Starting phenix.real_space_refine on Mon Aug 10 05:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23or_69132/08_2026/23or_69132.map" } resolution = 3.11 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= -0.000 sd= 0.054 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 P 384 5.49 5 S 72 5.16 5 C 25787 2.51 5 N 7121 2.21 5 O 8860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42224 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2981 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 10, 'TRANS': 356} Chain: "B" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5549 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 19, 'TRANS': 651} Chain breaks: 5 Chain: "C" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 56} Chain breaks: 1 Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 672 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 2 Chain: "E" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2981 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 10, 'TRANS': 356} Chain: "F" Number of atoms: 5540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5540 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 19, 'TRANS': 649} Chain breaks: 4 Chain: "G" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 56} Chain breaks: 1 Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 672 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 2 Chain: "I" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2981 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 10, 'TRANS': 356} Chain: "J" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5561 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 19, 'TRANS': 652} Chain breaks: 4 Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 56} Chain breaks: 1 Chain: "L" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 672 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 2 Chain: "M" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2981 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 10, 'TRANS': 356} Chain: "N" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5578 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 19, 'TRANS': 654} Chain breaks: 4 Chain: "O" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 56} Chain breaks: 1 Chain: "P" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 672 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 2 Time building chain proxies: 8.58, per 1000 atoms: 0.20 Number of scatterers: 42224 At special positions: 0 Unit cell: (115.644, 185.198, 232.126, 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) S 72 16.00 P 384 15.00 O 8860 8.00 N 7121 7.00 C 25787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7998 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 36 sheets defined 58.8% alpha, 10.8% beta 92 base pairs and 213 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.990A pdb=" N HIS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 96 through 100 removed outlier: 4.038A pdb=" N TYR A 99 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 100 " --> pdb=" O HIS A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.017A pdb=" N SER A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.521A pdb=" N LYS A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 215 through 227 removed outlier: 4.030A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 4.998A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.655A pdb=" N ILE A 304 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 344 removed outlier: 3.597A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 371 removed outlier: 3.539A pdb=" N ILE A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 removed outlier: 3.548A pdb=" N LYS B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.551A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.568A pdb=" N SER B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.799A pdb=" N ASN B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.717A pdb=" N ARG B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.517A pdb=" N ASP B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 187 " --> pdb=" O PHE B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.588A pdb=" N LYS B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.804A pdb=" N ASP B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 257 through 274 removed outlier: 3.748A pdb=" N ARG B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.644A pdb=" N VAL B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.569A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 382 through 388 removed outlier: 3.641A pdb=" N LEU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 490 through 501 Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.645A pdb=" N LEU B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 530 " --> pdb=" O ARG B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.614A pdb=" N LEU B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 removed outlier: 3.726A pdb=" N SER B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 669 through 682 removed outlier: 3.681A pdb=" N ASN B 682 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 692 Proline residue: B 689 - end of helix removed outlier: 4.228A pdb=" N THR B 692 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 713 Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 727 through 744 removed outlier: 3.591A pdb=" N GLU B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 17 Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.991A pdb=" N HIS E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 75 Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 96 through 100 removed outlier: 4.038A pdb=" N TYR E 99 " --> pdb=" O PRO E 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 100 " --> pdb=" O HIS E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 100' Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 140 through 149 removed outlier: 4.017A pdb=" N SER E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.521A pdb=" N LYS E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 214 Processing helix chain 'E' and resid 215 through 227 removed outlier: 4.030A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 4.998A pdb=" N THR E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 300 through 304 removed outlier: 3.654A pdb=" N ILE E 304 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 344 removed outlier: 3.597A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 371 removed outlier: 3.538A pdb=" N ILE E 352 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 51 removed outlier: 3.548A pdb=" N LYS F 36 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 40 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 removed outlier: 3.626A pdb=" N SER F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 101 through 108 removed outlier: 3.568A pdb=" N SER F 105 " --> pdb=" O PHE F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 removed outlier: 3.798A pdb=" N ASN F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 3.718A pdb=" N ARG F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 179 Processing helix chain 'F' and resid 183 through 187 removed outlier: 3.516A pdb=" N ASP F 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 187 " --> pdb=" O PHE F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 187' Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.589A pdb=" N LYS F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 removed outlier: 3.835A pdb=" N ASP F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 Processing helix chain 'F' and resid 257 through 274 removed outlier: 3.748A pdb=" N ARG F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 310 removed outlier: 3.779A pdb=" N VAL F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.568A pdb=" N LEU F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY F 347 " --> pdb=" O ILE F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 380 Processing helix chain 'F' and resid 382 through 388 removed outlier: 3.641A pdb=" N LEU F 388 " --> pdb=" O ASN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 408 through 415 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 427 through 435 Processing helix chain 'F' and resid 467 through 478 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 502 through 504 No H-bonds generated for 'chain 'F' and resid 502 through 504' Processing helix chain 'F' and resid 519 through 532 removed outlier: 3.645A pdb=" N LEU F 523 " --> pdb=" O SER F 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 548 Processing helix chain 'F' and resid 552 through 566 removed outlier: 3.614A pdb=" N LEU F 565 " --> pdb=" O GLY F 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 566 " --> pdb=" O ASP F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 636 removed outlier: 3.726A pdb=" N SER F 623 " --> pdb=" O ARG F 619 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE F 636 " --> pdb=" O VAL F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 651 Processing helix chain 'F' and resid 659 through 667 Processing helix chain 'F' and resid 669 through 682 removed outlier: 3.681A pdb=" N ASN F 682 " --> pdb=" O ASN F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 692 Proline residue: F 689 - end of helix removed outlier: 4.227A pdb=" N THR F 692 " --> pdb=" O PRO F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 713 Processing helix chain 'F' and resid 715 through 727 Processing helix chain 'F' and resid 727 through 744 removed outlier: 3.591A pdb=" N GLU F 744 " --> pdb=" O SER F 740 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 17 Processing helix chain 'I' and resid 23 through 30 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 58 through 71 removed outlier: 3.991A pdb=" N HIS I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 Processing helix chain 'I' and resid 89 through 95 Processing helix chain 'I' and resid 96 through 100 removed outlier: 4.038A pdb=" N TYR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY I 100 " --> pdb=" O HIS I 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 96 through 100' Processing helix chain 'I' and resid 116 through 125 Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 140 through 149 removed outlier: 4.016A pdb=" N SER I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I 148 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.521A pdb=" N LYS I 191 " --> pdb=" O PHE I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 214 Processing helix chain 'I' and resid 215 through 227 removed outlier: 4.030A pdb=" N ILE I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 283 removed outlier: 4.998A pdb=" N THR I 273 " --> pdb=" O SER I 269 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL I 274 " --> pdb=" O LYS I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 294 Processing helix chain 'I' and resid 300 through 304 removed outlier: 3.655A pdb=" N ILE I 304 " --> pdb=" O GLU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 344 removed outlier: 3.597A pdb=" N LYS I 315 " --> pdb=" O ASP I 311 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU I 336 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL I 337 " --> pdb=" O LEU I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 371 removed outlier: 3.539A pdb=" N ILE I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN I 371 " --> pdb=" O LYS I 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 51 removed outlier: 3.548A pdb=" N LYS J 36 " --> pdb=" O ASN J 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU J 40 " --> pdb=" O LYS J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 85 removed outlier: 3.690A pdb=" N SER J 85 " --> pdb=" O LYS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'J' and resid 101 through 108 removed outlier: 3.569A pdb=" N SER J 105 " --> pdb=" O PHE J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.799A pdb=" N ASN J 118 " --> pdb=" O ILE J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 154 removed outlier: 3.718A pdb=" N ARG J 147 " --> pdb=" O ASP J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 179 Processing helix chain 'J' and resid 183 through 187 removed outlier: 3.517A pdb=" N ASP J 186 " --> pdb=" O ASN J 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL J 187 " --> pdb=" O PHE J 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 183 through 187' Processing helix chain 'J' and resid 188 through 201 removed outlier: 3.588A pdb=" N LYS J 199 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 removed outlier: 3.551A pdb=" N ASP J 219 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 237 Processing helix chain 'J' and resid 257 through 274 removed outlier: 3.749A pdb=" N ARG J 274 " --> pdb=" O ILE J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 310 removed outlier: 3.644A pdb=" N VAL J 300 " --> pdb=" O ALA J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 347 removed outlier: 3.569A pdb=" N LEU J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY J 347 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 380 Processing helix chain 'J' and resid 382 through 388 removed outlier: 3.641A pdb=" N LEU J 388 " --> pdb=" O ASN J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 391 No H-bonds generated for 'chain 'J' and resid 389 through 391' Processing helix chain 'J' and resid 399 through 407 removed outlier: 3.522A pdb=" N LEU J 403 " --> pdb=" O GLY J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'J' and resid 417 through 421 Processing helix chain 'J' and resid 427 through 435 Processing helix chain 'J' and resid 467 through 478 Processing helix chain 'J' and resid 490 through 501 Processing helix chain 'J' and resid 502 through 504 No H-bonds generated for 'chain 'J' and resid 502 through 504' Processing helix chain 'J' and resid 519 through 532 removed outlier: 3.645A pdb=" N LEU J 523 " --> pdb=" O SER J 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 530 " --> pdb=" O ARG J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 542 through 548 Processing helix chain 'J' and resid 552 through 566 removed outlier: 3.615A pdb=" N LEU J 565 " --> pdb=" O GLY J 561 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR J 566 " --> pdb=" O ASP J 562 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 636 removed outlier: 3.726A pdb=" N SER J 623 " --> pdb=" O ARG J 619 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE J 636 " --> pdb=" O VAL J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 651 Processing helix chain 'J' and resid 659 through 667 Processing helix chain 'J' and resid 669 through 682 removed outlier: 3.681A pdb=" N ASN J 682 " --> pdb=" O ASN J 678 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 692 Proline residue: J 689 - end of helix removed outlier: 4.227A pdb=" N THR J 692 " --> pdb=" O PRO J 689 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 713 Processing helix chain 'J' and resid 715 through 727 Processing helix chain 'J' and resid 727 through 744 removed outlier: 3.592A pdb=" N GLU J 744 " --> pdb=" O SER J 740 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 17 Processing helix chain 'M' and resid 23 through 30 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.991A pdb=" N HIS M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 75 Processing helix chain 'M' and resid 89 through 95 Processing helix chain 'M' and resid 96 through 100 removed outlier: 4.039A pdb=" N TYR M 99 " --> pdb=" O PRO M 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY M 100 " --> pdb=" O HIS M 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 96 through 100' Processing helix chain 'M' and resid 116 through 125 Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 140 through 149 removed outlier: 4.017A pdb=" N SER M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL M 148 " --> pdb=" O ILE M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 177 Processing helix chain 'M' and resid 177 through 191 removed outlier: 3.521A pdb=" N LYS M 191 " --> pdb=" O PHE M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 215 through 227 removed outlier: 4.030A pdb=" N ILE M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 283 removed outlier: 4.998A pdb=" N THR M 273 " --> pdb=" O SER M 269 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL M 274 " --> pdb=" O LYS M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 294 Processing helix chain 'M' and resid 300 through 304 removed outlier: 3.655A pdb=" N ILE M 304 " --> pdb=" O GLU M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 344 removed outlier: 3.597A pdb=" N LYS M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU M 336 " --> pdb=" O TYR M 332 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL M 337 " --> pdb=" O LEU M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 371 removed outlier: 3.539A pdb=" N ILE M 352 " --> pdb=" O SER M 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN M 371 " --> pdb=" O LYS M 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 51 removed outlier: 3.548A pdb=" N LYS N 36 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU N 40 " --> pdb=" O LYS N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 85 removed outlier: 3.624A pdb=" N SER N 85 " --> pdb=" O LYS N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 Processing helix chain 'N' and resid 101 through 108 removed outlier: 3.616A pdb=" N SER N 105 " --> pdb=" O PHE N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 118 removed outlier: 3.799A pdb=" N ASN N 118 " --> pdb=" O ILE N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 154 removed outlier: 3.718A pdb=" N ARG N 147 " --> pdb=" O ASP N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 179 removed outlier: 3.706A pdb=" N LEU N 175 " --> pdb=" O PRO N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 187 removed outlier: 3.516A pdb=" N ASP N 186 " --> pdb=" O ASN N 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL N 187 " --> pdb=" O PHE N 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 183 through 187' Processing helix chain 'N' and resid 188 through 201 removed outlier: 3.589A pdb=" N LYS N 199 " --> pdb=" O PHE N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 219 removed outlier: 3.550A pdb=" N ASP N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 237 Processing helix chain 'N' and resid 257 through 274 removed outlier: 3.749A pdb=" N ARG N 274 " --> pdb=" O ILE N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 310 removed outlier: 3.777A pdb=" N VAL N 300 " --> pdb=" O ALA N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 347 removed outlier: 3.568A pdb=" N LEU N 339 " --> pdb=" O SER N 335 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY N 347 " --> pdb=" O ILE N 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 380 Processing helix chain 'N' and resid 382 through 388 removed outlier: 3.641A pdb=" N LEU N 388 " --> pdb=" O ASN N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 389 through 391 No H-bonds generated for 'chain 'N' and resid 389 through 391' Processing helix chain 'N' and resid 399 through 407 Processing helix chain 'N' and resid 408 through 415 Processing helix chain 'N' and resid 417 through 421 Processing helix chain 'N' and resid 427 through 435 Processing helix chain 'N' and resid 467 through 477 Processing helix chain 'N' and resid 490 through 501 Processing helix chain 'N' and resid 502 through 504 No H-bonds generated for 'chain 'N' and resid 502 through 504' Processing helix chain 'N' and resid 519 through 532 removed outlier: 3.645A pdb=" N LEU N 523 " --> pdb=" O SER N 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL N 530 " --> pdb=" O ARG N 526 " (cutoff:3.500A) Processing helix chain 'N' and resid 542 through 548 Processing helix chain 'N' and resid 552 through 566 removed outlier: 3.614A pdb=" N LEU N 565 " --> pdb=" O GLY N 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 566 " --> pdb=" O ASP N 562 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 636 removed outlier: 3.726A pdb=" N SER N 623 " --> pdb=" O ARG N 619 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE N 636 " --> pdb=" O VAL N 632 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 651 Processing helix chain 'N' and resid 659 through 667 Processing helix chain 'N' and resid 669 through 682 removed outlier: 3.680A pdb=" N ASN N 682 " --> pdb=" O ASN N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 684 through 692 Proline residue: N 689 - end of helix removed outlier: 4.227A pdb=" N THR N 692 " --> pdb=" O PRO N 689 " (cutoff:3.500A) Processing helix chain 'N' and resid 696 through 713 Processing helix chain 'N' and resid 715 through 727 Processing helix chain 'N' and resid 727 through 744 removed outlier: 3.592A pdb=" N GLU N 744 " --> pdb=" O SER N 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.507A pdb=" N SER A 196 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.970A pdb=" N GLN A 138 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.830A pdb=" N THR B 73 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE B 6 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 8 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 69 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 4.536A pdb=" N VAL B 352 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 422 through 425 removed outlier: 6.022A pdb=" N VAL B 395 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 394 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 448 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 396 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASP B 450 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR B 537 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 447 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET B 539 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS B 449 " --> pdb=" O MET B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 46 Processing sheet with id=AB2, first strand: chain 'E' and resid 194 through 198 removed outlier: 3.506A pdb=" N SER E 196 " --> pdb=" O LEU E 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 132 through 134 removed outlier: 6.970A pdb=" N GLN E 138 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AB5, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.830A pdb=" N THR F 73 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE F 6 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR F 71 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL F 8 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU F 69 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 156 through 160 removed outlier: 6.183A pdb=" N VAL F 282 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER F 332 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE F 284 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL F 352 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 422 through 425 removed outlier: 6.551A pdb=" N ILE F 394 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE F 448 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE F 396 " --> pdb=" O ILE F 448 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ASP F 450 " --> pdb=" O PHE F 396 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR F 537 " --> pdb=" O PHE F 445 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE F 447 " --> pdb=" O TYR F 537 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET F 539 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS F 449 " --> pdb=" O MET F 539 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 455 through 456 Processing sheet with id=AB9, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AC1, first strand: chain 'I' and resid 41 through 46 Processing sheet with id=AC2, first strand: chain 'I' and resid 194 through 198 removed outlier: 3.507A pdb=" N SER I 196 " --> pdb=" O LEU I 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 132 through 134 removed outlier: 6.970A pdb=" N GLN I 138 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 244 through 247 Processing sheet with id=AC5, first strand: chain 'J' and resid 16 through 20 removed outlier: 6.830A pdb=" N THR J 73 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE J 6 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR J 71 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL J 8 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU J 69 " --> pdb=" O VAL J 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 156 through 160 removed outlier: 4.537A pdb=" N VAL J 352 " --> pdb=" O ILE J 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 422 through 425 removed outlier: 6.023A pdb=" N VAL J 395 " --> pdb=" O TYR J 424 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE J 394 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE J 448 " --> pdb=" O ILE J 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE J 396 " --> pdb=" O ILE J 448 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ASP J 450 " --> pdb=" O PHE J 396 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR J 537 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE J 447 " --> pdb=" O TYR J 537 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET J 539 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS J 449 " --> pdb=" O MET J 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'J' and resid 455 through 456 Processing sheet with id=AC9, first strand: chain 'J' and resid 508 through 509 Processing sheet with id=AD1, first strand: chain 'M' and resid 41 through 46 Processing sheet with id=AD2, first strand: chain 'M' and resid 194 through 198 removed outlier: 3.507A pdb=" N SER M 196 " --> pdb=" O LEU M 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 132 through 134 removed outlier: 6.970A pdb=" N GLN M 138 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 244 through 247 Processing sheet with id=AD5, first strand: chain 'N' and resid 16 through 20 removed outlier: 6.831A pdb=" N THR N 73 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE N 6 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL N 8 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU N 69 " --> pdb=" O VAL N 8 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 156 through 160 removed outlier: 4.536A pdb=" N VAL N 352 " --> pdb=" O ILE N 368 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 422 through 425 removed outlier: 6.551A pdb=" N ILE N 394 " --> pdb=" O VAL N 446 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE N 448 " --> pdb=" O ILE N 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE N 396 " --> pdb=" O ILE N 448 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASP N 450 " --> pdb=" O PHE N 396 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR N 537 " --> pdb=" O PHE N 445 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE N 447 " --> pdb=" O TYR N 537 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET N 539 " --> pdb=" O ILE N 447 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS N 449 " --> pdb=" O MET N 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 455 through 456 Processing sheet with id=AD9, first strand: chain 'N' and resid 508 through 509 1730 hydrogen bonds defined for protein. 4998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 232 hydrogen bonds 440 hydrogen bond angles 0 basepair planarities 92 basepair parallelities 213 stacking parallelities Total time for adding SS restraints: 9.73 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5903 1.28 - 1.41: 12257 1.41 - 1.54: 24532 1.54 - 1.68: 1046 1.68 - 1.81: 121 Bond restraints: 43859 Sorted by residual: bond pdb=" CA SER N 177 " pdb=" C SER N 177 " ideal model delta sigma weight residual 1.524 1.389 0.134 1.29e-02 6.01e+03 1.08e+02 bond pdb=" C GLU F 286 " pdb=" O GLU F 286 " ideal model delta sigma weight residual 1.235 1.189 0.046 4.70e-03 4.53e+04 9.67e+01 bond pdb=" CA ASP J 165 " pdb=" C ASP J 165 " ideal model delta sigma weight residual 1.523 1.407 0.115 1.23e-02 6.61e+03 8.78e+01 bond pdb=" CA ARG M 155 " pdb=" C ARG M 155 " ideal model delta sigma weight residual 1.523 1.416 0.106 1.23e-02 6.61e+03 7.48e+01 bond pdb=" CA ARG I 155 " pdb=" C ARG I 155 " ideal model delta sigma weight residual 1.523 1.417 0.106 1.23e-02 6.61e+03 7.44e+01 ... (remaining 43854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 60303 5.50 - 10.99: 493 10.99 - 16.49: 59 16.49 - 21.99: 7 21.99 - 27.49: 2 Bond angle restraints: 60864 Sorted by residual: angle pdb=" N TYR N 483 " pdb=" CA TYR N 483 " pdb=" C TYR N 483 " ideal model delta sigma weight residual 111.36 132.16 -20.80 1.09e+00 8.42e-01 3.64e+02 angle pdb=" N GLY B 239 " pdb=" CA GLY B 239 " pdb=" C GLY B 239 " ideal model delta sigma weight residual 112.68 133.17 -20.49 1.26e+00 6.30e-01 2.65e+02 angle pdb=" N TYR F 483 " pdb=" CA TYR F 483 " pdb=" C TYR F 483 " ideal model delta sigma weight residual 111.28 128.90 -17.62 1.09e+00 8.42e-01 2.61e+02 angle pdb=" N LYS J 479 " pdb=" CA LYS J 479 " pdb=" C LYS J 479 " ideal model delta sigma weight residual 111.52 133.80 -22.28 1.40e+00 5.10e-01 2.53e+02 angle pdb=" N ILE B 164 " pdb=" CA ILE B 164 " pdb=" C ILE B 164 " ideal model delta sigma weight residual 108.11 86.66 21.45 1.40e+00 5.10e-01 2.35e+02 ... (remaining 60859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 24140 31.31 - 62.63: 2036 62.63 - 93.94: 229 93.94 - 125.26: 24 125.26 - 156.57: 12 Dihedral angle restraints: 26441 sinusoidal: 14095 harmonic: 12346 Sorted by residual: dihedral pdb=" O4' U K 23 " pdb=" C1' U K 23 " pdb=" N1 U K 23 " pdb=" C2 U K 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.43 156.57 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U G 23 " pdb=" C1' U G 23 " pdb=" N1 U G 23 " pdb=" C2 U G 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.43 156.57 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U O 23 " pdb=" C1' U O 23 " pdb=" N1 U O 23 " pdb=" C2 U O 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.44 156.56 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 26438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 6601 0.148 - 0.296: 334 0.296 - 0.444: 73 0.444 - 0.592: 20 0.592 - 0.740: 7 Chirality restraints: 7035 Sorted by residual: chirality pdb=" CA GLU F 286 " pdb=" N GLU F 286 " pdb=" C GLU F 286 " pdb=" CB GLU F 286 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA THR F 161 " pdb=" N THR F 161 " pdb=" C THR F 161 " pdb=" CB THR F 161 " both_signs ideal model delta sigma weight residual False 2.53 1.79 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LYS F 479 " pdb=" N LYS F 479 " pdb=" C LYS F 479 " pdb=" CB LYS F 479 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 7032 not shown) Planarity restraints: 6252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 236 " 0.032 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C ALA N 236 " -0.112 2.00e-02 2.50e+03 pdb=" O ALA N 236 " 0.042 2.00e-02 2.50e+03 pdb=" N ILE N 237 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 12 " -0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C LEU J 12 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU J 12 " -0.034 2.00e-02 2.50e+03 pdb=" N SER J 13 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 12 " 0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C LEU F 12 " -0.095 2.00e-02 2.50e+03 pdb=" O LEU F 12 " 0.034 2.00e-02 2.50e+03 pdb=" N SER F 13 " 0.034 2.00e-02 2.50e+03 ... (remaining 6249 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 29 2.34 - 2.98: 21000 2.98 - 3.62: 59764 3.62 - 4.26: 95328 4.26 - 4.90: 156060 Nonbonded interactions: 332181 Sorted by model distance: nonbonded pdb=" OE2 GLU B 404 " pdb=" NH1 ARG N 376 " model vdw 1.699 3.120 nonbonded pdb=" OE2 GLU F 404 " pdb=" NH1 ARG J 376 " model vdw 1.730 3.120 nonbonded pdb=" NH1 ARG B 376 " pdb=" OE2 GLU N 404 " model vdw 1.775 3.120 nonbonded pdb=" OP1 DA L 25 " pdb=" NZ LYS N 81 " model vdw 1.920 3.120 nonbonded pdb=" OG SER I 79 " pdb=" ND2 ASN J 65 " model vdw 1.973 3.120 ... (remaining 332176 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = (chain 'B' and (resid 2 through 237 or resid 256 through 744)) selection = (chain 'F' and (resid 2 through 166 or resid 168 through 744)) selection = (chain 'J' and (resid 2 through 166 or resid 168 through 237 or resid 256 throug \ h 744)) selection = (chain 'N' and (resid 2 through 166 or resid 168 through 237 or resid 256 throug \ h 744)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } 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 individual isotropic 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: 19.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 41.360 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.011 0.134 43859 Z= 0.822 Angle : 1.254 27.487 60864 Z= 0.863 Chirality : 0.083 0.740 7035 Planarity : 0.007 0.080 6252 Dihedral : 20.903 156.570 18443 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.51 % Allowed : 19.64 % Favored : 76.85 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.10 (0.13), residues: 4104 helix: 1.63 (0.11), residues: 2115 sheet: 1.68 (0.24), residues: 484 loop : -0.91 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 321 TYR 0.044 0.002 TYR F 223 PHE 0.040 0.002 PHE F 299 TRP 0.014 0.003 TRP F 173 HIS 0.024 0.002 HIS F 292 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.82 (43859) covalent geometry : angle 1.25352 / 0.86 (60864) hydrogen bonds : bond 0.18391 / 12.26 ( 1962) hydrogen bonds : angle 6.32580 / 4.41 ( 5438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 772 time to evaluate : 1.520 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: B 3 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8481 (tt) REVERT: B 44 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: B 260 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7554 (tttm) REVERT: B 273 THR cc_start: 0.8711 (m) cc_final: 0.8510 (p) REVERT: B 516 LYS cc_start: 0.6106 (mmmt) cc_final: 0.5735 (mmtp) REVERT: B 542 THR cc_start: 0.8360 (m) cc_final: 0.7948 (p) REVERT: B 643 VAL cc_start: 0.8187 (t) cc_final: 0.7970 (m) REVERT: B 648 LEU cc_start: 0.7793 (mt) cc_final: 0.7565 (mt) REVERT: B 680 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6801 (ptmt) REVERT: E 239 ILE cc_start: 0.8409 (mm) cc_final: 0.8205 (mt) REVERT: F 157 LEU cc_start: 0.8419 (mp) cc_final: 0.7813 (tp) REVERT: F 260 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7591 (tttm) REVERT: F 286 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: F 288 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: F 295 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8033 (mp) REVERT: F 509 MET cc_start: 0.6408 (ttt) cc_final: 0.6202 (ttp) REVERT: F 516 LYS cc_start: 0.5303 (mmmt) cc_final: 0.4906 (mtmt) REVERT: F 704 TYR cc_start: 0.8101 (t80) cc_final: 0.7734 (t80) REVERT: F 710 THR cc_start: 0.7729 (t) cc_final: 0.7509 (p) REVERT: J 81 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7829 (mttm) REVERT: J 85 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7601 (p) REVERT: J 234 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8037 (mtpp) REVERT: J 267 HIS cc_start: 0.8003 (t-90) cc_final: 0.7141 (m90) REVERT: J 470 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7622 (t80) REVERT: J 642 ILE cc_start: 0.7926 (mt) cc_final: 0.7705 (tt) REVERT: J 657 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7591 (mm-40) REVERT: N 157 LEU cc_start: 0.8411 (mp) cc_final: 0.8151 (tp) REVERT: N 166 LEU cc_start: 0.8418 (mt) cc_final: 0.8169 (mt) REVERT: N 174 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8015 (ttpt) REVERT: N 482 ASP cc_start: 0.7587 (t0) cc_final: 0.7185 (m-30) REVERT: N 484 TYR cc_start: 0.6272 (t80) cc_final: 0.6041 (t80) REVERT: N 529 LYS cc_start: 0.8047 (mttp) cc_final: 0.7766 (tptt) REVERT: N 680 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6061 (mptt) REVERT: N 681 ASN cc_start: 0.8327 (m-40) cc_final: 0.7718 (m110) outliers start: 136 outliers final: 42 residues processed: 879 average time/residue: 0.2479 time to fit residues: 355.3042 Evaluate side-chains 494 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 442 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 680 LYS Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 94 LYS Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 174 LYS Chi-restraints excluded: chain N residue 240 ASP Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 637 ASN Chi-restraints excluded: chain N residue 680 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN B 10 ASN B 26 ASN B 65 ASN B 88 ASN E 30 GLN F 88 ASN F 170 ASN F 292 HIS F 558 ASN J 65 ASN J 88 ASN J 350 GLN J 351 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 558 ASN M 38 ASN N 26 ASN N 88 ASN N 170 ASN N 292 HIS N 351 GLN N 551 GLN N 703 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.191439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122162 restraints weight = 50761.451| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.19 r_work: 0.3341 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43859 Z= 0.164 Angle : 0.637 9.545 60864 Z= 0.370 Chirality : 0.045 0.291 7035 Planarity : 0.005 0.069 6252 Dihedral : 20.764 153.405 9901 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.79 % Allowed : 19.59 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.46 (0.13), residues: 4104 helix: 1.95 (0.11), residues: 2126 sheet: 1.69 (0.23), residues: 512 loop : -0.79 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 31 TYR 0.026 0.001 TYR E 150 PHE 0.021 0.001 PHE N 725 TRP 0.013 0.001 TRP F 169 HIS 0.006 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (43859) covalent geometry : angle 0.63695 / 0.37 (60864) hydrogen bonds : bond 0.06265 / 4.23 ( 1962) hydrogen bonds : angle 4.31884 / 3.06 ( 5438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 447 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: A 102 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 156 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5449 (tppt) REVERT: B 3 ILE cc_start: 0.8804 (mt) cc_final: 0.8532 (tt) REVERT: B 21 ASP cc_start: 0.7950 (t0) cc_final: 0.7730 (t0) REVERT: B 44 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8527 (mtm-85) REVERT: B 215 VAL cc_start: 0.8217 (t) cc_final: 0.7959 (m) REVERT: B 260 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7225 (tttm) REVERT: B 273 THR cc_start: 0.8550 (m) cc_final: 0.8130 (p) REVERT: B 531 SER cc_start: 0.8136 (t) cc_final: 0.7569 (p) REVERT: B 551 GLN cc_start: 0.7775 (mp10) cc_final: 0.7544 (mp-120) REVERT: B 565 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6240 (mp) REVERT: B 626 ASN cc_start: 0.5637 (m-40) cc_final: 0.5219 (m110) REVERT: B 643 VAL cc_start: 0.7385 (t) cc_final: 0.7104 (m) REVERT: B 648 LEU cc_start: 0.7582 (mt) cc_final: 0.7180 (mt) REVERT: E 16 LYS cc_start: 0.7535 (tptp) cc_final: 0.7319 (mmmt) REVERT: E 203 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8938 (tt) REVERT: E 239 ILE cc_start: 0.8239 (mm) cc_final: 0.8038 (mt) REVERT: F 260 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7399 (tttm) REVERT: F 286 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: F 295 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8156 (mp) REVERT: F 509 MET cc_start: 0.4747 (ttt) cc_final: 0.4485 (ttp) REVERT: F 516 LYS cc_start: 0.5905 (mmmt) cc_final: 0.5666 (mtmt) REVERT: F 517 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5893 (ppt170) REVERT: F 533 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7918 (ptmm) REVERT: F 558 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7268 (t0) REVERT: F 704 TYR cc_start: 0.8286 (t80) cc_final: 0.7982 (t80) REVERT: F 710 THR cc_start: 0.8116 (t) cc_final: 0.7827 (p) REVERT: I 162 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8034 (mm) REVERT: I 294 TYR cc_start: 0.7177 (m-80) cc_final: 0.6958 (m-80) REVERT: J 65 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8347 (m-40) REVERT: J 81 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8283 (ttpt) REVERT: J 160 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: J 234 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6725 (mtpp) REVERT: J 286 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7694 (mm-30) REVERT: J 470 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7179 (t80) REVERT: J 529 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7784 (ttpp) REVERT: J 557 PHE cc_start: 0.6750 (m-10) cc_final: 0.6544 (m-10) REVERT: J 565 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5365 (mp) REVERT: J 642 ILE cc_start: 0.7870 (mt) cc_final: 0.7587 (tt) REVERT: J 678 ASN cc_start: 0.6501 (t0) cc_final: 0.5898 (m110) REVERT: J 683 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6737 (mp0) REVERT: J 735 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7497 (mm-30) REVERT: N 4 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: N 102 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8295 (tttm) REVERT: N 157 LEU cc_start: 0.8564 (mp) cc_final: 0.8203 (tp) REVERT: N 170 ASN cc_start: 0.8326 (m-40) cc_final: 0.8086 (m110) REVERT: N 183 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7456 (t0) REVERT: N 323 LYS cc_start: 0.8393 (mtpm) cc_final: 0.8192 (mtmt) REVERT: N 435 ASN cc_start: 0.8590 (t0) cc_final: 0.8227 (t0) REVERT: N 517 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4493 (ttp-110) REVERT: N 681 ASN cc_start: 0.7739 (m-40) cc_final: 0.7046 (m110) outliers start: 147 outliers final: 45 residues processed: 574 average time/residue: 0.2368 time to fit residues: 222.4843 Evaluate side-chains 456 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 392 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 349 ASP Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 562 ASP Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 183 ASN Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 452 ASP Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 163 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 422 optimal weight: 2.9990 chunk 350 optimal weight: 0.5980 chunk 424 optimal weight: 2.9990 chunk 428 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 398 optimal weight: 0.9980 chunk 378 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN B 384 ASN F 65 ASN F 170 ASN J 351 GLN J 384 ASN M 30 GLN N 65 ASN N 180 ASN N 351 GLN N 703 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.187798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128811 restraints weight = 50437.852| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.31 r_work: 0.3264 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 43859 Z= 0.155 Angle : 0.565 9.491 60864 Z= 0.330 Chirality : 0.043 0.255 7035 Planarity : 0.004 0.059 6252 Dihedral : 20.503 150.170 9841 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.27 % Allowed : 19.98 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.45 (0.13), residues: 4104 helix: 1.97 (0.11), residues: 2130 sheet: 1.58 (0.23), residues: 516 loop : -0.83 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 376 TYR 0.027 0.001 TYR F 457 PHE 0.019 0.001 PHE B 195 TRP 0.012 0.001 TRP B 559 HIS 0.006 0.001 HIS J 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (43859) covalent geometry : angle 0.56532 / 0.33 (60864) hydrogen bonds : bond 0.05470 / 3.64 ( 1962) hydrogen bonds : angle 4.05194 / 2.87 ( 5438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 412 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7692 (mtpp) REVERT: A 21 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: A 156 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5632 (tppt) REVERT: B 21 ASP cc_start: 0.7787 (t0) cc_final: 0.7379 (t0) REVERT: B 215 VAL cc_start: 0.8159 (t) cc_final: 0.7888 (m) REVERT: B 260 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7215 (tttm) REVERT: B 273 THR cc_start: 0.8540 (m) cc_final: 0.8136 (p) REVERT: B 516 LYS cc_start: 0.7055 (mmmm) cc_final: 0.6664 (mmtp) REVERT: B 531 SER cc_start: 0.8227 (t) cc_final: 0.7608 (p) REVERT: B 551 GLN cc_start: 0.7837 (mp10) cc_final: 0.7628 (mp-120) REVERT: B 558 ASN cc_start: 0.7873 (m110) cc_final: 0.7672 (m110) REVERT: B 565 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6211 (mp) REVERT: B 626 ASN cc_start: 0.5581 (m-40) cc_final: 0.5184 (m110) REVERT: B 643 VAL cc_start: 0.7235 (t) cc_final: 0.7034 (m) REVERT: B 644 LEU cc_start: 0.6923 (tt) cc_final: 0.6361 (mp) REVERT: B 711 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7419 (p) REVERT: B 721 GLN cc_start: 0.8105 (mp10) cc_final: 0.7768 (mm-40) REVERT: E 239 ILE cc_start: 0.8253 (mm) cc_final: 0.8007 (mt) REVERT: F 260 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7342 (tttm) REVERT: F 286 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: F 509 MET cc_start: 0.4706 (ttt) cc_final: 0.4399 (ttp) REVERT: F 516 LYS cc_start: 0.5777 (mmmt) cc_final: 0.5087 (ttpp) REVERT: F 517 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6122 (ppt170) REVERT: F 533 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7949 (ptmm) REVERT: F 704 TYR cc_start: 0.8453 (t80) cc_final: 0.8239 (t80) REVERT: F 710 THR cc_start: 0.8038 (t) cc_final: 0.7701 (p) REVERT: I 160 MET cc_start: 0.8548 (ttt) cc_final: 0.8305 (ttt) REVERT: I 162 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8055 (mm) REVERT: J 81 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8296 (ttpp) REVERT: J 105 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7309 (t) REVERT: J 160 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: J 234 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6595 (mtpp) REVERT: J 470 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6895 (t80) REVERT: J 529 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7762 (ttpp) REVERT: J 557 PHE cc_start: 0.7000 (m-10) cc_final: 0.6790 (m-10) REVERT: J 558 ASN cc_start: 0.7725 (m110) cc_final: 0.7358 (m110) REVERT: J 565 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5310 (mp) REVERT: J 642 ILE cc_start: 0.7862 (mt) cc_final: 0.7527 (tt) REVERT: J 672 PHE cc_start: 0.6159 (t80) cc_final: 0.5894 (m-80) REVERT: M 21 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: M 203 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8869 (tt) REVERT: M 330 ARG cc_start: 0.6868 (ttt-90) cc_final: 0.6647 (ttt-90) REVERT: N 102 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8188 (tttm) REVERT: N 157 LEU cc_start: 0.8462 (mp) cc_final: 0.8024 (tp) REVERT: N 199 LYS cc_start: 0.8482 (mttm) cc_final: 0.7786 (mtpt) REVERT: N 323 LYS cc_start: 0.8449 (mtpm) cc_final: 0.8242 (mtmt) REVERT: N 422 ASP cc_start: 0.8126 (m-30) cc_final: 0.7877 (t70) REVERT: N 509 MET cc_start: 0.4511 (tmm) cc_final: 0.4205 (tmm) REVERT: N 517 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.4537 (ttp-110) REVERT: N 679 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5419 (t80) REVERT: N 681 ASN cc_start: 0.7642 (m-40) cc_final: 0.7210 (m110) REVERT: N 704 TYR cc_start: 0.6904 (t80) cc_final: 0.6631 (t80) REVERT: N 708 LYS cc_start: 0.6275 (mmmm) cc_final: 0.5861 (mtpt) outliers start: 127 outliers final: 60 residues processed: 519 average time/residue: 0.2487 time to fit residues: 209.1056 Evaluate side-chains 446 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 368 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 698 VAL Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 368 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN E 114 ASN F 38 ASN F 65 ASN F 170 ASN F 558 ASN I 364 HIS J 678 ASN N 65 ASN N 703 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.184601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127847 restraints weight = 50560.842| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.35 r_work: 0.3210 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43859 Z= 0.201 Angle : 0.591 9.955 60864 Z= 0.341 Chirality : 0.044 0.267 7035 Planarity : 0.004 0.059 6252 Dihedral : 20.474 159.615 9837 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.87 % Allowed : 19.98 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.13 (0.13), residues: 4104 helix: 1.76 (0.11), residues: 2146 sheet: 1.11 (0.22), residues: 558 loop : -1.02 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 376 TYR 0.020 0.002 TYR J 331 PHE 0.022 0.002 PHE F 277 TRP 0.012 0.002 TRP N 559 HIS 0.008 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (43859) covalent geometry : angle 0.59128 / 0.34 (60864) hydrogen bonds : bond 0.05841 / 3.87 ( 1962) hydrogen bonds : angle 4.07812 / 2.89 ( 5438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 386 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7819 (mtpp) REVERT: A 21 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: A 156 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5621 (tppt) REVERT: B 3 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 21 ASP cc_start: 0.7764 (t0) cc_final: 0.7435 (t0) REVERT: B 260 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7347 (tttm) REVERT: B 307 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7181 (t80) REVERT: B 551 GLN cc_start: 0.7843 (mp10) cc_final: 0.7559 (mp10) REVERT: B 558 ASN cc_start: 0.8064 (m110) cc_final: 0.7748 (m110) REVERT: B 565 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6174 (mp) REVERT: B 626 ASN cc_start: 0.5589 (m-40) cc_final: 0.5285 (m-40) REVERT: B 641 GLU cc_start: 0.7339 (tp30) cc_final: 0.6974 (mt-10) REVERT: B 643 VAL cc_start: 0.7428 (t) cc_final: 0.7199 (m) REVERT: B 711 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7481 (p) REVERT: B 721 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: E 160 MET cc_start: 0.8047 (mtp) cc_final: 0.7565 (mtp) REVERT: E 200 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8120 (p0) REVERT: E 239 ILE cc_start: 0.8545 (mm) cc_final: 0.8292 (mt) REVERT: F 260 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7474 (tttm) REVERT: F 350 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: F 509 MET cc_start: 0.5140 (ttt) cc_final: 0.4836 (ttp) REVERT: F 516 LYS cc_start: 0.5904 (mmmt) cc_final: 0.5287 (ttpp) REVERT: F 517 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6583 (ppt170) REVERT: F 533 LYS cc_start: 0.8332 (ptpt) cc_final: 0.7985 (ptmm) REVERT: F 710 THR cc_start: 0.8171 (t) cc_final: 0.7853 (p) REVERT: I 7 ILE cc_start: 0.7752 (tt) cc_final: 0.7542 (tp) REVERT: J 160 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: J 234 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6711 (mtpp) REVERT: J 295 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8126 (mp) REVERT: J 359 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8187 (mmtt) REVERT: J 470 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7025 (t80) REVERT: J 529 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7963 (ttmm) REVERT: J 542 THR cc_start: 0.6897 (OUTLIER) cc_final: 0.6616 (p) REVERT: J 565 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5358 (mp) REVERT: J 642 ILE cc_start: 0.7971 (mt) cc_final: 0.7645 (tt) REVERT: M 21 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: N 102 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8245 (tttm) REVERT: N 199 LYS cc_start: 0.8512 (mttm) cc_final: 0.7901 (mtpt) REVERT: N 323 LYS cc_start: 0.8567 (mtpm) cc_final: 0.8268 (mtmt) REVERT: N 350 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: N 422 ASP cc_start: 0.8197 (m-30) cc_final: 0.7974 (t70) REVERT: N 509 MET cc_start: 0.4893 (tmm) cc_final: 0.4558 (tmm) REVERT: N 517 ARG cc_start: 0.5363 (OUTLIER) cc_final: 0.4505 (ttp-110) REVERT: N 558 ASN cc_start: 0.7096 (m110) cc_final: 0.6813 (m110) REVERT: N 681 ASN cc_start: 0.7744 (m-40) cc_final: 0.7295 (m110) outliers start: 150 outliers final: 77 residues processed: 518 average time/residue: 0.2714 time to fit residues: 229.6727 Evaluate side-chains 459 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 361 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 676 ILE Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 255 LYS Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 369 LYS Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 65 ASN Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 350 GLN Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 671 LEU Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 356 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 445 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 353 optimal weight: 0.6980 chunk 415 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN E 38 ASN F 38 ASN F 65 ASN J 678 ASN N 65 ASN N 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.183538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112627 restraints weight = 49547.665| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.17 r_work: 0.3213 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43859 Z= 0.130 Angle : 0.522 8.454 60864 Z= 0.305 Chirality : 0.041 0.261 7035 Planarity : 0.004 0.062 6252 Dihedral : 20.475 164.920 9837 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.91 % Allowed : 20.96 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.32 (0.13), residues: 4104 helix: 1.94 (0.11), residues: 2146 sheet: 1.20 (0.22), residues: 558 loop : -0.99 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 664 TYR 0.018 0.001 TYR J 331 PHE 0.020 0.001 PHE B 195 TRP 0.009 0.001 TRP B 559 HIS 0.004 0.001 HIS N 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (43859) covalent geometry : angle 0.52246 / 0.31 (60864) hydrogen bonds : bond 0.04830 / 3.20 ( 1962) hydrogen bonds : angle 3.94595 / 2.79 ( 5438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 378 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7766 (mtpp) REVERT: A 21 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 102 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8071 (t) REVERT: A 156 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5696 (tppt) REVERT: B 21 ASP cc_start: 0.7935 (t0) cc_final: 0.7529 (t0) REVERT: B 260 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7257 (tttm) REVERT: B 307 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7141 (t80) REVERT: B 350 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8282 (pt0) REVERT: B 451 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7584 (tt) REVERT: B 516 LYS cc_start: 0.6804 (mmmm) cc_final: 0.6603 (mmtp) REVERT: B 551 GLN cc_start: 0.7762 (mp10) cc_final: 0.7472 (mp10) REVERT: B 558 ASN cc_start: 0.8016 (m110) cc_final: 0.7707 (m110) REVERT: B 565 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6164 (mp) REVERT: B 626 ASN cc_start: 0.5528 (m-40) cc_final: 0.5080 (m110) REVERT: B 643 VAL cc_start: 0.7461 (t) cc_final: 0.7258 (m) REVERT: B 683 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.4587 (mm-30) REVERT: B 711 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7431 (p) REVERT: B 721 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: E 150 TYR cc_start: 0.7856 (t80) cc_final: 0.7654 (t80) REVERT: E 160 MET cc_start: 0.8043 (mtp) cc_final: 0.7369 (mtp) REVERT: E 239 ILE cc_start: 0.8357 (mm) cc_final: 0.8099 (mt) REVERT: F 260 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7352 (tttm) REVERT: F 509 MET cc_start: 0.4816 (ttt) cc_final: 0.4529 (ttp) REVERT: F 516 LYS cc_start: 0.5972 (mmmt) cc_final: 0.5342 (ttpp) REVERT: F 517 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6661 (ppt170) REVERT: F 542 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.7025 (p) REVERT: F 710 THR cc_start: 0.8166 (t) cc_final: 0.7854 (p) REVERT: I 296 LYS cc_start: 0.7238 (mmtt) cc_final: 0.7022 (mmtt) REVERT: J 33 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6329 (m110) REVERT: J 87 LYS cc_start: 0.7967 (mttt) cc_final: 0.7572 (pptt) REVERT: J 160 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: J 234 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6529 (mtpp) REVERT: J 359 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8195 (mmtt) REVERT: J 529 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7966 (ttmm) REVERT: J 542 THR cc_start: 0.6731 (OUTLIER) cc_final: 0.6471 (p) REVERT: J 558 ASN cc_start: 0.7823 (m-40) cc_final: 0.7466 (m110) REVERT: J 565 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5310 (mp) REVERT: J 642 ILE cc_start: 0.7866 (mt) cc_final: 0.7613 (tt) REVERT: M 21 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: M 203 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8967 (tt) REVERT: M 253 GLU cc_start: 0.8203 (pt0) cc_final: 0.7884 (pt0) REVERT: N 102 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8384 (tttm) REVERT: N 199 LYS cc_start: 0.8359 (mttm) cc_final: 0.7744 (mtpt) REVERT: N 323 LYS cc_start: 0.8559 (mtpm) cc_final: 0.8247 (mtmt) REVERT: N 422 ASP cc_start: 0.8358 (m-30) cc_final: 0.8074 (t70) REVERT: N 509 MET cc_start: 0.4632 (tmm) cc_final: 0.4298 (tmm) REVERT: N 517 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.4558 (ttm110) REVERT: N 558 ASN cc_start: 0.7021 (m110) cc_final: 0.6697 (m110) REVERT: N 681 ASN cc_start: 0.7600 (m-40) cc_final: 0.7158 (m110) outliers start: 113 outliers final: 61 residues processed: 478 average time/residue: 0.2807 time to fit residues: 218.0888 Evaluate side-chains 436 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 353 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 564 ILE Chi-restraints excluded: chain N residue 671 LEU Chi-restraints excluded: chain N residue 698 VAL Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 160 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 215 optimal weight: 50.0000 chunk 217 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 430 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 GLN B 384 ASN E 38 ASN E 364 HIS F 65 ASN F 267 HIS I 56 ASN J 678 ASN N 65 ASN N 351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108632 restraints weight = 49635.751| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.07 r_work: 0.3164 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 43859 Z= 0.213 Angle : 0.600 10.429 60864 Z= 0.341 Chirality : 0.044 0.261 7035 Planarity : 0.004 0.056 6252 Dihedral : 20.469 167.505 9831 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.63 % Allowed : 20.75 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.00 (0.13), residues: 4104 helix: 1.70 (0.11), residues: 2147 sheet: 1.00 (0.22), residues: 556 loop : -1.14 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 664 TYR 0.021 0.002 TYR J 331 PHE 0.025 0.002 PHE F 277 TRP 0.009 0.001 TRP B 559 HIS 0.007 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (43859) covalent geometry : angle 0.59958 / 0.34 (60864) hydrogen bonds : bond 0.05909 / 3.91 ( 1962) hydrogen bonds : angle 4.07074 / 2.88 ( 5438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 369 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7849 (mtpp) REVERT: A 21 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: A 156 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5827 (tppt) REVERT: B 21 ASP cc_start: 0.7989 (t0) cc_final: 0.7624 (t0) REVERT: B 260 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7215 (tttm) REVERT: B 307 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7108 (t80) REVERT: B 350 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: B 451 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7523 (tt) REVERT: B 532 ARG cc_start: 0.7937 (tpt170) cc_final: 0.7712 (tpm170) REVERT: B 551 GLN cc_start: 0.7772 (mp10) cc_final: 0.7435 (mp10) REVERT: B 558 ASN cc_start: 0.8078 (m110) cc_final: 0.7696 (m110) REVERT: B 565 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6224 (mp) REVERT: B 626 ASN cc_start: 0.5449 (m-40) cc_final: 0.5118 (m-40) REVERT: B 711 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 721 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: E 239 ILE cc_start: 0.8543 (mm) cc_final: 0.8291 (mt) REVERT: F 260 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7284 (tttm) REVERT: F 350 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: F 509 MET cc_start: 0.4871 (ttt) cc_final: 0.4583 (ttp) REVERT: F 516 LYS cc_start: 0.6252 (mmmt) cc_final: 0.5564 (ttpp) REVERT: F 517 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6734 (ppt170) REVERT: F 542 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7052 (p) REVERT: F 710 THR cc_start: 0.8233 (t) cc_final: 0.7894 (p) REVERT: I 134 ILE cc_start: 0.7813 (mm) cc_final: 0.7572 (mm) REVERT: I 255 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8342 (mppt) REVERT: I 296 LYS cc_start: 0.7398 (mmtt) cc_final: 0.7192 (mmtt) REVERT: J 234 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6540 (mtpp) REVERT: J 295 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8292 (mp) REVERT: J 359 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8155 (mmtt) REVERT: J 470 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6913 (t80) REVERT: J 529 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8177 (ttmm) REVERT: J 542 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6517 (p) REVERT: J 565 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.4921 (mm) REVERT: J 642 ILE cc_start: 0.7870 (mt) cc_final: 0.7595 (tt) REVERT: M 21 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: M 203 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9056 (tt) REVERT: N 102 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (tttm) REVERT: N 199 LYS cc_start: 0.8304 (mttm) cc_final: 0.7749 (mtpt) REVERT: N 323 LYS cc_start: 0.8564 (mtpm) cc_final: 0.8272 (mtmt) REVERT: N 350 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: N 422 ASP cc_start: 0.8362 (m-30) cc_final: 0.8069 (t70) REVERT: N 509 MET cc_start: 0.4563 (tmm) cc_final: 0.4234 (tmm) REVERT: N 517 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.4558 (ttm110) REVERT: N 558 ASN cc_start: 0.7077 (m110) cc_final: 0.6698 (m110) REVERT: N 681 ASN cc_start: 0.7660 (m-40) cc_final: 0.7219 (m110) outliers start: 141 outliers final: 82 residues processed: 492 average time/residue: 0.2735 time to fit residues: 218.5907 Evaluate side-chains 448 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 344 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 564 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 676 ILE Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 350 GLN Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 452 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 643 VAL Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 167 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 290 optimal weight: 0.0770 chunk 256 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 267 HIS J 678 ASN N 351 GLN N 703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.182360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112262 restraints weight = 49273.766| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43859 Z= 0.119 Angle : 0.513 7.877 60864 Z= 0.299 Chirality : 0.040 0.255 7035 Planarity : 0.004 0.060 6252 Dihedral : 20.479 168.404 9829 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.73 % Allowed : 21.71 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.26 (0.13), residues: 4104 helix: 1.93 (0.11), residues: 2147 sheet: 1.16 (0.22), residues: 552 loop : -1.07 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 664 TYR 0.018 0.001 TYR J 331 PHE 0.021 0.001 PHE B 195 TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (43859) covalent geometry : angle 0.51301 / 0.30 (60864) hydrogen bonds : bond 0.04533 / 3.00 ( 1962) hydrogen bonds : angle 3.90332 / 2.76 ( 5438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 369 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7887 (mtpp) REVERT: A 21 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: A 102 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8064 (t) REVERT: B 21 ASP cc_start: 0.7920 (t0) cc_final: 0.7528 (t0) REVERT: B 260 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7202 (tttm) REVERT: B 307 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 350 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: B 451 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (tt) REVERT: B 542 THR cc_start: 0.7992 (m) cc_final: 0.7480 (p) REVERT: B 551 GLN cc_start: 0.7779 (mp10) cc_final: 0.7488 (mp10) REVERT: B 558 ASN cc_start: 0.8087 (m110) cc_final: 0.7674 (m110) REVERT: B 565 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6254 (mp) REVERT: B 626 ASN cc_start: 0.5395 (m-40) cc_final: 0.5075 (m-40) REVERT: B 648 LEU cc_start: 0.6830 (mm) cc_final: 0.6579 (mm) REVERT: B 711 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7464 (p) REVERT: B 721 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: E 160 MET cc_start: 0.7953 (mtp) cc_final: 0.7441 (mtp) REVERT: E 239 ILE cc_start: 0.8358 (mm) cc_final: 0.8065 (mt) REVERT: F 260 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7265 (tttm) REVERT: F 509 MET cc_start: 0.4720 (ttt) cc_final: 0.4460 (ttp) REVERT: F 516 LYS cc_start: 0.6172 (mmmt) cc_final: 0.5501 (ttpp) REVERT: F 517 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6883 (ppt170) REVERT: F 542 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.7006 (p) REVERT: F 683 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: I 134 ILE cc_start: 0.7649 (mm) cc_final: 0.7439 (mm) REVERT: I 296 LYS cc_start: 0.7241 (mmtt) cc_final: 0.7009 (mmtt) REVERT: J 33 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6159 (m-40) REVERT: J 87 LYS cc_start: 0.7918 (mttt) cc_final: 0.7545 (pptt) REVERT: J 160 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: J 359 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8154 (mmtt) REVERT: J 470 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6917 (t80) REVERT: J 529 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8139 (ttmm) REVERT: J 542 THR cc_start: 0.6635 (OUTLIER) cc_final: 0.6406 (p) REVERT: J 558 ASN cc_start: 0.7845 (m-40) cc_final: 0.7542 (m110) REVERT: J 565 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5011 (mt) REVERT: J 642 ILE cc_start: 0.7848 (mt) cc_final: 0.7568 (tt) REVERT: J 678 ASN cc_start: 0.7979 (m-40) cc_final: 0.7499 (m110) REVERT: J 683 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: J 735 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7330 (mm-30) REVERT: M 21 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: M 203 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8947 (tt) REVERT: N 199 LYS cc_start: 0.8290 (mttm) cc_final: 0.7745 (mtpt) REVERT: N 323 LYS cc_start: 0.8577 (mtpm) cc_final: 0.8261 (mtmt) REVERT: N 422 ASP cc_start: 0.8345 (m-30) cc_final: 0.8060 (t70) REVERT: N 509 MET cc_start: 0.4629 (tmm) cc_final: 0.4308 (tmm) REVERT: N 517 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.4491 (ttp80) REVERT: N 558 ASN cc_start: 0.7110 (m110) cc_final: 0.6684 (m110) REVERT: N 679 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.5518 (t80) REVERT: N 681 ASN cc_start: 0.7646 (m-40) cc_final: 0.7212 (m110) outliers start: 106 outliers final: 64 residues processed: 461 average time/residue: 0.2692 time to fit residues: 202.4759 Evaluate side-chains 437 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 351 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 683 GLU Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 643 VAL Chi-restraints excluded: chain N residue 671 LEU Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 384 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 38 ASN F 65 ASN M 30 GLN N 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126109 restraints weight = 50176.315| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.32 r_work: 0.3193 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 43859 Z= 0.203 Angle : 0.590 11.034 60864 Z= 0.334 Chirality : 0.043 0.256 7035 Planarity : 0.004 0.057 6252 Dihedral : 20.427 168.249 9817 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.99 % Allowed : 21.71 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.00 (0.13), residues: 4104 helix: 1.75 (0.11), residues: 2149 sheet: 0.94 (0.22), residues: 552 loop : -1.20 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 664 TYR 0.026 0.002 TYR N 484 PHE 0.024 0.002 PHE F 277 TRP 0.007 0.001 TRP N 169 HIS 0.007 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (43859) covalent geometry : angle 0.59029 / 0.33 (60864) hydrogen bonds : bond 0.05622 / 3.72 ( 1962) hydrogen bonds : angle 4.00958 / 2.84 ( 5438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 345 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7979 (mtpp) REVERT: A 21 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: B 21 ASP cc_start: 0.7767 (t0) cc_final: 0.7466 (t0) REVERT: B 260 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7394 (tttm) REVERT: B 307 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7113 (t80) REVERT: B 451 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7636 (tt) REVERT: B 551 GLN cc_start: 0.7875 (mp10) cc_final: 0.7631 (mp10) REVERT: B 558 ASN cc_start: 0.8172 (m110) cc_final: 0.7723 (m110) REVERT: B 565 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6408 (mp) REVERT: B 626 ASN cc_start: 0.5424 (m-40) cc_final: 0.5061 (m-40) REVERT: B 644 LEU cc_start: 0.7154 (tt) cc_final: 0.6468 (mp) REVERT: B 711 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7420 (p) REVERT: B 721 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: E 239 ILE cc_start: 0.8635 (mm) cc_final: 0.8361 (mt) REVERT: F 260 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7423 (tttm) REVERT: F 509 MET cc_start: 0.5030 (ttt) cc_final: 0.4699 (ttp) REVERT: F 516 LYS cc_start: 0.6236 (mmmt) cc_final: 0.5546 (ttpp) REVERT: F 542 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7282 (p) REVERT: F 565 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5762 (tt) REVERT: F 683 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: I 8 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7352 (tt) REVERT: J 87 LYS cc_start: 0.8015 (mttt) cc_final: 0.7593 (pptt) REVERT: J 160 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: J 234 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6696 (mtpp) REVERT: J 295 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8240 (mp) REVERT: J 359 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8173 (mmtt) REVERT: J 470 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7124 (t80) REVERT: J 529 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8181 (ttmm) REVERT: J 542 THR cc_start: 0.6918 (OUTLIER) cc_final: 0.6676 (p) REVERT: J 558 ASN cc_start: 0.8040 (m-40) cc_final: 0.7825 (m110) REVERT: J 565 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.4938 (mt) REVERT: J 642 ILE cc_start: 0.7970 (mt) cc_final: 0.7691 (tt) REVERT: J 678 ASN cc_start: 0.7996 (m-40) cc_final: 0.7541 (m110) REVERT: J 683 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: J 735 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7348 (mm-30) REVERT: M 203 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9056 (tt) REVERT: N 199 LYS cc_start: 0.8425 (mttm) cc_final: 0.7958 (mtpt) REVERT: N 313 THR cc_start: 0.7629 (t) cc_final: 0.7404 (p) REVERT: N 350 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: N 422 ASP cc_start: 0.8288 (m-30) cc_final: 0.8062 (t70) REVERT: N 509 MET cc_start: 0.4840 (tmm) cc_final: 0.4472 (tmm) REVERT: N 517 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4586 (ttp80) REVERT: N 550 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: N 558 ASN cc_start: 0.7254 (m110) cc_final: 0.6847 (m110) REVERT: N 681 ASN cc_start: 0.7925 (m-40) cc_final: 0.7467 (m110) outliers start: 116 outliers final: 77 residues processed: 446 average time/residue: 0.2634 time to fit residues: 191.4420 Evaluate side-chains 436 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 337 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 422 ASP Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 683 GLU Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 350 GLN Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 550 GLU Chi-restraints excluded: chain N residue 643 VAL Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 274 optimal weight: 0.9980 chunk 331 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 218 optimal weight: 20.0000 chunk 409 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 369 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 38 ASN N 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.185285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129049 restraints weight = 50186.559| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.33 r_work: 0.3239 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43859 Z= 0.125 Angle : 0.520 8.753 60864 Z= 0.302 Chirality : 0.040 0.251 7035 Planarity : 0.004 0.062 6252 Dihedral : 20.444 168.400 9817 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.58 % Allowed : 22.20 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.22 (0.13), residues: 4104 helix: 1.93 (0.11), residues: 2148 sheet: 1.03 (0.22), residues: 556 loop : -1.11 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 664 TYR 0.018 0.001 TYR J 331 PHE 0.023 0.001 PHE B 195 TRP 0.009 0.001 TRP B 559 HIS 0.004 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (43859) covalent geometry : angle 0.51970 / 0.30 (60864) hydrogen bonds : bond 0.04524 / 2.99 ( 1962) hydrogen bonds : angle 3.88356 / 2.74 ( 5438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 346 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7983 (mtpp) REVERT: A 21 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: A 102 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7998 (t) REVERT: B 21 ASP cc_start: 0.7709 (t0) cc_final: 0.7435 (t0) REVERT: B 260 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7414 (tttm) REVERT: B 294 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7419 (mmmt) REVERT: B 307 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 451 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7614 (tt) REVERT: B 551 GLN cc_start: 0.7923 (mp10) cc_final: 0.7711 (mp10) REVERT: B 558 ASN cc_start: 0.8175 (m110) cc_final: 0.7863 (m110) REVERT: B 565 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6421 (mp) REVERT: B 626 ASN cc_start: 0.5401 (m-40) cc_final: 0.5084 (m-40) REVERT: B 657 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7767 (mm-40) REVERT: B 683 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4211 (mm-30) REVERT: B 721 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: E 160 MET cc_start: 0.7929 (mtp) cc_final: 0.7560 (mtp) REVERT: E 239 ILE cc_start: 0.8476 (mm) cc_final: 0.8176 (mt) REVERT: F 260 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7428 (tttm) REVERT: F 509 MET cc_start: 0.4968 (ttt) cc_final: 0.4746 (ttp) REVERT: F 516 LYS cc_start: 0.6290 (mmmt) cc_final: 0.5602 (ttpp) REVERT: F 542 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7316 (p) REVERT: F 565 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5812 (tt) REVERT: F 683 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5855 (mp0) REVERT: I 8 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7244 (tt) REVERT: J 33 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6200 (m-40) REVERT: J 87 LYS cc_start: 0.7994 (mttt) cc_final: 0.7657 (pptt) REVERT: J 160 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: J 234 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6707 (mtpp) REVERT: J 359 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8194 (mmtt) REVERT: J 470 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7134 (t80) REVERT: J 481 PHE cc_start: 0.7198 (m-80) cc_final: 0.6944 (m-80) REVERT: J 529 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8184 (ttmm) REVERT: J 542 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6656 (p) REVERT: J 558 ASN cc_start: 0.8023 (m-40) cc_final: 0.7720 (m110) REVERT: J 565 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5006 (mt) REVERT: J 642 ILE cc_start: 0.7959 (mt) cc_final: 0.7675 (tt) REVERT: J 678 ASN cc_start: 0.7993 (m-40) cc_final: 0.7500 (m110) REVERT: J 683 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: J 735 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7349 (mm-30) REVERT: M 203 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8974 (tt) REVERT: M 244 GLU cc_start: 0.8921 (tt0) cc_final: 0.8707 (tt0) REVERT: N 199 LYS cc_start: 0.8415 (mttm) cc_final: 0.7973 (mtpt) REVERT: N 313 THR cc_start: 0.7503 (t) cc_final: 0.7257 (p) REVERT: N 323 LYS cc_start: 0.8643 (mtpm) cc_final: 0.8364 (mtmt) REVERT: N 509 MET cc_start: 0.4840 (tmm) cc_final: 0.4475 (tmm) REVERT: N 517 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.4608 (ttp80) REVERT: N 558 ASN cc_start: 0.7285 (m110) cc_final: 0.6868 (m110) REVERT: N 679 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5407 (t80) REVERT: N 681 ASN cc_start: 0.7886 (m-40) cc_final: 0.7442 (m110) outliers start: 100 outliers final: 67 residues processed: 433 average time/residue: 0.2768 time to fit residues: 194.2610 Evaluate side-chains 427 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 338 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 484 TYR Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 683 GLU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 105 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 183 ASN Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 192 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 389 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 366 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 393 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 426 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS B 384 ASN F 38 ASN F 65 ASN F 267 HIS N 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123688 restraints weight = 49410.711| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.17 r_work: 0.3201 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43859 Z= 0.205 Angle : 0.588 8.822 60864 Z= 0.333 Chirality : 0.043 0.251 7035 Planarity : 0.004 0.055 6252 Dihedral : 20.422 167.441 9817 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.55 % Allowed : 22.33 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.99 (0.13), residues: 4104 helix: 1.77 (0.11), residues: 2146 sheet: 0.89 (0.22), residues: 550 loop : -1.22 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 664 TYR 0.023 0.002 TYR J 307 PHE 0.023 0.002 PHE F 277 TRP 0.007 0.001 TRP J 173 HIS 0.007 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (43859) covalent geometry : angle 0.58765 / 0.33 (60864) hydrogen bonds : bond 0.05588 / 3.70 ( 1962) hydrogen bonds : angle 3.99489 / 2.82 ( 5438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 341 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8239 (mtpt) cc_final: 0.8008 (mtpp) REVERT: A 21 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: B 21 ASP cc_start: 0.8059 (t0) cc_final: 0.7756 (t0) REVERT: B 307 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 451 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 558 ASN cc_start: 0.8232 (m110) cc_final: 0.7923 (m110) REVERT: B 565 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6488 (mp) REVERT: B 644 LEU cc_start: 0.7329 (tt) cc_final: 0.6668 (mp) REVERT: B 657 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 685 PHE cc_start: 0.6811 (t80) cc_final: 0.6207 (p90) REVERT: B 721 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: E 239 ILE cc_start: 0.8723 (mm) cc_final: 0.8468 (mt) REVERT: F 350 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: F 509 MET cc_start: 0.5138 (ttt) cc_final: 0.4796 (ttp) REVERT: F 516 LYS cc_start: 0.6403 (mmmt) cc_final: 0.5634 (ttpp) REVERT: F 542 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7327 (p) REVERT: F 565 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5973 (tt) REVERT: F 683 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: I 8 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7410 (tt) REVERT: I 367 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7074 (mttt) REVERT: J 33 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6537 (m-40) REVERT: J 87 LYS cc_start: 0.8068 (mttt) cc_final: 0.7595 (pptt) REVERT: J 160 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: J 234 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7016 (mtpp) REVERT: J 359 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8227 (mmtt) REVERT: J 470 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7239 (t80) REVERT: J 529 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8326 (ttmm) REVERT: J 542 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6782 (p) REVERT: J 565 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.4889 (mt) REVERT: J 642 ILE cc_start: 0.7976 (mt) cc_final: 0.7709 (tt) REVERT: J 678 ASN cc_start: 0.8097 (m-40) cc_final: 0.7603 (m110) REVERT: J 683 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: J 735 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7569 (mm-30) REVERT: M 203 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9116 (tt) REVERT: N 199 LYS cc_start: 0.8484 (mttm) cc_final: 0.8024 (mtpt) REVERT: N 509 MET cc_start: 0.4733 (tmm) cc_final: 0.4348 (tmm) REVERT: N 517 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.4497 (ttp80) REVERT: N 558 ASN cc_start: 0.7343 (m110) cc_final: 0.6979 (m110) REVERT: N 679 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5479 (t80) REVERT: N 681 ASN cc_start: 0.7935 (m-40) cc_final: 0.7476 (m110) outliers start: 99 outliers final: 68 residues processed: 429 average time/residue: 0.2791 time to fit residues: 194.0469 Evaluate side-chains 419 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 330 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 GLN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 LEU Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 367 LYS Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 160 GLU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 275 THR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 452 ASP Chi-restraints excluded: chain J residue 470 PHE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 618 LEU Chi-restraints excluded: chain J residue 620 ILE Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 683 GLU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 236 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 183 ASN Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 298 SER Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 414 optimal weight: 0.0170 chunk 269 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 441 optimal weight: 20.0000 chunk 267 optimal weight: 0.0980 chunk 131 optimal weight: 0.6980 chunk 413 optimal weight: 0.0470 chunk 396 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN B 267 HIS B 351 GLN B 681 ASN E 38 ASN F 38 ASN F 267 HIS F 522 ASN J 351 GLN ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.185501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127939 restraints weight = 50564.968| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.30 r_work: 0.3238 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43859 Z= 0.112 Angle : 0.503 8.439 60864 Z= 0.291 Chirality : 0.039 0.293 7035 Planarity : 0.004 0.059 6252 Dihedral : 20.445 166.828 9817 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.88 % Allowed : 23.05 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.41 (0.13), residues: 4104 helix: 2.12 (0.11), residues: 2126 sheet: 1.13 (0.22), residues: 556 loop : -1.02 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 664 TYR 0.018 0.001 TYR N 331 PHE 0.023 0.001 PHE B 195 TRP 0.008 0.001 TRP B 559 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (43859) covalent geometry : angle 0.50302 / 0.29 (60864) hydrogen bonds : bond 0.03913 / 2.59 ( 1962) hydrogen bonds : angle 3.78931 / 2.68 ( 5438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12841.95 seconds wall clock time: 220 minutes 10.59 seconds (13210.59 seconds total)