cc_final: 0.8409 (mttp) REVERT: A 219 ILE cc_start: 0.9474 (mt) cc_final: 0.9265 (mt) REVERT: A 341 GLU cc_start: 0.8829 (mp0) cc_final: 0.8592 (pm20) REVERT: A 395 ASP cc_start: 0.8430 (t0) cc_final: 0.8044 (t0) REVERT: A 409 TRP cc_start: 0.8573 (t-100) cc_final: 0.8325 (t-100) REVERT: B 33 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7347 (t0) REVERT: B 39 ASP cc_start: 0.7755 (m-30) cc_final: 0.7377 (m-30) REVERT: B 40 ASP cc_start: 0.8443 (p0) cc_final: 0.7877 (p0) REVERT: B 70 ASP cc_start: 0.7750 (p0) cc_final: 0.7060 (p0) REVERT: B 92 ARG cc_start: 0.2694 (mtt180) cc_final: 0.1892 (mtm180) REVERT: B 122 ASN cc_start: 0.8821 (m110) cc_final: 0.8618 (m-40) REVERT: B 146 HIS cc_start: 0.5015 (OUTLIER) cc_final: 0.4649 (m170) REVERT: B 176 TYR cc_start: 0.7395 (m-80) cc_final: 0.6661 (m-80) REVERT: B 258 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8453 (Cg_exo) REVERT: B 278 LYS cc_start: 0.9295 (mtmm) cc_final: 0.9064 (mttp) REVERT: B 305 ASP cc_start: 0.8844 (t0) cc_final: 0.8518 (t0) REVERT: B 330 TRP cc_start: 0.9066 (t-100) cc_final: 0.8516 (t-100) REVERT: C 32 THR cc_start: 0.9124 (m) cc_final: 0.8776 (p) REVERT: C 97 ASP cc_start: 0.8050 (p0) cc_final: 0.7749 (p0) REVERT: C 100 ASN cc_start: 0.8292 (m-40) cc_final: 0.7843 (m-40) REVERT: C 139 ASN cc_start: 0.8317 (t0) cc_final: 0.7946 (m-40) REVERT: C 262 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7489 (pt0) REVERT: C 307 ILE cc_start: 0.6663 (mt) cc_final: 0.6368 (mt) REVERT: C 362 GLN cc_start: 0.7963 (pm20) cc_final: 0.7624 (pm20) REVERT: C 409 TRP cc_start: 0.8297 (m100) cc_final: 0.7498 (m100) REVERT: D 18 TYR cc_start: 0.8603 (t80) cc_final: 0.8342 (t80) REVERT: D 33 ASN cc_start: 0.8241 (m-40) cc_final: 0.8040 (m-40) REVERT: D 82 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8578 (mtmt) REVERT: D 137 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8180 (ptp90) REVERT: D 272 HIS cc_start: 0.8257 (t-170) cc_final: 0.8002 (t70) REVERT: D 273 THR cc_start: 0.9212 (m) cc_final: 0.8643 (p) REVERT: E 119 GLN cc_start: 0.7634 (pm20) cc_final: 0.7406 (pm20) REVERT: E 130 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8078 (tpp80) REVERT: E 160 GLU cc_start: 0.8280 (pt0) cc_final: 0.7955 (pm20) REVERT: E 194 GLU cc_start: 0.8740 (tp30) cc_final: 0.8293 (tp30) REVERT: F 119 GLN cc_start: 0.8231 (pt0) cc_final: 0.7456 (pm20) REVERT: F 127 VAL cc_start: 0.8955 (t) cc_final: 0.8685 (m) REVERT: F 184 TYR cc_start: 0.7014 (m-80) cc_final: 0.6632 (m-80) REVERT: F 207 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8450 (tmtt) REVERT: F 214 ILE cc_start: 0.8877 (mm) cc_final: 0.8499 (pt) REVERT: G 10 VAL cc_start: 0.9073 (t) cc_final: 0.8796 (m) REVERT: G 21 ARG cc_start: 0.8479 (tmm-80) cc_final: 0.8064 (tmm-80) REVERT: G 27 LEU cc_start: 0.8411 (tp) cc_final: 0.7904 (tp) REVERT: G 37 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7490 (mp0) REVERT: G 62 CYS cc_start: 0.4584 (m) cc_final: 0.4250 (m) REVERT: G 160 LYS cc_start: 0.9151 (pptt) cc_final: 0.8846 (mmtm) REVERT: G 170 PHE cc_start: 0.8091 (t80) cc_final: 0.7665 (t80) REVERT: G 206 SER cc_start: 0.9651 (m) cc_final: 0.9308 (t) REVERT: G 218 ASP cc_start: 0.7644 (t0) cc_final: 0.7170 (t0) REVERT: G 220 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8195 (ptp90) REVERT: G 257 PHE cc_start: 0.8597 (m-80) cc_final: 0.8317 (m-80) REVERT: G 273 TYR cc_start: 0.8632 (p90) cc_final: 0.8092 (p90) REVERT: G 324 ARG cc_start: 0.7659 (ptp-170) cc_final: 0.7418 (ptp90) REVERT: G 364 ASN cc_start: 0.8943 (t0) cc_final: 0.8564 (t0) REVERT: H 82 LYS cc_start: 0.8557 (mttt) cc_final: 0.7955 (mttm) REVERT: H 134 PHE cc_start: 0.9291 (p90) cc_final: 0.9033 (p90) REVERT: H 200 GLU cc_start: 0.7593 (tt0) cc_final: 0.7116 (tt0) REVERT: H 305 ASP cc_start: 0.8588 (t0) cc_final: 0.8307 (t0) REVERT: H 362 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8431 (mtp-110) REVERT: I 115 MET cc_start: 0.6270 (mmp) cc_final: 0.5733 (mmm) REVERT: I 130 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7208 (mtt180) REVERT: I 152 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7716 (mmtt) REVERT: I 212 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.7503 (mmm-85) REVERT: J 9 ASN cc_start: 0.9284 (t0) cc_final: 0.8758 (t0) REVERT: J 15 TYR cc_start: 0.8285 (t80) cc_final: 0.7769 (t80) REVERT: J 133 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8409 (mm) REVERT: J 195 MET cc_start: 0.9018 (mpp) cc_final: 0.8792 (mpp) REVERT: J 218 ASP cc_start: 0.8271 (t0) cc_final: 0.7759 (t0) REVERT: J 230 HIS cc_start: 0.8867 (t-90) cc_final: 0.8319 (t-90) REVERT: J 246 ASN cc_start: 0.8157 (t0) cc_final: 0.7753 (t0) REVERT: J 257 PHE cc_start: 0.8480 (m-80) cc_final: 0.7806 (m-80) REVERT: J 271 CYS cc_start: 0.6411 (m) cc_final: 0.6048 (m) REVERT: J 307 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (mm) REVERT: J 368 SER cc_start: 0.8685 (t) cc_final: 0.8342 (t) REVERT: J 372 LYS cc_start: 0.8786 (tptt) cc_final: 0.8372 (tppt) REVERT: J 409 TRP cc_start: 0.8501 (m100) cc_final: 0.8220 (m100) REVERT: K 38 SER cc_start: 0.9287 (t) cc_final: 0.9023 (p) REVERT: K 279 TRP cc_start: 0.9125 (p-90) cc_final: 0.8706 (p-90) REVERT: K 341 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: K 366 TYR cc_start: 0.8391 (m-80) cc_final: 0.7891 (m-80) REVERT: L 110 LYS cc_start: 0.8010 (mmtm) cc_final: 0.6858 (pttm) REVERT: L 168 MET cc_start: 0.9283 (ppp) cc_final: 0.8836 (tmm) REVERT: W 72 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.4792 (p) REVERT: W 90 LYS cc_start: 0.8611 (mtpt) cc_final: 0.7727 (tmtt) REVERT: W 106 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6539 (pm20) outliers start: 209 outliers final: 162 residues processed: 1017 average time/residue: 0.2015 time to fit residues: 338.7600 Evaluate side-chains 1028 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 858 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 162 ILE 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 353 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 ILE 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 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 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 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 330 VAL Chi-restraints excluded: chain C residue 335 THR 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 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 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 295 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 121 ASN 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 5 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 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 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 146 HIS Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 236 TRP Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 277 THR 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 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 33 ASN 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 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 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 153 optimal weight: 0.0770 chunk 344 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 415 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 400 optimal weight: 9.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS L 187 HIS X 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123887 restraints weight = 64309.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127813 restraints weight = 31622.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130341 restraints weight = 19610.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131919 restraints weight = 14266.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132917 restraints weight = 11698.809| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33733 Z= 0.161 Angle : 0.691 10.383 45942 Z= 0.356 Chirality : 0.047 0.440 5080 Planarity : 0.005 0.073 5924 Dihedral : 6.243 82.079 4614 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 5.04 % Allowed : 22.62 % Favored : 72.34 % 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 are not related in a simple way. whole: -0.71 (0.13), residues: 4240 helix: 0.82 (0.25), residues: 392 sheet: -0.79 (0.15), residues: 1107 loop : -0.47 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 220 TYR 0.035 0.002 TYR I 161 PHE 0.028 0.002 PHE I 198 TRP 0.014 0.001 TRP J 89 HIS 0.020 0.001 HIS L 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (33660) covalent geometry : angle 0.68348 / 0.35 (45796) SS BOND : bond 0.00369 / 0.24 ( 73) SS BOND : angle 1.97452 / 1.26 ( 146) hydrogen bonds : bond 0.03681 / 2.47 ( 1197) hydrogen bonds : angle 6.06243 / 4.17 ( 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 1110 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 928 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8498 (m-80) cc_final: 0.8124 (m-80) REVERT: A 75 ASP cc_start: 0.7746 (t0) cc_final: 0.6719 (t0) REVERT: A 219 ILE cc_start: 0.9417 (mt) cc_final: 0.9072 (mt) REVERT: A 262 GLU cc_start: 0.8307 (tt0) cc_final: 0.8045 (tt0) REVERT: A 367 VAL cc_start: 0.9685 (OUTLIER) cc_final: 0.9464 (m) REVERT: A 395 ASP cc_start: 0.8441 (t0) cc_final: 0.8031 (t0) REVERT: A 409 TRP cc_start: 0.8564 (t-100) cc_final: 0.8286 (t-100) REVERT: B 30 LYS cc_start: 0.9130 (tptt) cc_final: 0.8289 (tttt) REVERT: B 32 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8032 (tp30) REVERT: B 33 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7423 (t0) REVERT: B 70 ASP cc_start: 0.7664 (p0) cc_final: 0.6910 (p0) REVERT: B 92 ARG cc_start: 0.2547 (mtt180) cc_final: 0.1683 (mtm180) REVERT: B 122 ASN cc_start: 0.8818 (m110) cc_final: 0.8608 (m-40) REVERT: B 176 TYR cc_start: 0.7388 (m-80) cc_final: 0.6638 (m-80) REVERT: B 258 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8321 (Cg_exo) REVERT: B 305 ASP cc_start: 0.8861 (t0) cc_final: 0.8515 (t0) REVERT: B 329 VAL cc_start: 0.9399 (t) cc_final: 0.9172 (m) REVERT: B 330 TRP cc_start: 0.9026 (t-100) cc_final: 0.8486 (t-100) REVERT: C 32 THR cc_start: 0.9089 (m) cc_final: 0.8784 (p) REVERT: C 93 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8645 (tp40) REVERT: C 97 ASP cc_start: 0.8090 (p0) cc_final: 0.7734 (p0) REVERT: C 195 MET cc_start: 0.8859 (mpp) cc_final: 0.8546 (mpp) REVERT: C 262 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7548 (pt0) REVERT: C 307 ILE cc_start: 0.6623 (mt) cc_final: 0.6379 (mt) REVERT: C 362 GLN cc_start: 0.7852 (pm20) cc_final: 0.7483 (pm20) REVERT: C 409 TRP cc_start: 0.8291 (m100) cc_final: 0.7493 (m100) REVERT: D 137 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8026 (ptp90) REVERT: D 272 HIS cc_start: 0.8182 (t-170) cc_final: 0.7794 (t70) REVERT: D 273 THR cc_start: 0.9180 (m) cc_final: 0.8496 (p) REVERT: E 160 GLU cc_start: 0.8326 (pt0) cc_final: 0.7972 (pm20) REVERT: E 168 MET cc_start: 0.7059 (ptp) cc_final: 0.6668 (ptm) REVERT: E 186 TRP cc_start: 0.7601 (t60) cc_final: 0.6664 (t60) REVERT: E 194 GLU cc_start: 0.8704 (tp30) cc_final: 0.8297 (tp30) REVERT: E 257 GLU cc_start: 0.8052 (mp0) cc_final: 0.7562 (mp0) REVERT: F 119 GLN cc_start: 0.8268 (pt0) cc_final: 0.7490 (pm20) REVERT: F 127 VAL cc_start: 0.8923 (t) cc_final: 0.8693 (m) REVERT: F 184 TYR cc_start: 0.6993 (m-80) cc_final: 0.6772 (m-80) REVERT: F 186 TRP cc_start: 0.7779 (t60) cc_final: 0.7385 (t60) REVERT: F 207 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8436 (tmtt) REVERT: F 243 ASN cc_start: 0.8495 (t0) cc_final: 0.8275 (t0) REVERT: G 10 VAL cc_start: 0.9001 (t) cc_final: 0.8752 (m) REVERT: G 27 LEU cc_start: 0.8447 (tp) cc_final: 0.7908 (tp) REVERT: G 37 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7490 (mp0) REVERT: G 62 CYS cc_start: 0.4405 (m) cc_final: 0.4075 (m) REVERT: G 160 LYS cc_start: 0.9144 (pptt) cc_final: 0.8682 (mmtm) REVERT: G 170 PHE cc_start: 0.8047 (t80) cc_final: 0.7585 (t80) REVERT: G 206 SER cc_start: 0.9644 (m) cc_final: 0.9301 (t) REVERT: G 218 ASP cc_start: 0.7605 (t0) cc_final: 0.6941 (t0) REVERT: G 220 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.7898 (ptp90) REVERT: G 235 GLN cc_start: 0.8985 (pt0) cc_final: 0.8514 (pt0) REVERT: G 257 PHE cc_start: 0.8590 (m-80) cc_final: 0.8288 (m-80) REVERT: G 273 TYR cc_start: 0.8652 (p90) cc_final: 0.8180 (p90) REVERT: G 281 ASP cc_start: 0.8761 (t0) cc_final: 0.7899 (p0) REVERT: G 364 ASN cc_start: 0.8960 (t0) cc_final: 0.8552 (t0) REVERT: H 30 LYS cc_start: 0.9110 (ptmt) cc_final: 0.8888 (ptmm) REVERT: H 46 GLN cc_start: 0.6779 (tt0) cc_final: 0.6399 (tt0) REVERT: H 82 LYS cc_start: 0.8466 (mttt) cc_final: 0.8037 (mtmm) REVERT: H 155 TYR cc_start: 0.7663 (m-80) cc_final: 0.7323 (m-80) REVERT: H 200 GLU cc_start: 0.7591 (tt0) cc_final: 0.7091 (tt0) REVERT: H 305 ASP cc_start: 0.8582 (t0) cc_final: 0.8363 (t0) REVERT: H 362 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.8464 (mtp-110) REVERT: I 115 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5738 (mmm) REVERT: I 130 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7251 (mtt180) REVERT: I 136 HIS cc_start: 0.7478 (p90) cc_final: 0.7251 (p90) REVERT: I 152 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7591 (mmtt) REVERT: I 212 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8441 (mmm-85) REVERT: J 9 ASN cc_start: 0.9319 (t0) cc_final: 0.8739 (t0) REVERT: J 15 TYR cc_start: 0.8270 (t80) cc_final: 0.7723 (t80) REVERT: J 63 CYS cc_start: 0.5194 (t) cc_final: 0.4803 (t) REVERT: J 133 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8431 (mm) REVERT: J 195 MET cc_start: 0.9006 (mpp) cc_final: 0.8648 (mpp) REVERT: J 218 ASP cc_start: 0.8228 (t0) cc_final: 0.7716 (t0) REVERT: J 230 HIS cc_start: 0.8783 (t-90) cc_final: 0.8556 (t70) REVERT: J 246 ASN cc_start: 0.8238 (t0) cc_final: 0.7735 (t0) REVERT: J 257 PHE cc_start: 0.8382 (m-80) cc_final: 0.7843 (m-80) REVERT: J 262 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7631 (mp0) REVERT: J 271 CYS cc_start: 0.6487 (m) cc_final: 0.6102 (m) REVERT: J 307 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8043 (mm) REVERT: J 333 HIS cc_start: 0.7965 (m90) cc_final: 0.7503 (m170) REVERT: J 362 GLN cc_start: 0.8164 (tp40) cc_final: 0.7941 (tp-100) REVERT: J 372 LYS cc_start: 0.8750 (tptt) cc_final: 0.8521 (tppt) REVERT: J 409 TRP cc_start: 0.8492 (m100) cc_final: 0.8237 (m100) REVERT: K 15 PHE cc_start: 0.8617 (t80) cc_final: 0.8307 (t80) REVERT: K 38 SER cc_start: 0.9248 (t) cc_final: 0.8965 (p) REVERT: K 78 ASP cc_start: 0.8628 (t0) cc_final: 0.8364 (t70) REVERT: K 168 MET cc_start: 0.8223 (mmp) cc_final: 0.7827 (mmp) REVERT: K 272 HIS cc_start: 0.8634 (t70) cc_final: 0.7546 (t70) REVERT: K 279 TRP cc_start: 0.9107 (p-90) cc_final: 0.8715 (p-90) REVERT: K 341 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: K 366 TYR cc_start: 0.8376 (m-80) cc_final: 0.7889 (m-80) REVERT: L 110 LYS cc_start: 0.8008 (mmtm) cc_final: 0.6808 (pttm) REVERT: L 168 MET cc_start: 0.9204 (ppp) cc_final: 0.8812 (tmm) REVERT: L 250 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7364 (mtpt) REVERT: W 90 LYS cc_start: 0.8666 (mtpt) cc_final: 0.7766 (tmtt) REVERT: X 77 PHE cc_start: 0.6575 (t80) cc_final: 0.6134 (t80) REVERT: Y 83 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.4399 (pm20) REVERT: Y 84 CYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6989 (t) outliers start: 182 outliers final: 143 residues processed: 1019 average time/residue: 0.2044 time to fit residues: 344.6471 Evaluate side-chains 1016 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 863 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 162 ILE 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 367 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN 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 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 93 GLN 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 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 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 295 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 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 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 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 50 GLN 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 307 THR Chi-restraints excluded: chain H residue 311 ILE 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 215 LEU 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 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 84 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 75 SER Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 395 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 386 optimal weight: 7.9990 chunk 93 optimal weight: 0.0980 chunk 134 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS G 235 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 355 HIS ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN L 145 GLN L 187 HIS L 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124128 restraints weight = 64381.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128071 restraints weight = 31599.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130591 restraints weight = 19544.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132140 restraints weight = 14207.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133162 restraints weight = 11654.085| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4356 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= 0.162 Angle : 0.689 11.774 45942 Z= 0.354 Chirality : 0.047 0.403 5080 Planarity : 0.005 0.051 5924 Dihedral : 6.201 82.460 4614 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 5.20 % Allowed : 22.76 % Favored : 72.04 % 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 are not related in a simple way. whole: -0.70 (0.13), residues: 4240 helix: 0.90 (0.25), residues: 392 sheet: -0.81 (0.15), residues: 1136 loop : -0.46 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 131 TYR 0.026 0.002 TYR I 161 PHE 0.027 0.002 PHE K 100 TRP 0.023 0.001 TRP K 330 HIS 0.014 0.001 HIS L 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (33660) covalent geometry : angle 0.68201 / 0.35 (45796) SS BOND : bond 0.00346 / 0.24 ( 73) SS BOND : angle 1.86657 / 1.22 ( 146) hydrogen bonds : bond 0.03608 / 2.42 ( 1197) hydrogen bonds : angle 5.99694 / 4.12 ( 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 1076 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 888 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8489 (m-80) cc_final: 0.8172 (m-80) REVERT: A 69 LYS cc_start: 0.8834 (ptmm) cc_final: 0.8567 (ptmt) REVERT: A 75 ASP cc_start: 0.7468 (t0) cc_final: 0.6523 (t0) REVERT: A 143 HIS cc_start: 0.8375 (m90) cc_final: 0.8012 (m-70) REVERT: A 219 ILE cc_start: 0.9330 (mt) cc_final: 0.9037 (mt) REVERT: A 395 ASP cc_start: 0.8449 (t0) cc_final: 0.8115 (t0) REVERT: A 409 TRP cc_start: 0.8611 (t-100) cc_final: 0.8377 (t-100) REVERT: B 30 LYS cc_start: 0.9153 (tptt) cc_final: 0.8265 (tttt) REVERT: B 33 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7351 (t0) REVERT: B 70 ASP cc_start: 0.7635 (p0) cc_final: 0.6866 (p0) REVERT: B 78 ASP cc_start: 0.7738 (t0) cc_final: 0.7378 (t0) REVERT: B 92 ARG cc_start: 0.2968 (mtt180) cc_final: 0.1994 (mtm180) REVERT: B 176 TYR cc_start: 0.7352 (m-80) cc_final: 0.6509 (m-80) REVERT: B 258 PRO cc_start: 0.8598 (Cg_endo) cc_final: 0.8304 (Cg_exo) REVERT: B 305 ASP cc_start: 0.8865 (t0) cc_final: 0.8512 (t0) REVERT: B 330 TRP cc_start: 0.9046 (t-100) cc_final: 0.8540 (t-100) REVERT: B 357 ILE cc_start: 0.9436 (pt) cc_final: 0.9228 (tt) REVERT: C 32 THR cc_start: 0.9136 (m) cc_final: 0.8819 (p) REVERT: C 93 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8638 (tp40) REVERT: C 97 ASP cc_start: 0.8140 (p0) cc_final: 0.7814 (p0) REVERT: C 100 ASN cc_start: 0.8186 (m-40) cc_final: 0.7821 (m-40) REVERT: C 139 ASN cc_start: 0.8298 (t0) cc_final: 0.7910 (m-40) REVERT: C 195 MET cc_start: 0.8854 (mpp) cc_final: 0.8603 (mpp) REVERT: C 262 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7576 (pt0) REVERT: C 307 ILE cc_start: 0.6989 (mt) cc_final: 0.6757 (mt) REVERT: C 362 GLN cc_start: 0.7783 (pm20) cc_final: 0.7457 (pm20) REVERT: C 395 ASP cc_start: 0.8302 (t0) cc_final: 0.8074 (t0) REVERT: C 409 TRP cc_start: 0.8308 (m100) cc_final: 0.7579 (m100) REVERT: D 131 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: D 137 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8054 (ptp90) REVERT: D 261 LEU cc_start: 0.9337 (tp) cc_final: 0.8951 (tt) REVERT: D 272 HIS cc_start: 0.8092 (t-170) cc_final: 0.7682 (t70) REVERT: D 305 ASP cc_start: 0.8181 (t0) cc_final: 0.7935 (t0) REVERT: E 140 LYS cc_start: 0.7241 (tptp) cc_final: 0.6970 (tptt) REVERT: E 168 MET cc_start: 0.7094 (ptp) cc_final: 0.6759 (ptm) REVERT: E 194 GLU cc_start: 0.8652 (tp30) cc_final: 0.8348 (mm-30) REVERT: E 257 GLU cc_start: 0.8096 (mp0) cc_final: 0.7566 (mp0) REVERT: F 119 GLN cc_start: 0.8298 (pt0) cc_final: 0.7529 (pm20) REVERT: F 127 VAL cc_start: 0.8852 (t) cc_final: 0.8621 (m) REVERT: F 152 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8281 (mtmt) REVERT: F 156 MET cc_start: 0.8782 (tmm) cc_final: 0.8196 (pmm) REVERT: F 157 TYR cc_start: 0.7749 (m-80) cc_final: 0.6698 (m-80) REVERT: F 184 TYR cc_start: 0.6990 (m-80) cc_final: 0.6777 (m-80) REVERT: F 186 TRP cc_start: 0.7750 (t60) cc_final: 0.7449 (t60) REVERT: F 197 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8313 (ttm170) REVERT: F 207 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8441 (tmtt) REVERT: F 243 ASN cc_start: 0.8588 (t0) cc_final: 0.8366 (t0) REVERT: G 10 VAL cc_start: 0.9043 (t) cc_final: 0.8808 (m) REVERT: G 27 LEU cc_start: 0.8379 (tp) cc_final: 0.7856 (tp) REVERT: G 37 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7535 (mp0) REVERT: G 62 CYS cc_start: 0.4244 (m) cc_final: 0.3957 (m) REVERT: G 160 LYS cc_start: 0.9140 (pptt) cc_final: 0.8684 (mmtm) REVERT: G 170 PHE cc_start: 0.8019 (t80) cc_final: 0.7554 (t80) REVERT: G 206 SER cc_start: 0.9631 (m) cc_final: 0.9290 (t) REVERT: G 218 ASP cc_start: 0.7606 (t0) cc_final: 0.6934 (t0) REVERT: G 220 ARG cc_start: 0.8474 (ptp-170) cc_final: 0.7893 (ptp90) REVERT: G 235 GLN cc_start: 0.9043 (pt0) cc_final: 0.8529 (pt0) REVERT: G 257 PHE cc_start: 0.8652 (m-80) cc_final: 0.8298 (m-80) REVERT: G 263 VAL cc_start: 0.9320 (t) cc_final: 0.9033 (m) REVERT: G 273 TYR cc_start: 0.8681 (p90) cc_final: 0.8292 (p90) REVERT: G 281 ASP cc_start: 0.8827 (t0) cc_final: 0.7984 (p0) REVERT: G 364 ASN cc_start: 0.8892 (t0) cc_final: 0.8446 (t0) REVERT: H 30 LYS cc_start: 0.9117 (ptmt) cc_final: 0.8807 (ptmm) REVERT: H 46 GLN cc_start: 0.6651 (tt0) cc_final: 0.6272 (tt0) REVERT: H 82 LYS cc_start: 0.8426 (mttt) cc_final: 0.8013 (mtmm) REVERT: H 155 TYR cc_start: 0.7701 (m-80) cc_final: 0.7394 (m-80) REVERT: H 200 GLU cc_start: 0.7590 (tt0) cc_final: 0.7086 (tt0) REVERT: H 305 ASP cc_start: 0.8601 (t0) cc_final: 0.8381 (t0) REVERT: H 327 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8140 (pp20) REVERT: H 337 ARG cc_start: 0.8829 (mtt-85) cc_final: 0.8596 (mtt-85) REVERT: H 362 ARG cc_start: 0.8936 (mmm-85) cc_final: 0.8449 (mtp-110) REVERT: I 130 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7325 (mtt180) REVERT: I 152 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7589 (mmtm) REVERT: I 197 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7108 (mmt180) REVERT: I 212 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: J 9 ASN cc_start: 0.9347 (t0) cc_final: 0.8889 (t0) REVERT: J 15 TYR cc_start: 0.8259 (t80) cc_final: 0.7734 (t80) REVERT: J 133 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8458 (mm) REVERT: J 195 MET cc_start: 0.8977 (mpp) cc_final: 0.8593 (mpp) REVERT: J 218 ASP cc_start: 0.8250 (t0) cc_final: 0.7789 (t0) REVERT: J 230 HIS cc_start: 0.8817 (t-90) cc_final: 0.8602 (t70) REVERT: J 246 ASN cc_start: 0.8212 (t0) cc_final: 0.7704 (t0) REVERT: J 257 PHE cc_start: 0.8376 (m-80) cc_final: 0.7867 (m-80) REVERT: J 262 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7616 (mp0) REVERT: J 271 CYS cc_start: 0.6507 (m) cc_final: 0.6083 (m) REVERT: J 307 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (mm) REVERT: J 372 LYS cc_start: 0.8745 (tptt) cc_final: 0.8356 (tppt) REVERT: J 409 TRP cc_start: 0.8425 (m100) cc_final: 0.8165 (m100) REVERT: K 15 PHE cc_start: 0.8600 (t80) cc_final: 0.8279 (t80) REVERT: K 38 SER cc_start: 0.9241 (t) cc_final: 0.8919 (p) REVERT: K 78 ASP cc_start: 0.8589 (t0) cc_final: 0.8326 (t70) REVERT: K 131 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7350 (ptp-110) REVERT: K 137 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8452 (mtp85) REVERT: K 168 MET cc_start: 0.8355 (mmp) cc_final: 0.7740 (mmp) REVERT: K 272 HIS cc_start: 0.8581 (t70) cc_final: 0.7499 (t70) REVERT: K 279 TRP cc_start: 0.9120 (p-90) cc_final: 0.8711 (p-90) REVERT: K 330 TRP cc_start: 0.9394 (t-100) cc_final: 0.9143 (t-100) REVERT: K 341 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: K 366 TYR cc_start: 0.8376 (m-80) cc_final: 0.7900 (m-80) REVERT: L 110 LYS cc_start: 0.8013 (mmtm) cc_final: 0.6854 (pttm) REVERT: L 168 MET cc_start: 0.9240 (ppp) cc_final: 0.8860 (tmm) REVERT: L 250 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7358 (mtpt) REVERT: W 88 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7529 (ttm-80) REVERT: W 90 LYS cc_start: 0.8682 (mtpt) cc_final: 0.7805 (tmtt) REVERT: W 106 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: X 77 PHE cc_start: 0.6734 (t80) cc_final: 0.6363 (t80) REVERT: Y 83 GLN cc_start: 0.6080 (OUTLIER) cc_final: 0.4802 (pm20) REVERT: Y 84 CYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6958 (t) REVERT: Y 90 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7818 (tptm) outliers start: 188 outliers final: 144 residues processed: 986 average time/residue: 0.2016 time to fit residues: 331.0030 Evaluate side-chains 1012 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 857 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 162 ILE 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 370 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 273 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 396 CYS 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 93 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 103 LEU 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 19 CYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 131 ARG 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 237 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain 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 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 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 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 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 50 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 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 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 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 208 LEU 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 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 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 V residue 84 CYS Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain X residue 57 ASP 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 75 SER Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 136 optimal weight: 0.8980 chunk 384 optimal weight: 10.0000 chunk 323 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS D 33 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN W 37 GLN Y 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125218 restraints weight = 64163.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129159 restraints weight = 31609.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131684 restraints weight = 19581.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133282 restraints weight = 14266.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134237 restraints weight = 11672.879| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33733 Z= 0.146 Angle : 0.681 11.515 45942 Z= 0.349 Chirality : 0.046 0.364 5080 Planarity : 0.005 0.043 5924 Dihedral : 6.028 83.171 4613 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 4.90 % Allowed : 23.75 % Favored : 71.35 % 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 are not related in a simple way. whole: -0.62 (0.13), residues: 4240 helix: 0.84 (0.25), residues: 410 sheet: -0.72 (0.15), residues: 1126 loop : -0.41 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 220 TYR 0.031 0.002 TYR C 233 PHE 0.027 0.002 PHE K 100 TRP 0.025 0.001 TRP K 330 HIS 0.011 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (33660) covalent geometry : angle 0.67390 / 0.35 (45796) SS BOND : bond 0.00432 / 0.31 ( 73) SS BOND : angle 1.83412 / 1.19 ( 146) hydrogen bonds : bond 0.03552 / 2.38 ( 1197) hydrogen bonds : angle 5.90930 / 4.05 ( 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 1063 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 886 time to evaluate : 1.408 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 24 TYR cc_start: 0.8463 (m-80) cc_final: 0.8164 (m-80) REVERT: A 69 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8457 (ptmt) REVERT: A 75 ASP cc_start: 0.7543 (t0) cc_final: 0.6518 (t0) REVERT: A 102 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 143 HIS cc_start: 0.8378 (m90) cc_final: 0.8099 (m-70) REVERT: A 219 ILE cc_start: 0.9317 (mt) cc_final: 0.9094 (mt) REVERT: A 395 ASP cc_start: 0.8382 (t0) cc_final: 0.8064 (t0) REVERT: A 409 TRP cc_start: 0.8574 (t-100) cc_final: 0.8301 (t-100) REVERT: B 30 LYS cc_start: 0.9092 (tptt) cc_final: 0.8255 (tttt) REVERT: B 33 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7361 (t0) REVERT: B 70 ASP cc_start: 0.7618 (p0) cc_final: 0.6830 (p0) REVERT: B 78 ASP cc_start: 0.8411 (t0) cc_final: 0.8198 (t0) REVERT: B 92 ARG cc_start: 0.2754 (mtt180) cc_final: 0.1985 (mtm180) REVERT: B 176 TYR cc_start: 0.7417 (m-80) cc_final: 0.6619 (m-80) REVERT: B 258 PRO cc_start: 0.8520 (Cg_endo) cc_final: 0.8230 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9373 (mt) cc_final: 0.9131 (mp) REVERT: B 305 ASP cc_start: 0.8842 (t0) cc_final: 0.8515 (t0) REVERT: B 330 TRP cc_start: 0.9020 (t-100) cc_final: 0.8581 (t-100) REVERT: C 32 THR cc_start: 0.9117 (m) cc_final: 0.8813 (p) REVERT: C 93 GLN cc_start: 0.8731 (mm110) cc_final: 0.8479 (tp40) REVERT: C 97 ASP cc_start: 0.8210 (p0) cc_final: 0.7818 (p0) REVERT: C 262 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7607 (pt0) REVERT: C 307 ILE cc_start: 0.6977 (mt) cc_final: 0.6754 (mt) REVERT: C 362 GLN cc_start: 0.7843 (pm20) cc_final: 0.7520 (pm20) REVERT: C 395 ASP cc_start: 0.8372 (t0) cc_final: 0.8104 (t0) REVERT: C 409 TRP cc_start: 0.8313 (m100) cc_final: 0.7582 (m100) REVERT: D 137 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8033 (ptp90) REVERT: D 272 HIS cc_start: 0.8065 (t-170) cc_final: 0.7611 (t70) REVERT: D 295 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8632 (tp) REVERT: D 305 ASP cc_start: 0.8158 (t0) cc_final: 0.7937 (t0) REVERT: D 330 TRP cc_start: 0.9342 (t-100) cc_final: 0.9008 (t-100) REVERT: E 140 LYS cc_start: 0.7345 (tptp) cc_final: 0.7043 (tptt) REVERT: E 160 GLU cc_start: 0.8281 (pt0) cc_final: 0.7905 (pm20) REVERT: E 168 MET cc_start: 0.7114 (ptp) cc_final: 0.6881 (ptm) REVERT: E 194 GLU cc_start: 0.8647 (tp30) cc_final: 0.8257 (mm-30) REVERT: E 257 GLU cc_start: 0.8085 (mp0) cc_final: 0.7525 (mp0) REVERT: F 127 VAL cc_start: 0.8832 (t) cc_final: 0.8602 (m) REVERT: F 152 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8292 (mtmt) REVERT: F 156 MET cc_start: 0.8788 (tmm) cc_final: 0.8165 (pmm) REVERT: F 157 TYR cc_start: 0.7626 (m-80) cc_final: 0.6723 (m-80) REVERT: F 179 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7355 (mmtt) REVERT: F 184 TYR cc_start: 0.7032 (m-80) cc_final: 0.6698 (m-80) REVERT: F 186 TRP cc_start: 0.7795 (t60) cc_final: 0.7451 (t60) REVERT: F 197 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8301 (ttm170) REVERT: F 207 LYS cc_start: 0.9082 (tmmt) cc_final: 0.8414 (tmtt) REVERT: F 214 ILE cc_start: 0.8909 (mm) cc_final: 0.8531 (pt) REVERT: F 243 ASN cc_start: 0.8613 (t0) cc_final: 0.8328 (t0) REVERT: G 10 VAL cc_start: 0.9082 (t) cc_final: 0.8846 (m) REVERT: G 27 LEU cc_start: 0.8402 (tp) cc_final: 0.7840 (tp) REVERT: G 37 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7536 (mp0) REVERT: G 157 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7131 (tpp80) REVERT: G 160 LYS cc_start: 0.9136 (pptt) cc_final: 0.8659 (mmtm) REVERT: G 162 ILE cc_start: 0.8568 (mt) cc_final: 0.8068 (mm) REVERT: G 170 PHE cc_start: 0.7988 (t80) cc_final: 0.7542 (t80) REVERT: G 206 SER cc_start: 0.9629 (m) cc_final: 0.9299 (t) REVERT: G 212 ASP cc_start: 0.8851 (p0) cc_final: 0.8499 (p0) REVERT: G 218 ASP cc_start: 0.7567 (t0) cc_final: 0.5669 (t0) REVERT: G 220 ARG cc_start: 0.8499 (ptp-170) cc_final: 0.7526 (ptp90) REVERT: G 235 GLN cc_start: 0.9042 (pt0) cc_final: 0.8298 (pt0) REVERT: G 257 PHE cc_start: 0.8644 (m-80) cc_final: 0.8254 (m-80) REVERT: G 263 VAL cc_start: 0.9323 (t) cc_final: 0.9082 (m) REVERT: G 273 TYR cc_start: 0.8686 (p90) cc_final: 0.8331 (p90) REVERT: G 281 ASP cc_start: 0.8820 (t0) cc_final: 0.7966 (p0) REVERT: G 364 ASN cc_start: 0.8903 (t0) cc_final: 0.8461 (t0) REVERT: H 30 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8776 (ptmm) REVERT: H 46 GLN cc_start: 0.6647 (tt0) cc_final: 0.6226 (tt0) REVERT: H 82 LYS cc_start: 0.8403 (mttt) cc_final: 0.8059 (mtmm) REVERT: H 155 TYR cc_start: 0.7634 (m-80) cc_final: 0.7355 (m-80) REVERT: H 200 GLU cc_start: 0.7677 (tt0) cc_final: 0.7306 (tt0) REVERT: H 305 ASP cc_start: 0.8628 (t0) cc_final: 0.8425 (t0) REVERT: H 327 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: H 337 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8573 (mtt-85) REVERT: H 362 ARG cc_start: 0.8969 (mmm-85) cc_final: 0.8497 (mtp-110) REVERT: I 130 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7310 (mtt180) REVERT: I 152 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7537 (mmtm) REVERT: I 197 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7238 (mmt180) REVERT: I 212 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: J 9 ASN cc_start: 0.9336 (t0) cc_final: 0.8878 (t0) REVERT: J 15 TYR cc_start: 0.8186 (t80) cc_final: 0.7688 (t80) REVERT: J 76 TYR cc_start: 0.8782 (t80) cc_final: 0.8481 (t80) REVERT: J 133 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8452 (mm) REVERT: J 195 MET cc_start: 0.8975 (mpp) cc_final: 0.8602 (mpp) REVERT: J 218 ASP cc_start: 0.8211 (t0) cc_final: 0.7758 (t0) REVERT: J 246 ASN cc_start: 0.8169 (t0) cc_final: 0.7667 (t0) REVERT: J 257 PHE cc_start: 0.8353 (m-80) cc_final: 0.7858 (m-80) REVERT: J 262 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7590 (mp0) REVERT: J 307 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (mm) REVERT: J 368 SER cc_start: 0.8607 (t) cc_final: 0.7594 (t) REVERT: J 372 LYS cc_start: 0.8711 (tptt) cc_final: 0.8280 (tppt) REVERT: J 409 TRP cc_start: 0.8402 (m100) cc_final: 0.8151 (m100) REVERT: K 15 PHE cc_start: 0.8549 (t80) cc_final: 0.8278 (t80) REVERT: K 38 SER cc_start: 0.9227 (t) cc_final: 0.8899 (p) REVERT: K 78 ASP cc_start: 0.8549 (t0) cc_final: 0.8308 (t70) REVERT: K 131 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7334 (ptp-110) REVERT: K 168 MET cc_start: 0.8227 (mmp) cc_final: 0.7907 (mmp) REVERT: K 180 LEU cc_start: 0.9133 (mt) cc_final: 0.8932 (mt) REVERT: K 272 HIS cc_start: 0.8560 (t70) cc_final: 0.7196 (t70) REVERT: K 279 TRP cc_start: 0.9117 (p-90) cc_final: 0.8743 (p-90) REVERT: K 330 TRP cc_start: 0.9357 (t-100) cc_final: 0.9144 (t-100) REVERT: K 341 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: K 366 TYR cc_start: 0.8351 (m-80) cc_final: 0.7866 (m-80) REVERT: L 110 LYS cc_start: 0.7951 (mmtm) cc_final: 0.6842 (pttm) REVERT: L 156 MET cc_start: 0.9005 (ppp) cc_final: 0.8470 (ppp) REVERT: L 168 MET cc_start: 0.9266 (ppp) cc_final: 0.8974 (tmm) REVERT: L 250 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7353 (mtpt) REVERT: W 90 LYS cc_start: 0.8708 (mtpt) cc_final: 0.7856 (tmtt) REVERT: W 106 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: X 77 PHE cc_start: 0.6743 (t80) cc_final: 0.6321 (t80) REVERT: Y 83 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.4858 (pm20) REVERT: Y 84 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6968 (t) REVERT: Y 90 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7904 (tttt) outliers start: 177 outliers final: 138 residues processed: 977 average time/residue: 0.2042 time to fit residues: 331.0240 Evaluate side-chains 996 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 846 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 102 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 162 ILE 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 370 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain 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 295 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 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 314 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 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 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 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 237 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 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 117 ASN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 129 LEU 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 208 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 102 LEU 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 145 GLN 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 76 ASP Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain W residue 85 VAL 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 Y residue 33 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 138 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 344 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 373 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 186 ASN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** 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 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125233 restraints weight = 63935.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129139 restraints weight = 31613.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131640 restraints weight = 19667.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133245 restraints weight = 14367.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134133 restraints weight = 11763.610| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33733 Z= 0.150 Angle : 0.683 11.337 45942 Z= 0.349 Chirality : 0.046 0.347 5080 Planarity : 0.005 0.042 5924 Dihedral : 5.947 82.330 4613 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 4.54 % Allowed : 24.39 % Favored : 71.07 % 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 are not related in a simple way. whole: -0.54 (0.13), residues: 4240 helix: 1.26 (0.26), residues: 374 sheet: -0.65 (0.15), residues: 1113 loop : -0.42 (0.12), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 131 TYR 0.033 0.002 TYR C 233 PHE 0.018 0.001 PHE W 38 TRP 0.017 0.001 TRP K 330 HIS 0.013 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (33660) covalent geometry : angle 0.67608 / 0.35 (45796) SS BOND : bond 0.00401 / 0.29 ( 73) SS BOND : angle 1.83217 / 1.19 ( 146) hydrogen bonds : bond 0.03535 / 2.38 ( 1197) hydrogen bonds : angle 5.85615 / 4.02 ( 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 1033 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 869 time to evaluate : 1.352 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: 0.8680 (mtmt) cc_final: 0.8446 (mttt) REVERT: A 69 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8513 (ptmt) REVERT: A 75 ASP cc_start: 0.7531 (t0) cc_final: 0.6529 (t0) REVERT: A 102 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: A 143 HIS cc_start: 0.8478 (m90) cc_final: 0.8111 (m-70) REVERT: A 219 ILE cc_start: 0.9309 (mt) cc_final: 0.9073 (mt) REVERT: A 395 ASP cc_start: 0.8390 (t0) cc_final: 0.8054 (t0) REVERT: A 409 TRP cc_start: 0.8585 (t-100) cc_final: 0.8343 (t-100) REVERT: B 30 LYS cc_start: 0.9150 (tptt) cc_final: 0.8289 (tttt) REVERT: B 33 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7362 (t0) REVERT: B 70 ASP cc_start: 0.7637 (p0) cc_final: 0.6884 (p0) REVERT: B 92 ARG cc_start: 0.2863 (mtt180) cc_final: 0.2085 (mtm180) REVERT: B 176 TYR cc_start: 0.7402 (m-80) cc_final: 0.6559 (m-80) REVERT: B 258 PRO cc_start: 0.8488 (Cg_endo) cc_final: 0.8199 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9368 (mt) cc_final: 0.9114 (mp) REVERT: B 305 ASP cc_start: 0.8863 (t0) cc_final: 0.8472 (t0) REVERT: B 330 TRP cc_start: 0.8981 (t-100) cc_final: 0.8527 (t-100) REVERT: C 32 THR cc_start: 0.9097 (m) cc_final: 0.8802 (p) REVERT: C 93 GLN cc_start: 0.8766 (mm110) cc_final: 0.8503 (tp40) REVERT: C 97 ASP cc_start: 0.8220 (p0) cc_final: 0.7891 (p0) REVERT: C 100 ASN cc_start: 0.8008 (m-40) cc_final: 0.7696 (m-40) REVERT: C 139 ASN cc_start: 0.8378 (t0) cc_final: 0.7964 (m-40) REVERT: C 196 LYS cc_start: 0.9209 (mtmm) cc_final: 0.8966 (mtmm) REVERT: C 262 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7623 (pt0) REVERT: C 362 GLN cc_start: 0.7838 (pm20) cc_final: 0.7510 (pm20) REVERT: C 409 TRP cc_start: 0.8317 (m100) cc_final: 0.7575 (m100) REVERT: D 55 GLN cc_start: 0.8544 (tt0) cc_final: 0.8282 (tt0) REVERT: D 131 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7918 (mtm-85) REVERT: D 137 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8061 (ptp90) REVERT: D 272 HIS cc_start: 0.8042 (t-170) cc_final: 0.7595 (t70) REVERT: D 295 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8610 (tp) REVERT: D 323 ARG cc_start: 0.9267 (ptm160) cc_final: 0.8906 (ttm-80) REVERT: E 140 LYS cc_start: 0.7406 (tptp) cc_final: 0.7125 (tptt) REVERT: E 168 MET cc_start: 0.7128 (ptp) cc_final: 0.6868 (ptm) REVERT: E 194 GLU cc_start: 0.8592 (tp30) cc_final: 0.8218 (mm-30) REVERT: E 257 GLU cc_start: 0.8081 (mp0) cc_final: 0.7405 (mp0) REVERT: F 156 MET cc_start: 0.8824 (tmm) cc_final: 0.8245 (pmm) REVERT: F 157 TYR cc_start: 0.7597 (m-80) cc_final: 0.6794 (m-80) REVERT: F 186 TRP cc_start: 0.7807 (t60) cc_final: 0.7469 (t60) REVERT: F 207 LYS cc_start: 0.9089 (tmmt) cc_final: 0.8401 (tmtt) REVERT: F 214 ILE cc_start: 0.8932 (mm) cc_final: 0.8492 (pt) REVERT: F 243 ASN cc_start: 0.8601 (t0) cc_final: 0.8316 (t0) REVERT: G 10 VAL cc_start: 0.9082 (t) cc_final: 0.8839 (m) REVERT: G 37 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7550 (mp0) REVERT: G 160 LYS cc_start: 0.9110 (pptt) cc_final: 0.8600 (mmtm) REVERT: G 162 ILE cc_start: 0.8535 (mt) cc_final: 0.8041 (mm) REVERT: G 170 PHE cc_start: 0.8033 (t80) cc_final: 0.7522 (t80) REVERT: G 206 SER cc_start: 0.9624 (m) cc_final: 0.9279 (t) REVERT: G 216 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7818 (ttm-80) REVERT: G 218 ASP cc_start: 0.7581 (t0) cc_final: 0.5630 (t0) REVERT: G 220 ARG cc_start: 0.8539 (ptp-170) cc_final: 0.7529 (ptp90) REVERT: G 235 GLN cc_start: 0.9046 (pt0) cc_final: 0.8455 (pt0) REVERT: G 257 PHE cc_start: 0.8647 (m-80) cc_final: 0.8212 (m-80) REVERT: G 263 VAL cc_start: 0.9319 (t) cc_final: 0.9082 (m) REVERT: G 273 TYR cc_start: 0.8697 (p90) cc_final: 0.8329 (p90) REVERT: G 281 ASP cc_start: 0.8799 (t0) cc_final: 0.7947 (p0) REVERT: G 364 ASN cc_start: 0.8912 (t0) cc_final: 0.8451 (t0) REVERT: H 46 GLN cc_start: 0.6737 (tt0) cc_final: 0.6323 (tt0) REVERT: H 82 LYS cc_start: 0.8382 (mttt) cc_final: 0.7951 (mtmm) REVERT: H 155 TYR cc_start: 0.7639 (m-80) cc_final: 0.7377 (m-80) REVERT: H 305 ASP cc_start: 0.8669 (t0) cc_final: 0.8466 (t0) REVERT: H 337 ARG cc_start: 0.8786 (mtt-85) cc_final: 0.8490 (mtt-85) REVERT: H 362 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8498 (mtp-110) REVERT: I 130 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7294 (mtt180) REVERT: I 152 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7513 (mmtm) REVERT: I 197 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7228 (mmt180) REVERT: I 212 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8463 (mmm-85) REVERT: J 9 ASN cc_start: 0.9333 (t0) cc_final: 0.8901 (t0) REVERT: J 15 TYR cc_start: 0.8235 (t80) cc_final: 0.7775 (t80) REVERT: J 76 TYR cc_start: 0.8784 (t80) cc_final: 0.8461 (t80) REVERT: J 133 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8467 (mm) REVERT: J 195 MET cc_start: 0.8976 (mpp) cc_final: 0.8647 (mpp) REVERT: J 218 ASP cc_start: 0.8235 (t0) cc_final: 0.7794 (t0) REVERT: J 246 ASN cc_start: 0.8158 (t0) cc_final: 0.7641 (t0) REVERT: J 262 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7578 (mp0) REVERT: J 307 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7940 (mm) REVERT: J 362 GLN cc_start: 0.8105 (tp40) cc_final: 0.7838 (tp-100) REVERT: J 372 LYS cc_start: 0.8627 (tptt) cc_final: 0.8358 (tppt) REVERT: J 409 TRP cc_start: 0.8395 (m100) cc_final: 0.8151 (m100) REVERT: K 15 PHE cc_start: 0.8548 (t80) cc_final: 0.8306 (t80) REVERT: K 38 SER cc_start: 0.9190 (t) cc_final: 0.8869 (p) REVERT: K 78 ASP cc_start: 0.8565 (t0) cc_final: 0.8312 (t70) REVERT: K 94 LEU cc_start: 0.9313 (mt) cc_final: 0.9092 (mp) REVERT: K 104 GLN cc_start: 0.8944 (mm110) cc_final: 0.8504 (tp40) REVERT: K 168 MET cc_start: 0.8258 (mmp) cc_final: 0.7934 (mmp) REVERT: K 272 HIS cc_start: 0.8572 (t70) cc_final: 0.7174 (t70) REVERT: K 279 TRP cc_start: 0.9123 (p-90) cc_final: 0.8749 (p-90) REVERT: K 366 TYR cc_start: 0.8345 (m-80) cc_final: 0.7881 (m-80) REVERT: L 110 LYS cc_start: 0.7950 (mmtm) cc_final: 0.6909 (pttm) REVERT: L 156 MET cc_start: 0.9109 (ppp) cc_final: 0.8773 (ppp) REVERT: L 168 MET cc_start: 0.9273 (ppp) cc_final: 0.8943 (tmm) REVERT: W 90 LYS cc_start: 0.8730 (mtpt) cc_final: 0.7847 (tmtt) REVERT: W 106 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: X 77 PHE cc_start: 0.6765 (t80) cc_final: 0.6367 (t80) REVERT: Y 83 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.4850 (pm20) REVERT: Y 84 CYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7120 (t) outliers start: 164 outliers final: 136 residues processed: 955 average time/residue: 0.2001 time to fit residues: 317.3612 Evaluate side-chains 987 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 841 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 102 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 162 ILE 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 370 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 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 295 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 339 LEU 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 131 ARG 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 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 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 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 157 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 27 SER 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 327 GLU 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 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 124 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 137 TYR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 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 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 187 HIS Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain V residue 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 106 GLU 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 Chi-restraints excluded: chain Y residue 84 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 359 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 392 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 395 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 316 optimal weight: 0.0670 chunk 157 optimal weight: 0.6980 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN L 145 GLN W 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126358 restraints weight = 64445.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130280 restraints weight = 31884.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132814 restraints weight = 19805.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134433 restraints weight = 14448.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135449 restraints weight = 11820.567| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33733 Z= 0.144 Angle : 0.693 11.488 45942 Z= 0.353 Chirality : 0.047 0.363 5080 Planarity : 0.005 0.062 5924 Dihedral : 5.929 81.808 4613 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 4.40 % Allowed : 24.83 % Favored : 70.76 % 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 are not related in a simple way. whole: -0.59 (0.13), residues: 4240 helix: 1.19 (0.26), residues: 380 sheet: -0.67 (0.15), residues: 1121 loop : -0.46 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 131 TYR 0.034 0.002 TYR C 233 PHE 0.026 0.002 PHE B 280 TRP 0.036 0.001 TRP L 186 HIS 0.034 0.001 HIS L 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (33660) covalent geometry : angle 0.68741 / 0.35 (45796) SS BOND : bond 0.00353 / 0.24 ( 73) SS BOND : angle 1.75556 / 1.16 ( 146) hydrogen bonds : bond 0.03480 / 2.35 ( 1197) hydrogen bonds : angle 5.84993 / 4.01 ( 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 1011 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 852 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8456 (mttt) REVERT: A 24 TYR cc_start: 0.8301 (m-80) cc_final: 0.7970 (m-80) REVERT: A 75 ASP cc_start: 0.7517 (t0) cc_final: 0.6514 (t0) REVERT: A 102 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: A 219 ILE cc_start: 0.9303 (mt) cc_final: 0.9068 (mt) REVERT: A 395 ASP cc_start: 0.8377 (t0) cc_final: 0.8031 (t0) REVERT: A 409 TRP cc_start: 0.8584 (t-100) cc_final: 0.8337 (t-100) REVERT: B 30 LYS cc_start: 0.9151 (tptt) cc_final: 0.8354 (tttt) REVERT: B 32 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7861 (tp30) REVERT: B 33 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7351 (t0) REVERT: B 70 ASP cc_start: 0.7634 (p0) cc_final: 0.6856 (p0) REVERT: B 92 ARG cc_start: 0.3301 (mtt180) cc_final: 0.2518 (mtm180) REVERT: B 156 ASP cc_start: 0.8479 (t0) cc_final: 0.8233 (m-30) REVERT: B 176 TYR cc_start: 0.7406 (m-80) cc_final: 0.6523 (m-80) REVERT: B 258 PRO cc_start: 0.8434 (Cg_endo) cc_final: 0.8146 (Cg_exo) REVERT: B 287 LEU cc_start: 0.9371 (mt) cc_final: 0.9112 (mp) REVERT: B 305 ASP cc_start: 0.8851 (t0) cc_final: 0.8494 (t0) REVERT: B 330 TRP cc_start: 0.8971 (t-100) cc_final: 0.8467 (t-100) REVERT: C 32 THR cc_start: 0.9094 (m) cc_final: 0.8806 (p) REVERT: C 93 GLN cc_start: 0.8717 (mm110) cc_final: 0.8440 (tp40) REVERT: C 97 ASP cc_start: 0.8252 (p0) cc_final: 0.7883 (p0) REVERT: C 196 LYS cc_start: 0.9217 (mtmm) cc_final: 0.9005 (mtmm) REVERT: C 262 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7632 (pt0) REVERT: C 362 GLN cc_start: 0.7810 (pm20) cc_final: 0.7518 (pm20) REVERT: C 409 TRP cc_start: 0.8306 (m100) cc_final: 0.7557 (m100) REVERT: D 131 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: D 137 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7962 (ptp90) REVERT: D 272 HIS cc_start: 0.8003 (t-170) cc_final: 0.7590 (t70) REVERT: D 295 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8567 (tp) REVERT: D 323 ARG cc_start: 0.9245 (ptm160) cc_final: 0.8889 (ttm-80) REVERT: E 140 LYS cc_start: 0.7405 (tptp) cc_final: 0.7136 (tptt) REVERT: E 168 MET cc_start: 0.7201 (ptp) cc_final: 0.6952 (ptm) REVERT: E 194 GLU cc_start: 0.8597 (tp30) cc_final: 0.8245 (mm-30) REVERT: E 257 GLU cc_start: 0.8066 (mp0) cc_final: 0.7376 (mp0) REVERT: F 119 GLN cc_start: 0.8381 (pt0) cc_final: 0.7627 (pm20) REVERT: F 156 MET cc_start: 0.8827 (tmm) cc_final: 0.8260 (pmm) REVERT: F 157 TYR cc_start: 0.7602 (m-80) cc_final: 0.6838 (m-80) REVERT: F 179 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7369 (mmtt) REVERT: F 186 TRP cc_start: 0.7808 (t60) cc_final: 0.7476 (t60) REVERT: F 198 PHE cc_start: 0.8450 (m-80) cc_final: 0.8135 (m-80) REVERT: F 207 LYS cc_start: 0.9076 (tmmt) cc_final: 0.8382 (tmtt) REVERT: F 214 ILE cc_start: 0.8914 (mm) cc_final: 0.8553 (pt) REVERT: F 243 ASN cc_start: 0.8609 (t0) cc_final: 0.8325 (t0) REVERT: G 10 VAL cc_start: 0.9089 (t) cc_final: 0.8845 (m) REVERT: G 27 LEU cc_start: 0.8503 (tp) cc_final: 0.8208 (tp) REVERT: G 37 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7553 (mp0) REVERT: G 160 LYS cc_start: 0.9106 (pptt) cc_final: 0.8597 (mmtm) REVERT: G 162 ILE cc_start: 0.8579 (mt) cc_final: 0.8078 (mm) REVERT: G 170 PHE cc_start: 0.7974 (t80) cc_final: 0.7447 (t80) REVERT: G 206 SER cc_start: 0.9605 (m) cc_final: 0.9261 (t) REVERT: G 212 ASP cc_start: 0.8837 (p0) cc_final: 0.8492 (p0) REVERT: G 216 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7816 (ttm-80) REVERT: G 218 ASP cc_start: 0.7598 (t0) cc_final: 0.5679 (t0) REVERT: G 220 ARG cc_start: 0.8510 (ptp-170) cc_final: 0.7518 (ptp90) REVERT: G 235 GLN cc_start: 0.9026 (pt0) cc_final: 0.8303 (pt0) REVERT: G 257 PHE cc_start: 0.8635 (m-80) cc_final: 0.8209 (m-80) REVERT: G 263 VAL cc_start: 0.9308 (t) cc_final: 0.9068 (m) REVERT: G 273 TYR cc_start: 0.8684 (p90) cc_final: 0.8316 (p90) REVERT: G 281 ASP cc_start: 0.8787 (t0) cc_final: 0.7947 (p0) REVERT: G 364 ASN cc_start: 0.8917 (t0) cc_final: 0.8458 (t0) REVERT: H 46 GLN cc_start: 0.6650 (tt0) cc_final: 0.6260 (tt0) REVERT: H 82 LYS cc_start: 0.8316 (mttt) cc_final: 0.7845 (mttm) REVERT: H 155 TYR cc_start: 0.7608 (m-80) cc_final: 0.7304 (m-80) REVERT: H 337 ARG cc_start: 0.8769 (mtt-85) cc_final: 0.8467 (mtt-85) REVERT: H 362 ARG cc_start: 0.8954 (mmm-85) cc_final: 0.8514 (mmm-85) REVERT: I 152 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7512 (mmtm) REVERT: I 197 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7084 (mmt180) REVERT: I 212 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8468 (mmm-85) REVERT: J 9 ASN cc_start: 0.9335 (t0) cc_final: 0.8886 (t0) REVERT: J 15 TYR cc_start: 0.8227 (t80) cc_final: 0.7770 (t80) REVERT: J 76 TYR cc_start: 0.8767 (t80) cc_final: 0.8481 (t80) REVERT: J 133 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8451 (mm) REVERT: J 195 MET cc_start: 0.8968 (mpp) cc_final: 0.8661 (mpp) REVERT: J 218 ASP cc_start: 0.8202 (t0) cc_final: 0.7771 (t0) REVERT: J 246 ASN cc_start: 0.8147 (t0) cc_final: 0.7609 (t0) REVERT: J 262 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7635 (mp0) REVERT: J 307 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7887 (mm) REVERT: J 362 GLN cc_start: 0.8035 (tp40) cc_final: 0.7770 (tp-100) REVERT: J 409 TRP cc_start: 0.8382 (m100) cc_final: 0.8143 (m100) REVERT: K 15 PHE cc_start: 0.8571 (t80) cc_final: 0.8313 (t80) REVERT: K 38 SER cc_start: 0.9128 (t) cc_final: 0.8811 (p) REVERT: K 78 ASP cc_start: 0.8563 (t0) cc_final: 0.8333 (t70) REVERT: K 104 GLN cc_start: 0.8972 (mm110) cc_final: 0.8452 (tp40) REVERT: K 168 MET cc_start: 0.8219 (mmp) cc_final: 0.7862 (mmp) REVERT: K 236 TRP cc_start: 0.8676 (m-10) cc_final: 0.8467 (m-10) REVERT: K 272 HIS cc_start: 0.8526 (t70) cc_final: 0.7203 (t70) REVERT: K 279 TRP cc_start: 0.9122 (p-90) cc_final: 0.8747 (p-90) REVERT: K 366 TYR cc_start: 0.8348 (m-80) cc_final: 0.7928 (m-80) REVERT: L 110 LYS cc_start: 0.7918 (mmtm) cc_final: 0.6785 (pttm) REVERT: L 156 MET cc_start: 0.9137 (ppp) cc_final: 0.8808 (ppp) REVERT: L 168 MET cc_start: 0.9276 (ppp) cc_final: 0.8981 (tmm) REVERT: W 90 LYS cc_start: 0.8718 (mtpt) cc_final: 0.7860 (tmtt) REVERT: W 106 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: X 77 PHE cc_start: 0.6760 (t80) cc_final: 0.6416 (t80) REVERT: Y 83 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.4838 (pm20) REVERT: Y 90 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7566 (tttt) outliers start: 159 outliers final: 135 residues processed: 936 average time/residue: 0.1918 time to fit residues: 298.2168 Evaluate side-chains 963 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 819 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 102 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ILE 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 370 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 124 CYS 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 273 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 339 LEU 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 131 ARG 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 295 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 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 F residue 164 VAL 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 157 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 27 SER 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 327 GLU 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 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 97 ASP Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 145 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 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 84 CYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain W residue 85 VAL 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 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: 8.9990 chunk 160 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 413 optimal weight: 0.0970 chunk 173 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 354 optimal weight: 0.7980 overall best weight: 1.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 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 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 233 GLN ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124906 restraints weight = 64477.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128806 restraints weight = 32041.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131317 restraints weight = 19970.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132911 restraints weight = 14588.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133867 restraints weight = 11965.108| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33733 Z= 0.168 Angle : 0.693 11.200 45942 Z= 0.355 Chirality : 0.047 0.312 5080 Planarity : 0.005 0.045 5924 Dihedral : 5.911 81.430 4613 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 4.29 % Allowed : 25.06 % Favored : 70.65 % 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 are not related in a simple way. whole: -0.63 (0.13), residues: 4240 helix: 1.10 (0.26), residues: 392 sheet: -0.76 (0.15), residues: 1150 loop : -0.44 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.035 0.002 TYR C 233 PHE 0.026 0.002 PHE D 134 TRP 0.023 0.001 TRP K 330 HIS 0.012 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (33660) covalent geometry : angle 0.68499 / 0.35 (45796) SS BOND : bond 0.00502 / 0.37 ( 73) SS BOND : angle 1.95317 / 1.29 ( 146) hydrogen bonds : bond 0.03495 / 2.36 ( 1197) hydrogen bonds : angle 5.85888 / 4.01 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7970.16 seconds wall clock time: 138 minutes 8.62 seconds (8288.62 seconds total)