Starting phenix.real_space_refine on Sun Jun 7 13:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tam_55751/06_2026/9tam_55751.map" } resolution = 2.96 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= 0.051 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Fe 32 7.16 5 P 18 5.49 5 S 265 5.16 5 C 24617 2.51 5 N 6174 2.21 5 O 7055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38164 Number of models: 1 Model: "" Number of chains: 37 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "I" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1185 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 135} Chain: "J" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1237 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "L" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4685 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} Chain: "N" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3673 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 463} Chain: "B" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1601 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2402 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "A" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'TRANS': 105} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' CA': 2, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' CA': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'3PE': 1, '7PH': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'3PE': 1, '7PH': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 310 Unusual residues: {'3PE': 4, 'UQ8': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'3PE': 2, '7PH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5407 SG CYS E 92 80.254 82.937 32.309 1.00 34.56 S ATOM 5441 SG CYS E 97 82.732 84.975 29.821 1.00 19.20 S ATOM 5745 SG CYS E 137 85.865 78.224 30.484 1.00 16.25 S ATOM 8701 SG CYS F 354 77.041 71.877 53.407 1.00 4.02 S ATOM 8721 SG CYS F 357 78.048 75.590 50.033 1.00 5.67 S ATOM 9042 SG CYS F 398 79.008 69.411 48.146 1.00 3.17 S ATOM 8677 SG CYS F 351 73.327 70.958 48.096 1.00 3.43 S ATOM 10236 SG CYS G 114 63.853 78.255 69.188 1.00 0.67 S ATOM 10176 SG CYS G 105 64.651 84.488 70.496 1.00 0.88 S ATOM 10196 SG CYS G 108 59.492 81.991 67.650 1.00 3.47 S ATOM 10590 SG CYS G 156 65.183 71.665 60.869 1.00 1.50 S ATOM 10571 SG CYS G 153 63.662 76.606 57.584 1.00 2.66 S ATOM 10619 SG CYS G 159 60.473 71.474 57.078 1.00 1.01 S ATOM 10967 SG CYS G 203 60.279 74.250 62.424 1.00 1.55 S ATOM 11192 SG CYS G 230 43.224 61.953 71.972 1.00 6.28 S ATOM 11477 SG CYS G 265 44.280 61.998 66.040 1.00 3.27 S ATOM 11240 SG CYS G 237 47.460 58.261 70.287 1.00 1.82 S ATOM 11216 SG CYS G 233 41.789 57.231 68.750 1.00 3.56 S ATOM 9637 SG CYS G 36 70.760 66.727 60.122 1.00 1.17 S ATOM 9713 SG CYS G 47 72.459 70.478 62.061 1.00 1.13 S ATOM 9739 SG CYS G 50 76.325 65.321 64.619 1.00 4.40 S ATOM 9888 SG CYS G 69 74.316 63.202 61.776 1.00 5.95 S ATOM 16989 SG CYS I 102 63.151 93.164 91.769 1.00 2.52 S ATOM 16964 SG CYS I 99 57.686 96.059 92.614 1.00 4.25 S ATOM 17007 SG CYS I 105 60.107 95.265 87.028 1.00 2.78 S ATOM 16722 SG CYS I 70 58.430 90.323 90.339 1.00 1.54 S ATOM 17036 SG CYS I 109 60.365 95.523 78.410 1.00 2.32 S ATOM 16699 SG CYS I 66 57.027 91.793 82.311 1.00 0.87 S ATOM 16659 SG CYS I 60 53.964 94.212 77.702 1.00 4.32 S ATOM 16677 SG CYS I 63 58.670 89.999 76.754 1.00 0.84 S ATOM 32786 SG CYS B 129 59.761 91.940 103.880 1.00 4.37 S ATOM 32343 SG CYS B 64 60.464 97.792 105.467 1.00 10.47 S ATOM 32337 SG CYS B 63 65.524 94.713 105.618 1.00 11.26 S ATOM 33003 SG CYS B 158 62.226 95.012 100.239 1.00 9.86 S Time building chain proxies: 9.53, per 1000 atoms: 0.25 Number of scatterers: 38164 At special positions: 0 Unit cell: (117.15, 160.05, 283.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 3 19.99 S 265 16.00 P 18 15.00 O 7055 8.00 N 6174 7.00 C 24617 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: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8618 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 27 sheets defined 60.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.524A pdb=" N GLY C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.320A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.513A pdb=" N GLY C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.507A pdb=" N THR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 268 through 274' Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.661A pdb=" N GLU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 300 through 330 Processing helix chain 'C' and resid 335 through 355 removed outlier: 3.916A pdb=" N THR C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 415 through 423 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 462 through 487 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'C' and resid 563 through 577 removed outlier: 4.048A pdb=" N ALA C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.731A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.039A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.793A pdb=" N GLY E 140 " --> pdb=" O CYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 164 removed outlier: 3.756A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 17 removed outlier: 4.280A pdb=" N ARG F 16 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.647A pdb=" N GLY F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.530A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.756A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.688A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.560A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.547A pdb=" N ILE F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.129A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.523A pdb=" N GLU F 406 " --> pdb=" O PRO F 402 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.695A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 150 through 153 Processing helix chain 'G' and resid 157 through 164 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.822A pdb=" N VAL G 181 " --> pdb=" O HIS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.337A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 265 through 271 Processing helix chain 'G' and resid 272 through 277 removed outlier: 3.556A pdb=" N LEU G 277 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 310 removed outlier: 3.665A pdb=" N ALA G 300 " --> pdb=" O ASN G 296 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN G 310 " --> pdb=" O ASP G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 344 through 360 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'G' and resid 383 through 388 Processing helix chain 'G' and resid 388 through 400 Processing helix chain 'G' and resid 400 through 410 removed outlier: 3.950A pdb=" N ARG G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 478 through 494 removed outlier: 3.541A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 3.935A pdb=" N ILE G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 547 Processing helix chain 'G' and resid 550 through 561 Processing helix chain 'G' and resid 578 through 589 Processing helix chain 'G' and resid 600 through 605 removed outlier: 3.504A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 618 removed outlier: 3.585A pdb=" N SER G 618 " --> pdb=" O PHE G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 664 Processing helix chain 'G' and resid 670 through 682 Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.738A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 Processing helix chain 'G' and resid 824 through 829 removed outlier: 3.868A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) Processing helix chain 'G' and resid 832 through 837 removed outlier: 4.174A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 845 through 853 Processing helix chain 'G' and resid 894 through 898 removed outlier: 3.548A pdb=" N ALA G 898 " --> pdb=" O PRO G 895 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.623A pdb=" N VAL I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 58 removed outlier: 3.709A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 73 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 79 through 85 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 89 through 113 removed outlier: 5.588A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.823A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 159 removed outlier: 3.561A pdb=" N SER J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.620A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 removed outlier: 3.662A pdb=" N ARG K 86 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.587A pdb=" N VAL K 95 " --> pdb=" O ILE K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 26 through 56 removed outlier: 3.529A pdb=" N ILE L 32 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.714A pdb=" N VAL L 91 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 Processing helix chain 'L' and resid 135 through 155 removed outlier: 3.621A pdb=" N GLY L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY L 147 " --> pdb=" O TRP L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 193 Processing helix chain 'L' and resid 203 through 208 Processing helix chain 'L' and resid 214 through 229 removed outlier: 3.762A pdb=" N GLY L 224 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY L 225 " --> pdb=" O MET L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 242 removed outlier: 4.290A pdb=" N ALA L 240 " --> pdb=" O GLN L 236 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA L 242 " --> pdb=" O TRP L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 254 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 269 through 275 Processing helix chain 'L' and resid 276 through 299 removed outlier: 4.121A pdb=" N LEU L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS L 281 " --> pdb=" O PRO L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 317 removed outlier: 3.782A pdb=" N GLY L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 325 removed outlier: 5.293A pdb=" N LEU L 323 " --> pdb=" O MET L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 337 Processing helix chain 'L' and resid 339 through 356 Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 367 through 371 removed outlier: 3.701A pdb=" N LYS L 370 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 388 Processing helix chain 'L' and resid 395 through 410 removed outlier: 4.245A pdb=" N GLU L 401 " --> pdb=" O PHE L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 429 removed outlier: 3.936A pdb=" N VAL L 416 " --> pdb=" O ILE L 412 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 417 " --> pdb=" O ASN L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 437 Processing helix chain 'L' and resid 453 through 464 Processing helix chain 'L' and resid 486 through 513 removed outlier: 4.371A pdb=" N GLY L 498 " --> pdb=" O GLU L 494 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 499 " --> pdb=" O ILE L 495 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 537 removed outlier: 3.844A pdb=" N ASN L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 549 removed outlier: 3.617A pdb=" N LEU L 544 " --> pdb=" O GLY L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 549 through 561 Processing helix chain 'L' and resid 563 through 569 Processing helix chain 'L' and resid 570 through 584 Processing helix chain 'L' and resid 585 through 587 No H-bonds generated for 'chain 'L' and resid 585 through 587' Processing helix chain 'L' and resid 590 through 613 Processing helix chain 'M' and resid 3 through 6 Processing helix chain 'M' and resid 7 through 18 Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 26 through 51 removed outlier: 3.867A pdb=" N GLY M 51 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 55 Processing helix chain 'M' and resid 84 through 105 Processing helix chain 'M' and resid 112 through 133 removed outlier: 4.067A pdb=" N PHE M 116 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.851A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 156 Processing helix chain 'M' and resid 163 through 201 removed outlier: 3.761A pdb=" N ARG M 167 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 234 removed outlier: 3.838A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 250 removed outlier: 3.857A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 275 removed outlier: 3.940A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.619A pdb=" N SER M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 removed outlier: 3.561A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY M 360 " --> pdb=" O PHE M 356 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR M 363 " --> pdb=" O CYS M 359 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG M 365 " --> pdb=" O GLN M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 396 removed outlier: 3.714A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 416 removed outlier: 6.548A pdb=" N MET M 409 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE M 410 " --> pdb=" O GLY M 406 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 444 removed outlier: 3.527A pdb=" N THR M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 489 removed outlier: 3.535A pdb=" N THR M 488 " --> pdb=" O PRO M 484 " (cutoff:3.500A) Processing helix chain 'M' and resid 489 through 502 Processing helix chain 'N' and resid 8 through 10 No H-bonds generated for 'chain 'N' and resid 8 through 10' Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 51 Processing helix chain 'N' and resid 51 through 59 Processing helix chain 'N' and resid 70 through 97 Proline residue: N 93 - end of helix removed outlier: 4.282A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 122 Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.894A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 182 Processing helix chain 'N' and resid 185 through 193 removed outlier: 3.604A pdb=" N LEU N 189 " --> pdb=" O PHE N 186 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY N 190 " --> pdb=" O VAL N 187 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS N 191 " --> pdb=" O ALA N 188 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN N 192 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 193 " --> pdb=" O GLY N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 218 removed outlier: 3.670A pdb=" N GLY N 213 " --> pdb=" O LEU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 261 removed outlier: 4.190A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 288 removed outlier: 3.872A pdb=" N ASN N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.675A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 312 " --> pdb=" O TYR N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.671A pdb=" N VAL N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 357 removed outlier: 4.080A pdb=" N ASP N 357 " --> pdb=" O PRO N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 369 through 384 Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.564A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 431 removed outlier: 4.079A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 432 through 434 No H-bonds generated for 'chain 'N' and resid 432 through 434' Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 481 Processing helix chain 'B' and resid 35 through 52 removed outlier: 3.955A pdb=" N ASN B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.553A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.613A pdb=" N LYS B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.585A pdb=" N TYR B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 removed outlier: 4.666A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 37 Processing helix chain 'H' and resid 55 through 69 removed outlier: 4.302A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 97 removed outlier: 3.693A pdb=" N LEU H 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) Proline residue: H 87 - end of helix removed outlier: 4.859A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 Processing helix chain 'H' and resid 115 through 137 removed outlier: 3.969A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.999A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.546A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 207 Processing helix chain 'H' and resid 231 through 257 removed outlier: 3.550A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR H 242 " --> pdb=" O PHE H 238 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 289 Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.562A pdb=" N ILE H 304 " --> pdb=" O PHE H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 325 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.549A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 6.320A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.152A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER C 97 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 79 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 99 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 77 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS C 101 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.631A pdb=" N VAL C 124 " --> pdb=" O ASP C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 217 through 219 removed outlier: 3.501A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 241 through 242 removed outlier: 3.665A pdb=" N SER C 579 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AA6, first strand: chain 'C' and resid 531 through 538 removed outlier: 3.503A pdb=" N ARG C 558 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 131 Processing sheet with id=AA8, first strand: chain 'F' and resid 168 through 173 Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.574A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET F 327 " --> pdb=" O TRP F 290 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP F 290 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL F 329 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.693A pdb=" N THR G 77 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AB3, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AB4, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AB5, first strand: chain 'G' and resid 224 through 225 removed outlier: 3.514A pdb=" N ARG G 250 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 292 through 294 removed outlier: 6.540A pdb=" N VAL G 592 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU G 610 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL G 594 " --> pdb=" O LEU G 610 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY G 316 " --> pdb=" O TYR G 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 447 through 450 removed outlier: 3.813A pdb=" N TRP G 447 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR G 532 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 500 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE G 534 " --> pdb=" O ILE G 500 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER G 502 " --> pdb=" O ILE G 534 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 620 through 623 Processing sheet with id=AB9, first strand: chain 'G' and resid 704 through 705 removed outlier: 6.500A pdb=" N LEU G 704 " --> pdb=" O THR G 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 870 through 871 removed outlier: 3.733A pdb=" N LYS G 906 " --> pdb=" O SER G 861 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER G 863 " --> pdb=" O ASP G 904 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE G 842 " --> pdb=" O GLU G 874 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.845A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AC5, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AC6, first strand: chain 'M' and resid 66 through 72 removed outlier: 3.647A pdb=" N TRP M 71 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.571A pdb=" N MET N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AC9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.618A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 123 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ILE B 155 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 125 " --> pdb=" O ILE B 155 " (cutoff:3.500A) 2010 hydrogen bonds defined for protein. 5796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 15734 1.41 - 1.63: 22413 1.63 - 1.85: 432 1.85 - 2.07: 0 2.07 - 2.30: 92 Bond restraints: 38671 Sorted by residual: bond pdb=" O11 7PH H 403 " pdb=" P 7PH H 403 " ideal model delta sigma weight residual 1.611 1.828 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O11 7PH J 203 " pdb=" P 7PH J 203 " ideal model delta sigma weight residual 1.611 1.827 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O11 7PH J 202 " pdb=" P 7PH J 202 " ideal model delta sigma weight residual 1.611 1.827 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" O11 7PH M 603 " pdb=" P 7PH M 603 " ideal model delta sigma weight residual 1.611 1.826 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" O11 7PH M 602 " pdb=" P 7PH M 602 " ideal model delta sigma weight residual 1.611 1.826 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 38666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.53: 52367 12.53 - 25.06: 10 25.06 - 37.60: 0 37.60 - 50.13: 0 50.13 - 62.66: 5 Bond angle restraints: 52382 Sorted by residual: angle pdb=" O13 7PH M 602 " pdb=" P 7PH M 602 " pdb=" O14 7PH M 602 " ideal model delta sigma weight residual 54.30 116.96 -62.66 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH J 202 " pdb=" P 7PH J 202 " pdb=" O14 7PH J 202 " ideal model delta sigma weight residual 54.30 116.92 -62.62 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH M 603 " pdb=" P 7PH M 603 " pdb=" O14 7PH M 603 " ideal model delta sigma weight residual 54.30 116.91 -62.61 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH H 403 " pdb=" P 7PH H 403 " pdb=" O14 7PH H 403 " ideal model delta sigma weight residual 54.30 116.85 -62.55 3.00e+00 1.11e-01 4.35e+02 angle pdb=" O13 7PH J 203 " pdb=" P 7PH J 203 " pdb=" O14 7PH J 203 " ideal model delta sigma weight residual 54.30 116.84 -62.54 3.00e+00 1.11e-01 4.35e+02 ... (remaining 52377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 21845 35.02 - 70.04: 990 70.04 - 105.06: 74 105.06 - 140.07: 4 140.07 - 175.09: 3 Dihedral angle restraints: 22916 sinusoidal: 9441 harmonic: 13475 Sorted by residual: dihedral pdb=" C20 UQ8 N 505 " pdb=" C19 UQ8 N 505 " pdb=" C21 UQ8 N 505 " pdb=" C22 UQ8 N 505 " ideal model delta sinusoidal sigma weight residual 289.14 114.05 175.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C41 UQ8 N 505 " pdb=" C42 UQ8 N 505 " pdb=" C43 UQ8 N 505 " pdb=" C44 UQ8 N 505 " ideal model delta sinusoidal sigma weight residual 114.10 -96.89 -149.01 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C41 UQ8 N 506 " pdb=" C42 UQ8 N 506 " pdb=" C43 UQ8 N 506 " pdb=" C44 UQ8 N 506 " ideal model delta sinusoidal sigma weight residual 114.10 -98.20 -147.70 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 22913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.227: 5769 4.227 - 8.453: 0 8.453 - 12.680: 0 12.680 - 16.906: 0 16.906 - 21.133: 28 Chirality restraints: 5797 Sorted by residual: chirality pdb="FE4 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S3 SF4 G1001 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.45 -21.00 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.43 -20.99 2.00e-01 2.50e+01 1.10e+04 ... (remaining 5794 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 34 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C GLY A 34 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY A 34 " -0.025 2.00e-02 2.50e+03 pdb=" N TRP A 35 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 95 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL L 95 " -0.061 2.00e-02 2.50e+03 pdb=" O VAL L 95 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY L 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 493 " -0.014 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C LEU L 493 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU L 493 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU L 494 " -0.018 2.00e-02 2.50e+03 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2727 2.74 - 3.28: 38110 3.28 - 3.82: 68992 3.82 - 4.36: 84330 4.36 - 4.90: 140612 Nonbonded interactions: 334771 Sorted by model distance: nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.197 3.040 nonbonded pdb=" O HOH G1181 " pdb=" O HOH G1184 " model vdw 2.202 3.040 nonbonded pdb=" O HOH G1168 " pdb=" O HOH G1189 " model vdw 2.230 3.040 nonbonded pdb=" O GLY N 385 " pdb=" O HOH N 601 " model vdw 2.230 3.040 nonbonded pdb=" O HOH G1110 " pdb=" O HOH G1114 " model vdw 2.248 3.040 ... (remaining 334766 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 30.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 42.920 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 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 : 0.012 0.721 38707 Z= 0.427 Angle : 1.070 62.662 52475 Z= 0.456 Chirality : 1.437 21.133 5797 Planarity : 0.005 0.117 6536 Dihedral : 18.341 175.093 14298 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 4.43 % Allowed : 20.90 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.88 (0.13), residues: 4683 helix: 1.52 (0.10), residues: 2562 sheet: 0.12 (0.32), residues: 282 loop : -0.65 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 529 TYR 0.017 0.001 TYR L 428 PHE 0.031 0.001 PHE H 268 TRP 0.013 0.001 TRP L 543 HIS 0.005 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.33 (38671) covalent geometry : angle 0.94570 / 0.45 (52382) hydrogen bonds : bond 0.14441 / 9.59 ( 2008) hydrogen bonds : angle 5.85636 / 4.16 ( 5796) metal coordination : bond 0.35506 / 21.31 ( 36) metal coordination : angle 11.91327 / 8.58 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 917 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.3485 (tt0) cc_final: 0.3241 (tt0) REVERT: C 333 MET cc_start: 0.4621 (ptt) cc_final: 0.4252 (ppp) REVERT: G 298 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: G 870 THR cc_start: 0.6315 (m) cc_final: 0.6029 (p) REVERT: I 32 MET cc_start: 0.4590 (mmt) cc_final: 0.3334 (ptp) REVERT: L 358 HIS cc_start: 0.5253 (p-80) cc_final: 0.4403 (t70) REVERT: L 433 ILE cc_start: 0.0988 (OUTLIER) cc_final: 0.0312 (mm) REVERT: L 440 LYS cc_start: 0.5822 (ttpp) cc_final: 0.5289 (pptt) REVERT: L 449 LYS cc_start: 0.4214 (tptp) cc_final: 0.2944 (ttmt) REVERT: M 97 LEU cc_start: 0.4136 (mt) cc_final: 0.3857 (mt) REVERT: M 323 MET cc_start: 0.2945 (mmm) cc_final: 0.2342 (mmm) REVERT: M 330 ILE cc_start: 0.3574 (mm) cc_final: 0.3343 (mm) REVERT: M 405 VAL cc_start: 0.4407 (OUTLIER) cc_final: 0.4202 (p) REVERT: B 45 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: B 190 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6425 (mt0) outliers start: 171 outliers final: 30 residues processed: 1042 average time/residue: 0.6650 time to fit residues: 859.8366 Evaluate side-chains 572 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 537 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 896 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain L residue 25 TRP Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 433 ILE Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 221 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.5980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 HIS ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN F 341 ASN G 54 GLN G 151 ASN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 482 GLN G 490 GLN G 571 ASN G 867 ASN J 75 ASN J 115 ASN K 91 ASN L 2 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 487 HIS M 206 ASN M 322 HIS M 348 HIS N 124 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 HIS ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.203277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.166993 restraints weight = 57828.568| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.13 r_work: 0.3986 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.255 38707 Z= 0.391 Angle : 2.513 50.910 52475 Z= 1.438 Chirality : 0.440 6.467 5797 Planarity : 0.005 0.064 6536 Dihedral : 11.073 165.228 5999 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 5.16 % Allowed : 25.00 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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 (0.12), residues: 4683 helix: 1.58 (0.10), residues: 2577 sheet: 0.02 (0.32), residues: 286 loop : -0.53 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 148 TYR 0.032 0.002 TYR M 435 PHE 0.029 0.002 PHE L 397 TRP 0.022 0.001 TRP M 63 HIS 0.013 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.39 (38671) covalent geometry : angle 2.19335 / 1.43 (52382) hydrogen bonds : bond 0.04070 / 2.73 ( 2008) hydrogen bonds : angle 4.83102 / 3.38 ( 5796) metal coordination : bond 0.03456 / 2.22 ( 36) metal coordination : angle 29.19879 / 20.22 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 603 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6517 (ttp) cc_final: 0.6289 (tpp) REVERT: C 135 ASN cc_start: 0.5325 (OUTLIER) cc_final: 0.4494 (t0) REVERT: C 155 LEU cc_start: 0.5902 (pt) cc_final: 0.5440 (mt) REVERT: C 200 LYS cc_start: 0.4306 (OUTLIER) cc_final: 0.4051 (ptmm) REVERT: C 333 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.3910 (ppp) REVERT: C 341 THR cc_start: 0.8012 (m) cc_final: 0.7775 (p) REVERT: E 143 MET cc_start: 0.7195 (ttp) cc_final: 0.6871 (tmm) REVERT: F 21 LYS cc_start: 0.4190 (mmmt) cc_final: 0.3807 (mmmt) REVERT: F 73 TRP cc_start: 0.7919 (m-10) cc_final: 0.7247 (m-10) REVERT: F 281 MET cc_start: 0.7070 (pmm) cc_final: 0.5832 (mpp) REVERT: G 287 ARG cc_start: 0.6541 (tmm160) cc_final: 0.5679 (ttp80) REVERT: G 298 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: G 499 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7738 (tp) REVERT: G 608 LEU cc_start: 0.8204 (tp) cc_final: 0.7619 (mp) REVERT: G 642 ASP cc_start: 0.7358 (t0) cc_final: 0.7060 (t0) REVERT: G 827 SER cc_start: 0.7555 (t) cc_final: 0.7083 (p) REVERT: G 870 THR cc_start: 0.7989 (m) cc_final: 0.7787 (p) REVERT: I 32 MET cc_start: 0.4399 (mmt) cc_final: 0.3135 (ptt) REVERT: L 1 MET cc_start: 0.5547 (tmm) cc_final: 0.5230 (tpp) REVERT: L 140 TYR cc_start: 0.5361 (t80) cc_final: 0.4783 (t80) REVERT: L 158 TYR cc_start: 0.6288 (p90) cc_final: 0.5924 (p90) REVERT: L 168 MET cc_start: 0.2959 (ttp) cc_final: 0.2674 (ttp) REVERT: L 358 HIS cc_start: 0.6300 (p-80) cc_final: 0.4874 (t70) REVERT: L 365 MET cc_start: 0.4310 (tmm) cc_final: 0.3965 (ttt) REVERT: L 399 LYS cc_start: 0.6366 (mmtm) cc_final: 0.6074 (tmtt) REVERT: L 440 LYS cc_start: 0.5598 (ttpp) cc_final: 0.4886 (pptt) REVERT: L 449 LYS cc_start: 0.4714 (tptp) cc_final: 0.3463 (ttmt) REVERT: L 545 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.5071 (m-80) REVERT: L 549 PHE cc_start: 0.5945 (m-80) cc_final: 0.4904 (m-10) REVERT: M 146 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5666 (ppp) REVERT: M 177 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3945 (t80) REVERT: M 357 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5000 (mm) REVERT: M 405 VAL cc_start: 0.4792 (OUTLIER) cc_final: 0.4518 (p) REVERT: M 456 GLU cc_start: 0.7338 (tt0) cc_final: 0.5515 (tm-30) REVERT: M 493 ILE cc_start: 0.7212 (mt) cc_final: 0.6863 (mm) REVERT: N 117 ILE cc_start: 0.7028 (mt) cc_final: 0.6757 (mt) REVERT: B 5 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5343 (tp) REVERT: B 45 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7845 (mmp) REVERT: B 200 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: H 80 ARG cc_start: 0.6469 (ptm160) cc_final: 0.6155 (ptm160) REVERT: H 88 MET cc_start: 0.8303 (mtp) cc_final: 0.7991 (mtp) REVERT: H 192 GLN cc_start: 0.7564 (mm110) cc_final: 0.7329 (mm110) REVERT: H 209 ARG cc_start: 0.6131 (mmm-85) cc_final: 0.5886 (mmm-85) REVERT: H 228 GLU cc_start: 0.7968 (tp30) cc_final: 0.7768 (tp30) REVERT: H 241 GLU cc_start: 0.8543 (tt0) cc_final: 0.7454 (mp0) REVERT: H 279 MET cc_start: 0.6281 (mtt) cc_final: 0.5865 (mtm) outliers start: 199 outliers final: 56 residues processed: 750 average time/residue: 0.5992 time to fit residues: 566.2194 Evaluate side-chains 573 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 15 PHE Chi-restraints excluded: chain L residue 25 TRP Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 432 MET Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 361 SER Chi-restraints excluded: chain N residue 476 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 79 optimal weight: 0.0040 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 456 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 314 optimal weight: 0.7980 chunk 204 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN G 151 ASN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 GLN G 348 GLN G 490 GLN G 505 ASN G 724 HIS J 75 ASN J 115 ASN L 135 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS M 322 HIS N 121 ASN N 404 GLN B 92 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169300 restraints weight = 58434.455| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.91 r_work: 0.3970 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38707 Z= 0.388 Angle : 2.500 50.586 52475 Z= 1.433 Chirality : 0.441 6.399 5797 Planarity : 0.004 0.057 6536 Dihedral : 10.485 154.935 5962 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 5.16 % Allowed : 25.29 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 1.08 (0.12), residues: 4683 helix: 1.66 (0.10), residues: 2580 sheet: -0.02 (0.31), residues: 287 loop : -0.48 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 430 TYR 0.031 0.002 TYR G 797 PHE 0.029 0.002 PHE L 183 TRP 0.041 0.001 TRP H 302 HIS 0.013 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.01135 / 0.39 (38671) covalent geometry : angle 2.18256 / 1.43 (52382) hydrogen bonds : bond 0.03760 / 2.51 ( 2008) hydrogen bonds : angle 4.60270 / 3.21 ( 5796) metal coordination : bond 0.03187 / 2.07 ( 36) metal coordination : angle 29.04133 / 20.09 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 562 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 ASN cc_start: 0.5533 (OUTLIER) cc_final: 0.4715 (t0) REVERT: C 155 LEU cc_start: 0.5930 (pt) cc_final: 0.5374 (mt) REVERT: C 333 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.3859 (ppp) REVERT: C 341 THR cc_start: 0.8037 (m) cc_final: 0.7765 (p) REVERT: C 394 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: C 399 LEU cc_start: 0.7198 (tt) cc_final: 0.6793 (pt) REVERT: E 143 MET cc_start: 0.7806 (ttp) cc_final: 0.7311 (tmm) REVERT: F 21 LYS cc_start: 0.4468 (mmmt) cc_final: 0.4097 (mmmt) REVERT: F 73 TRP cc_start: 0.7898 (m-10) cc_final: 0.7064 (m-10) REVERT: F 95 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: F 158 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7316 (ttpt) REVERT: F 281 MET cc_start: 0.6972 (pmm) cc_final: 0.5882 (mpp) REVERT: F 311 PHE cc_start: 0.6551 (m-80) cc_final: 0.6167 (m-80) REVERT: F 344 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7187 (tp30) REVERT: G 5 THR cc_start: 0.7314 (t) cc_final: 0.7004 (m) REVERT: G 287 ARG cc_start: 0.6748 (tmm160) cc_final: 0.5864 (ttp80) REVERT: G 298 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: G 482 GLN cc_start: 0.7326 (tp40) cc_final: 0.7117 (tp-100) REVERT: G 499 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7856 (tp) REVERT: G 608 LEU cc_start: 0.8370 (tp) cc_final: 0.7758 (mp) REVERT: G 642 ASP cc_start: 0.7372 (t0) cc_final: 0.7054 (t0) REVERT: G 827 SER cc_start: 0.7782 (t) cc_final: 0.7248 (p) REVERT: G 874 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: J 85 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7491 (ttp-110) REVERT: K 99 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7535 (mtp85) REVERT: L 140 TYR cc_start: 0.5300 (t80) cc_final: 0.4546 (t80) REVERT: L 168 MET cc_start: 0.3007 (ttp) cc_final: 0.2801 (ttp) REVERT: L 358 HIS cc_start: 0.6392 (p-80) cc_final: 0.5088 (t70) REVERT: L 365 MET cc_start: 0.4284 (tmm) cc_final: 0.3776 (ttm) REVERT: L 399 LYS cc_start: 0.6431 (mmtm) cc_final: 0.6162 (tmtt) REVERT: L 440 LYS cc_start: 0.5694 (ttpp) cc_final: 0.4948 (pptt) REVERT: L 449 LYS cc_start: 0.4850 (tptp) cc_final: 0.3627 (ttmt) REVERT: L 545 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: L 547 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7460 (mmmt) REVERT: L 549 PHE cc_start: 0.5868 (m-80) cc_final: 0.4864 (m-10) REVERT: M 5 TRP cc_start: 0.4650 (m-10) cc_final: 0.4325 (m-10) REVERT: M 65 SER cc_start: 0.6630 (OUTLIER) cc_final: 0.6144 (m) REVERT: M 69 MET cc_start: 0.6869 (tmm) cc_final: 0.6451 (tmm) REVERT: M 121 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.5036 (mmp) REVERT: M 145 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.5086 (tpp) REVERT: M 146 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5792 (ppp) REVERT: M 373 MET cc_start: 0.6611 (mmm) cc_final: 0.6215 (mpp) REVERT: M 456 GLU cc_start: 0.7344 (tt0) cc_final: 0.5449 (tm-30) REVERT: M 493 ILE cc_start: 0.7123 (mt) cc_final: 0.6898 (mm) REVERT: M 499 TRP cc_start: 0.6820 (t60) cc_final: 0.6551 (t60) REVERT: N 117 ILE cc_start: 0.7165 (mt) cc_final: 0.6911 (mt) REVERT: N 211 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7765 (mt) REVERT: B 44 ASP cc_start: 0.8182 (t0) cc_final: 0.7878 (t70) REVERT: B 45 MET cc_start: 0.8455 (ttp) cc_final: 0.7976 (mmp) REVERT: B 200 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: H 13 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8504 (tt) REVERT: H 16 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (tm) REVERT: H 88 MET cc_start: 0.8402 (mtp) cc_final: 0.8107 (mtp) REVERT: H 228 GLU cc_start: 0.8120 (tp30) cc_final: 0.7647 (tp30) REVERT: H 241 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7460 (mp0) REVERT: H 281 MET cc_start: 0.6854 (ppp) cc_final: 0.6641 (ppp) REVERT: A 98 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7092 (p) outliers start: 199 outliers final: 68 residues processed: 690 average time/residue: 0.6067 time to fit residues: 526.5151 Evaluate side-chains 587 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 502 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 25 TRP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 476 SER Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 108 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 360 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 269 optimal weight: 0.0970 chunk 442 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN G 302 GLN J 75 ASN J 115 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN N 46 ASN B 92 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 192 GLN H 312 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.199048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.166467 restraints weight = 57687.828| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.05 r_work: 0.3933 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38707 Z= 0.389 Angle : 2.500 50.641 52475 Z= 1.434 Chirality : 0.441 6.417 5797 Planarity : 0.004 0.083 6536 Dihedral : 10.298 150.426 5951 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 5.11 % Allowed : 25.54 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 1.03 (0.12), residues: 4683 helix: 1.61 (0.10), residues: 2578 sheet: 0.05 (0.32), residues: 281 loop : -0.53 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 600 TYR 0.028 0.002 TYR M 435 PHE 0.022 0.002 PHE E 122 TRP 0.023 0.001 TRP H 302 HIS 0.010 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.39 (38671) covalent geometry : angle 2.18277 / 1.43 (52382) hydrogen bonds : bond 0.03731 / 2.49 ( 2008) hydrogen bonds : angle 4.54771 / 3.17 ( 5796) metal coordination : bond 0.02947 / 1.90 ( 36) metal coordination : angle 29.02862 / 20.06 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 541 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6125 (tpp) REVERT: C 135 ASN cc_start: 0.5545 (OUTLIER) cc_final: 0.4708 (t0) REVERT: C 317 ASN cc_start: 0.8529 (t0) cc_final: 0.8083 (t0) REVERT: C 333 MET cc_start: 0.4357 (OUTLIER) cc_final: 0.3644 (ppp) REVERT: C 394 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: C 399 LEU cc_start: 0.7180 (tt) cc_final: 0.6787 (pt) REVERT: E 143 MET cc_start: 0.7871 (ttp) cc_final: 0.7432 (tmm) REVERT: F 21 LYS cc_start: 0.4775 (mmmt) cc_final: 0.4406 (mmmt) REVERT: F 73 TRP cc_start: 0.7947 (m-10) cc_final: 0.7046 (m-10) REVERT: F 95 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: F 158 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7334 (ttpt) REVERT: F 281 MET cc_start: 0.6939 (pmm) cc_final: 0.6056 (mpp) REVERT: F 311 PHE cc_start: 0.6439 (m-80) cc_final: 0.5952 (m-80) REVERT: F 312 GLU cc_start: 0.8295 (pm20) cc_final: 0.7650 (mp0) REVERT: F 344 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7328 (tp30) REVERT: G 287 ARG cc_start: 0.6882 (tmm160) cc_final: 0.5936 (ttp80) REVERT: G 298 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: G 482 GLN cc_start: 0.7258 (tp40) cc_final: 0.6958 (tp-100) REVERT: G 499 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8014 (tp) REVERT: G 608 LEU cc_start: 0.8367 (tp) cc_final: 0.7745 (mp) REVERT: G 642 ASP cc_start: 0.7456 (t0) cc_final: 0.7111 (t0) REVERT: G 740 MET cc_start: 0.8013 (ppp) cc_final: 0.7507 (ptp) REVERT: G 827 SER cc_start: 0.7762 (t) cc_final: 0.7471 (p) REVERT: G 868 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7034 (p) REVERT: G 874 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6437 (tp30) REVERT: J 84 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7236 (mm-30) REVERT: K 99 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7573 (mtp85) REVERT: L 53 PHE cc_start: 0.3804 (m-80) cc_final: 0.3413 (m-10) REVERT: L 140 TYR cc_start: 0.5559 (t80) cc_final: 0.5096 (t80) REVERT: L 158 TYR cc_start: 0.6185 (p90) cc_final: 0.5760 (p90) REVERT: L 340 PHE cc_start: -0.2274 (OUTLIER) cc_final: -0.2492 (p90) REVERT: L 358 HIS cc_start: 0.6406 (p-80) cc_final: 0.5117 (t70) REVERT: L 399 LYS cc_start: 0.6464 (mmtm) cc_final: 0.6173 (tmtt) REVERT: L 449 LYS cc_start: 0.4752 (tptp) cc_final: 0.3449 (mtmt) REVERT: L 549 PHE cc_start: 0.6006 (m-80) cc_final: 0.5757 (m-80) REVERT: L 581 LYS cc_start: 0.7697 (mmmt) cc_final: 0.7024 (mmpt) REVERT: M 5 TRP cc_start: 0.4659 (m-10) cc_final: 0.4258 (m-10) REVERT: M 65 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.5986 (m) REVERT: M 66 GLU cc_start: 0.7132 (tm-30) cc_final: 0.5414 (tp30) REVERT: M 69 MET cc_start: 0.6898 (tmm) cc_final: 0.6468 (tmm) REVERT: M 145 MET cc_start: 0.5351 (OUTLIER) cc_final: 0.5148 (tpp) REVERT: M 146 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5590 (ppp) REVERT: M 303 TRP cc_start: 0.4480 (OUTLIER) cc_final: 0.3991 (m-90) REVERT: M 357 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5399 (mm) REVERT: M 374 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4452 (pmt) REVERT: N 49 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7271 (mt) REVERT: N 100 ASP cc_start: 0.5278 (t0) cc_final: 0.5076 (t0) REVERT: N 117 ILE cc_start: 0.7373 (mt) cc_final: 0.7146 (mt) REVERT: N 211 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7677 (mt) REVERT: B 44 ASP cc_start: 0.8258 (t0) cc_final: 0.7964 (t70) REVERT: B 45 MET cc_start: 0.8577 (ttp) cc_final: 0.7950 (mmp) REVERT: B 142 VAL cc_start: 0.7778 (t) cc_final: 0.7570 (p) REVERT: B 170 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8064 (mpt) REVERT: B 200 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: H 13 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8542 (tt) REVERT: H 16 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8043 (tm) REVERT: H 80 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6122 (ptm160) REVERT: H 88 MET cc_start: 0.8383 (mtp) cc_final: 0.8050 (mtp) REVERT: H 228 GLU cc_start: 0.8072 (tp30) cc_final: 0.7678 (tp30) REVERT: H 241 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 98 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7172 (p) outliers start: 197 outliers final: 78 residues processed: 677 average time/residue: 0.5847 time to fit residues: 502.0577 Evaluate side-chains 609 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 506 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 TYR Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 361 SER Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 412 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 415 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 251 optimal weight: 0.7980 chunk 444 optimal weight: 3.9990 chunk 395 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 GLN G 574 HIS J 115 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS M 308 GLN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.197520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162798 restraints weight = 57423.445| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.13 r_work: 0.3911 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38707 Z= 0.392 Angle : 2.503 50.666 52475 Z= 1.435 Chirality : 0.441 6.413 5797 Planarity : 0.004 0.054 6536 Dihedral : 10.208 148.873 5949 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 5.01 % Allowed : 26.32 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.95 (0.12), residues: 4683 helix: 1.56 (0.10), residues: 2576 sheet: 0.06 (0.32), residues: 284 loop : -0.58 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 600 TYR 0.030 0.002 TYR L 264 PHE 0.029 0.002 PHE L 183 TRP 0.041 0.002 TRP N 470 HIS 0.034 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.39 (38671) covalent geometry : angle 2.18599 / 1.43 (52382) hydrogen bonds : bond 0.03789 / 2.53 ( 2008) hydrogen bonds : angle 4.51704 / 3.16 ( 5796) metal coordination : bond 0.03148 / 2.02 ( 36) metal coordination : angle 29.02159 / 20.04 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 531 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6232 (tpp) REVERT: C 135 ASN cc_start: 0.5576 (OUTLIER) cc_final: 0.4716 (t0) REVERT: C 140 GLU cc_start: 0.5965 (tt0) cc_final: 0.5528 (mt-10) REVERT: C 333 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.3732 (ppp) REVERT: C 394 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.5962 (m-80) REVERT: C 399 LEU cc_start: 0.7217 (tt) cc_final: 0.6804 (pt) REVERT: C 487 ASN cc_start: 0.7208 (m-40) cc_final: 0.6767 (m110) REVERT: C 528 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6210 (mtp) REVERT: E 143 MET cc_start: 0.7935 (ttp) cc_final: 0.7372 (tmm) REVERT: F 21 LYS cc_start: 0.4963 (mmmt) cc_final: 0.4611 (mmmt) REVERT: F 73 TRP cc_start: 0.8045 (m-10) cc_final: 0.7053 (m-10) REVERT: F 95 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: F 281 MET cc_start: 0.6937 (pmm) cc_final: 0.6230 (mpp) REVERT: F 311 PHE cc_start: 0.6322 (m-80) cc_final: 0.6014 (m-80) REVERT: F 344 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7263 (tp30) REVERT: G 247 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7677 (mt-10) REVERT: G 287 ARG cc_start: 0.6831 (tmm160) cc_final: 0.5672 (ttp80) REVERT: G 298 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: G 454 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: G 482 GLN cc_start: 0.7290 (tp40) cc_final: 0.6978 (tp-100) REVERT: G 499 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8193 (tp) REVERT: G 608 LEU cc_start: 0.8348 (tp) cc_final: 0.7681 (mp) REVERT: G 642 ASP cc_start: 0.7540 (t0) cc_final: 0.7213 (t0) REVERT: G 740 MET cc_start: 0.7994 (ppp) cc_final: 0.7603 (tmt) REVERT: G 827 SER cc_start: 0.7841 (t) cc_final: 0.7327 (p) REVERT: G 868 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7051 (p) REVERT: G 874 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6559 (tp30) REVERT: G 901 HIS cc_start: 0.6273 (p90) cc_final: 0.6028 (p90) REVERT: I 161 LYS cc_start: 0.4584 (ptmt) cc_final: 0.4291 (tttm) REVERT: K 46 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7374 (t80) REVERT: L 53 PHE cc_start: 0.3789 (m-80) cc_final: 0.3417 (m-10) REVERT: L 135 ASN cc_start: 0.2698 (OUTLIER) cc_final: 0.1670 (m110) REVERT: L 140 TYR cc_start: 0.5871 (t80) cc_final: 0.5297 (t80) REVERT: L 143 TRP cc_start: 0.3613 (t-100) cc_final: 0.3222 (t-100) REVERT: L 340 PHE cc_start: -0.2310 (OUTLIER) cc_final: -0.2540 (p90) REVERT: L 358 HIS cc_start: 0.6279 (p-80) cc_final: 0.5092 (t70) REVERT: L 399 LYS cc_start: 0.6579 (mmtm) cc_final: 0.6195 (tmtt) REVERT: L 449 LYS cc_start: 0.4769 (tptp) cc_final: 0.3437 (ttmt) REVERT: L 483 THR cc_start: 0.3034 (OUTLIER) cc_final: 0.2828 (t) REVERT: L 545 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.5106 (m-80) REVERT: L 549 PHE cc_start: 0.6262 (m-80) cc_final: 0.6014 (m-80) REVERT: L 568 MET cc_start: 0.6508 (tmm) cc_final: 0.6042 (ttm) REVERT: L 581 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7111 (mmpt) REVERT: M 5 TRP cc_start: 0.4656 (m-10) cc_final: 0.4175 (m-10) REVERT: M 65 SER cc_start: 0.6600 (OUTLIER) cc_final: 0.6002 (m) REVERT: M 146 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.4722 (ppp) REVERT: M 203 TRP cc_start: 0.6449 (OUTLIER) cc_final: 0.6063 (m-10) REVERT: M 265 LYS cc_start: 0.5437 (mmmt) cc_final: 0.5154 (mmmm) REVERT: M 291 MET cc_start: 0.5972 (mpp) cc_final: 0.5768 (mmt) REVERT: M 303 TRP cc_start: 0.4384 (OUTLIER) cc_final: 0.3876 (m-90) REVERT: M 323 MET cc_start: 0.4984 (mmm) cc_final: 0.3810 (mmm) REVERT: M 357 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5472 (mm) REVERT: M 373 MET cc_start: 0.6861 (mmm) cc_final: 0.6589 (mpp) REVERT: M 460 MET cc_start: 0.3275 (OUTLIER) cc_final: 0.2730 (pmt) REVERT: M 493 ILE cc_start: 0.7087 (mt) cc_final: 0.6833 (mm) REVERT: N 1 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5794 (ttm) REVERT: N 49 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7373 (mt) REVERT: N 200 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: N 211 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (mt) REVERT: B 44 ASP cc_start: 0.8254 (t70) cc_final: 0.8009 (t70) REVERT: B 45 MET cc_start: 0.8642 (ttp) cc_final: 0.8010 (mmp) REVERT: B 170 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7948 (mpt) REVERT: B 200 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: H 13 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (tt) REVERT: H 16 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8064 (tm) REVERT: H 148 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6563 (ptt180) REVERT: H 228 GLU cc_start: 0.8115 (tp30) cc_final: 0.7721 (tp30) REVERT: H 241 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: H 323 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6886 (mt0) REVERT: A 98 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7314 (p) outliers start: 193 outliers final: 86 residues processed: 663 average time/residue: 0.5901 time to fit residues: 497.0795 Evaluate side-chains 607 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 488 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 787 LEU Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 361 SER Chi-restraints excluded: chain N residue 476 SER Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 78 optimal weight: 7.9990 chunk 320 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN G 151 ASN G 302 GLN G 490 GLN G 574 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN J 115 ASN L 2 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 GLN H 312 ASN H 325 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.194006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160901 restraints weight = 56974.801| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.99 r_work: 0.3862 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38707 Z= 0.398 Angle : 2.513 50.831 52475 Z= 1.439 Chirality : 0.442 6.512 5797 Planarity : 0.005 0.048 6536 Dihedral : 10.317 145.337 5947 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 5.78 % Allowed : 26.12 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.69 (0.12), residues: 4683 helix: 1.36 (0.10), residues: 2572 sheet: -0.05 (0.31), residues: 282 loop : -0.71 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 108 TYR 0.030 0.002 TYR N 423 PHE 0.025 0.002 PHE M 356 TRP 0.032 0.002 TRP H 302 HIS 0.011 0.002 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.40 (38671) covalent geometry : angle 2.19787 / 1.44 (52382) hydrogen bonds : bond 0.04135 / 2.76 ( 2008) hydrogen bonds : angle 4.57562 / 3.20 ( 5796) metal coordination : bond 0.03460 / 2.19 ( 36) metal coordination : angle 29.03042 / 20.02 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 545 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6566 (tpp) REVERT: C 135 ASN cc_start: 0.5665 (OUTLIER) cc_final: 0.4810 (t0) REVERT: C 244 ASP cc_start: 0.3996 (OUTLIER) cc_final: 0.3078 (t0) REVERT: C 333 MET cc_start: 0.4305 (OUTLIER) cc_final: 0.3887 (ppp) REVERT: C 394 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: C 399 LEU cc_start: 0.7157 (tt) cc_final: 0.6747 (pt) REVERT: C 487 ASN cc_start: 0.7360 (m-40) cc_final: 0.6782 (m110) REVERT: C 488 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6044 (ttm) REVERT: C 528 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6320 (mtp) REVERT: E 143 MET cc_start: 0.7970 (ttp) cc_final: 0.7470 (tmm) REVERT: F 73 TRP cc_start: 0.8047 (m-10) cc_final: 0.6855 (m-10) REVERT: F 132 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5537 (tp) REVERT: F 221 THR cc_start: 0.7750 (m) cc_final: 0.7425 (p) REVERT: F 281 MET cc_start: 0.6910 (pmm) cc_final: 0.6451 (mpp) REVERT: F 312 GLU cc_start: 0.8253 (pm20) cc_final: 0.7714 (mp0) REVERT: F 333 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5684 (tp) REVERT: F 344 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7271 (tp30) REVERT: G 247 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7801 (mt-10) REVERT: G 287 ARG cc_start: 0.6836 (tmm160) cc_final: 0.5632 (ttp80) REVERT: G 298 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: G 306 ASP cc_start: 0.7153 (t0) cc_final: 0.6423 (t0) REVERT: G 482 GLN cc_start: 0.7292 (tp40) cc_final: 0.6962 (tp-100) REVERT: G 496 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7488 (mtpt) REVERT: G 608 LEU cc_start: 0.8312 (tp) cc_final: 0.7665 (mp) REVERT: G 642 ASP cc_start: 0.7721 (t0) cc_final: 0.7434 (t0) REVERT: G 740 MET cc_start: 0.8016 (ppp) cc_final: 0.7718 (tmt) REVERT: G 827 SER cc_start: 0.7902 (t) cc_final: 0.7373 (p) REVERT: G 868 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7155 (p) REVERT: G 874 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: G 901 HIS cc_start: 0.6161 (p90) cc_final: 0.5944 (p90) REVERT: J 75 ASN cc_start: 0.8267 (t0) cc_final: 0.8029 (t0) REVERT: J 84 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7277 (mm-30) REVERT: K 46 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7751 (t80) REVERT: K 62 TYR cc_start: 0.8661 (t80) cc_final: 0.8420 (t80) REVERT: L 52 PHE cc_start: 0.6398 (t80) cc_final: 0.6171 (t80) REVERT: L 53 PHE cc_start: 0.3805 (m-80) cc_final: 0.3427 (m-10) REVERT: L 107 MET cc_start: 0.4310 (mmm) cc_final: 0.3930 (mmm) REVERT: L 135 ASN cc_start: 0.2852 (OUTLIER) cc_final: 0.1963 (m110) REVERT: L 140 TYR cc_start: 0.6346 (t80) cc_final: 0.5863 (t80) REVERT: L 207 HIS cc_start: 0.4242 (t-90) cc_final: 0.3972 (t-170) REVERT: L 320 PHE cc_start: 0.6875 (m-80) cc_final: 0.5580 (m-80) REVERT: L 334 HIS cc_start: 0.2755 (OUTLIER) cc_final: 0.2351 (t70) REVERT: L 340 PHE cc_start: -0.2785 (OUTLIER) cc_final: -0.3041 (p90) REVERT: L 358 HIS cc_start: 0.6249 (p-80) cc_final: 0.5022 (t70) REVERT: L 399 LYS cc_start: 0.6660 (mmtm) cc_final: 0.6075 (tmtt) REVERT: L 432 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.5813 (mpt) REVERT: L 449 LYS cc_start: 0.4920 (tptp) cc_final: 0.3551 (ttmt) REVERT: L 483 THR cc_start: 0.2943 (OUTLIER) cc_final: 0.2722 (t) REVERT: L 545 TYR cc_start: 0.5657 (OUTLIER) cc_final: 0.5432 (m-80) REVERT: M 65 SER cc_start: 0.6826 (OUTLIER) cc_final: 0.6269 (m) REVERT: M 90 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6312 (mmp) REVERT: M 146 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5507 (ppp) REVERT: M 177 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.4330 (t80) REVERT: M 203 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: M 323 MET cc_start: 0.4787 (mmm) cc_final: 0.4474 (ppp) REVERT: M 374 MET cc_start: 0.5445 (pmt) cc_final: 0.4584 (pmt) REVERT: M 377 LEU cc_start: 0.4503 (mt) cc_final: 0.4300 (mp) REVERT: M 460 MET cc_start: 0.3434 (OUTLIER) cc_final: 0.2716 (pmt) REVERT: M 493 ILE cc_start: 0.7147 (mt) cc_final: 0.6852 (mm) REVERT: N 1 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.5547 (tmm) REVERT: N 43 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6537 (mp) REVERT: N 200 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: N 211 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7782 (mt) REVERT: N 376 MET cc_start: 0.7480 (tpt) cc_final: 0.7107 (mmp) REVERT: N 426 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6806 (mm) REVERT: B 45 MET cc_start: 0.8720 (ttp) cc_final: 0.8030 (mmp) REVERT: B 170 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7909 (mpt) REVERT: B 200 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 219 GLU cc_start: 0.5433 (mm-30) cc_final: 0.4968 (mm-30) REVERT: H 13 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8548 (tt) REVERT: H 16 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8118 (tm) REVERT: H 147 MET cc_start: 0.7245 (tpp) cc_final: 0.6958 (tpp) REVERT: H 209 ARG cc_start: 0.6585 (mmm-85) cc_final: 0.5650 (mmm-85) REVERT: H 228 GLU cc_start: 0.8193 (tp30) cc_final: 0.7864 (tp30) REVERT: H 241 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: H 281 MET cc_start: 0.6800 (ppp) cc_final: 0.6590 (ppp) REVERT: H 302 TRP cc_start: 0.6193 (m100) cc_final: 0.5981 (m100) REVERT: H 323 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6971 (mt0) REVERT: A 94 GLU cc_start: 0.8599 (mp0) cc_final: 0.8367 (mp0) REVERT: A 98 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (p) outliers start: 223 outliers final: 96 residues processed: 701 average time/residue: 0.5873 time to fit residues: 523.2594 Evaluate side-chains 621 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 489 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 787 LEU Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 896 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 334 HIS Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 MET Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 104 optimal weight: 0.6980 chunk 339 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 419 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 342 optimal weight: 0.6980 chunk 451 optimal weight: 0.9990 chunk 426 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 338 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN F 53 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN G 302 GLN G 490 GLN G 574 HIS I 115 GLN J 115 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN ** L 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.194381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160528 restraints weight = 56951.096| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.95 r_work: 0.3871 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38707 Z= 0.391 Angle : 2.511 50.660 52475 Z= 1.438 Chirality : 0.441 6.401 5797 Planarity : 0.004 0.072 6536 Dihedral : 10.238 141.926 5946 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 4.54 % Allowed : 28.29 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.70 (0.12), residues: 4683 helix: 1.37 (0.10), residues: 2571 sheet: -0.06 (0.31), residues: 288 loop : -0.71 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG L 108 TYR 0.058 0.002 TYR L 264 PHE 0.029 0.002 PHE C 63 TRP 0.034 0.001 TRP L 143 HIS 0.011 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.39 (38671) covalent geometry : angle 2.19605 / 1.43 (52382) hydrogen bonds : bond 0.03905 / 2.60 ( 2008) hydrogen bonds : angle 4.54998 / 3.17 ( 5796) metal coordination : bond 0.02835 / 1.82 ( 36) metal coordination : angle 29.01365 / 20.01 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 508 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6652 (tpp) REVERT: C 135 ASN cc_start: 0.5690 (OUTLIER) cc_final: 0.4862 (t0) REVERT: C 317 ASN cc_start: 0.8333 (t0) cc_final: 0.7887 (t0) REVERT: C 333 MET cc_start: 0.4372 (OUTLIER) cc_final: 0.3813 (ppp) REVERT: C 394 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5457 (m-80) REVERT: C 399 LEU cc_start: 0.7204 (tt) cc_final: 0.6778 (pt) REVERT: C 487 ASN cc_start: 0.7274 (m-40) cc_final: 0.6722 (m110) REVERT: C 488 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5628 (ttm) REVERT: C 528 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6354 (mtp) REVERT: E 143 MET cc_start: 0.7967 (ttp) cc_final: 0.7409 (tmm) REVERT: F 73 TRP cc_start: 0.8069 (m-10) cc_final: 0.6832 (m-10) REVERT: F 221 THR cc_start: 0.7790 (m) cc_final: 0.7475 (p) REVERT: F 281 MET cc_start: 0.6925 (pmm) cc_final: 0.6541 (mpp) REVERT: F 312 GLU cc_start: 0.8254 (pm20) cc_final: 0.7497 (mp0) REVERT: F 344 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7278 (tp30) REVERT: G 247 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7729 (mt-10) REVERT: G 287 ARG cc_start: 0.6799 (tmm160) cc_final: 0.5640 (ttp80) REVERT: G 298 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: G 306 ASP cc_start: 0.7130 (t0) cc_final: 0.6400 (t0) REVERT: G 482 GLN cc_start: 0.7300 (tp40) cc_final: 0.6968 (tp-100) REVERT: G 496 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7508 (mtpp) REVERT: G 608 LEU cc_start: 0.8326 (tp) cc_final: 0.7672 (mp) REVERT: G 740 MET cc_start: 0.7950 (ppp) cc_final: 0.7726 (tmt) REVERT: G 827 SER cc_start: 0.7827 (t) cc_final: 0.7277 (p) REVERT: G 868 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7147 (p) REVERT: G 874 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6448 (tp30) REVERT: I 153 MET cc_start: 0.7168 (mpt) cc_final: 0.6786 (mpt) REVERT: I 161 LYS cc_start: 0.5279 (tttm) cc_final: 0.4770 (ptmt) REVERT: J 75 ASN cc_start: 0.8310 (t0) cc_final: 0.8048 (t0) REVERT: J 84 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7293 (mm-30) REVERT: K 46 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7568 (t80) REVERT: L 1 MET cc_start: 0.5518 (tpp) cc_final: 0.4915 (tpt) REVERT: L 10 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7629 (tt) REVERT: L 53 PHE cc_start: 0.3760 (m-80) cc_final: 0.3403 (m-10) REVERT: L 88 MET cc_start: 0.1030 (ptt) cc_final: 0.0500 (ptm) REVERT: L 135 ASN cc_start: 0.2991 (OUTLIER) cc_final: 0.2118 (m110) REVERT: L 140 TYR cc_start: 0.6419 (t80) cc_final: 0.5881 (t80) REVERT: L 163 ASN cc_start: 0.6543 (m-40) cc_final: 0.6023 (t0) REVERT: L 200 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.4895 (pmm) REVERT: L 334 HIS cc_start: 0.2740 (OUTLIER) cc_final: 0.2096 (t70) REVERT: L 358 HIS cc_start: 0.6245 (p-80) cc_final: 0.4992 (t70) REVERT: L 399 LYS cc_start: 0.6656 (mmtm) cc_final: 0.6022 (tmtt) REVERT: L 432 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6168 (mtt) REVERT: L 440 LYS cc_start: 0.5679 (ttpp) cc_final: 0.5059 (tmmt) REVERT: L 449 LYS cc_start: 0.5000 (tptp) cc_final: 0.3597 (mtmt) REVERT: L 483 THR cc_start: 0.3147 (OUTLIER) cc_final: 0.2906 (t) REVERT: L 545 TYR cc_start: 0.5553 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: L 547 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7433 (mmmm) REVERT: M 45 GLN cc_start: 0.5722 (mm-40) cc_final: 0.5320 (mp10) REVERT: M 65 SER cc_start: 0.6887 (OUTLIER) cc_final: 0.6318 (m) REVERT: M 146 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.5449 (ppp) REVERT: M 177 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4439 (t80) REVERT: M 203 TRP cc_start: 0.6389 (OUTLIER) cc_final: 0.6071 (m-10) REVERT: M 303 TRP cc_start: 0.4340 (OUTLIER) cc_final: 0.3901 (m-90) REVERT: M 373 MET cc_start: 0.6780 (mmm) cc_final: 0.6443 (mpp) REVERT: M 374 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4521 (pmt) REVERT: M 460 MET cc_start: 0.3389 (OUTLIER) cc_final: 0.2601 (pmt) REVERT: M 493 ILE cc_start: 0.7130 (mt) cc_final: 0.6885 (mm) REVERT: N 1 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5287 (ttm) REVERT: N 100 ASP cc_start: 0.5777 (t0) cc_final: 0.5555 (t0) REVERT: N 200 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: N 211 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7632 (mt) REVERT: N 376 MET cc_start: 0.7380 (tpt) cc_final: 0.7146 (mmp) REVERT: N 388 MET cc_start: 0.6962 (mtm) cc_final: 0.6443 (pp-130) REVERT: B 45 MET cc_start: 0.8708 (ttp) cc_final: 0.7958 (mmp) REVERT: B 170 MET cc_start: 0.8270 (mpp) cc_final: 0.7864 (mpt) REVERT: B 200 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 219 GLU cc_start: 0.5428 (mm-30) cc_final: 0.5017 (mm-30) REVERT: H 13 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8512 (tt) REVERT: H 16 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8145 (tm) REVERT: H 148 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6928 (ppp80) REVERT: H 209 ARG cc_start: 0.6658 (mmm-85) cc_final: 0.5775 (mmm-85) REVERT: H 228 GLU cc_start: 0.8166 (tp30) cc_final: 0.7894 (tp30) REVERT: H 241 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: H 323 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7092 (mt0) REVERT: A 94 GLU cc_start: 0.8575 (mp0) cc_final: 0.8338 (mp0) REVERT: A 98 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7354 (p) REVERT: A 108 PHE cc_start: 0.7014 (t80) cc_final: 0.6629 (t80) outliers start: 175 outliers final: 86 residues processed: 633 average time/residue: 0.6265 time to fit residues: 500.3258 Evaluate side-chains 591 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 472 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 334 HIS Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 MET Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 75 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 180 optimal weight: 0.2980 chunk 232 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 348 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 309 optimal weight: 6.9990 chunk 403 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN F 53 GLN F 409 GLN G 49 GLN G 151 ASN G 490 GLN G 574 HIS G 901 HIS J 115 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.193694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.158855 restraints weight = 56537.175| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.17 r_work: 0.3855 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38707 Z= 0.395 Angle : 2.515 50.684 52475 Z= 1.440 Chirality : 0.441 6.410 5797 Planarity : 0.004 0.047 6536 Dihedral : 10.274 136.383 5946 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 4.54 % Allowed : 28.55 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.64 (0.12), residues: 4683 helix: 1.32 (0.10), residues: 2573 sheet: -0.09 (0.31), residues: 288 loop : -0.73 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 108 TYR 0.041 0.002 TYR L 264 PHE 0.026 0.002 PHE L 397 TRP 0.043 0.002 TRP F 15 HIS 0.014 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.39 (38671) covalent geometry : angle 2.20135 / 1.44 (52382) hydrogen bonds : bond 0.04020 / 2.67 ( 2008) hydrogen bonds : angle 4.58625 / 3.21 ( 5796) metal coordination : bond 0.03089 / 1.98 ( 36) metal coordination : angle 28.99294 / 19.99 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 496 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6692 (tpp) REVERT: C 135 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.4879 (t0) REVERT: C 216 MET cc_start: 0.4343 (mmm) cc_final: 0.4027 (mtt) REVERT: C 317 ASN cc_start: 0.8291 (t0) cc_final: 0.7865 (t0) REVERT: C 333 MET cc_start: 0.4297 (OUTLIER) cc_final: 0.3893 (ppp) REVERT: C 394 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.5591 (m-80) REVERT: C 399 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6802 (pt) REVERT: C 487 ASN cc_start: 0.7322 (m-40) cc_final: 0.6733 (m110) REVERT: C 488 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5495 (ttm) REVERT: C 528 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6704 (mmt) REVERT: E 143 MET cc_start: 0.8002 (ttp) cc_final: 0.7429 (tmm) REVERT: F 73 TRP cc_start: 0.8137 (m-10) cc_final: 0.6877 (m-10) REVERT: F 132 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5187 (tp) REVERT: F 221 THR cc_start: 0.7669 (m) cc_final: 0.7430 (p) REVERT: F 281 MET cc_start: 0.6906 (pmm) cc_final: 0.6571 (mpp) REVERT: F 312 GLU cc_start: 0.8273 (pm20) cc_final: 0.7590 (mp0) REVERT: F 333 ILE cc_start: 0.5896 (OUTLIER) cc_final: 0.5603 (tp) REVERT: F 344 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7328 (tp30) REVERT: G 247 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7790 (mt-10) REVERT: G 287 ARG cc_start: 0.6774 (tmm160) cc_final: 0.5693 (ttp80) REVERT: G 298 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: G 306 ASP cc_start: 0.7137 (t0) cc_final: 0.6388 (t0) REVERT: G 478 GLU cc_start: 0.6620 (mp0) cc_final: 0.6329 (mp0) REVERT: G 482 GLN cc_start: 0.7304 (tp40) cc_final: 0.6960 (tp-100) REVERT: G 496 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7516 (mtpp) REVERT: G 608 LEU cc_start: 0.8298 (tp) cc_final: 0.7658 (mp) REVERT: G 722 SER cc_start: 0.8541 (t) cc_final: 0.7926 (m) REVERT: G 740 MET cc_start: 0.7981 (ppp) cc_final: 0.7722 (tmt) REVERT: G 804 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7835 (tpp80) REVERT: G 827 SER cc_start: 0.7830 (t) cc_final: 0.7283 (p) REVERT: G 868 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7219 (p) REVERT: G 874 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6495 (tp30) REVERT: I 153 MET cc_start: 0.7179 (mpt) cc_final: 0.6825 (mpt) REVERT: J 75 ASN cc_start: 0.8311 (t0) cc_final: 0.8048 (t0) REVERT: K 46 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7643 (t80) REVERT: L 1 MET cc_start: 0.5472 (tpp) cc_final: 0.5077 (tpt) REVERT: L 10 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7545 (tt) REVERT: L 53 PHE cc_start: 0.3768 (m-80) cc_final: 0.3420 (m-10) REVERT: L 68 MET cc_start: 0.4816 (mpt) cc_final: 0.4391 (mpt) REVERT: L 88 MET cc_start: 0.0831 (ptt) cc_final: 0.0258 (ptm) REVERT: L 135 ASN cc_start: 0.3146 (OUTLIER) cc_final: 0.2316 (m110) REVERT: L 140 TYR cc_start: 0.6434 (t80) cc_final: 0.5872 (t80) REVERT: L 160 ASP cc_start: 0.5564 (t70) cc_final: 0.5353 (t70) REVERT: L 200 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.4907 (pmm) REVERT: L 357 HIS cc_start: 0.6750 (m-70) cc_final: 0.5884 (p-80) REVERT: L 399 LYS cc_start: 0.6663 (mmtm) cc_final: 0.6041 (tmtt) REVERT: L 440 LYS cc_start: 0.5622 (ttpp) cc_final: 0.5009 (tmmt) REVERT: L 449 LYS cc_start: 0.5043 (tptp) cc_final: 0.3619 (mtmt) REVERT: L 483 THR cc_start: 0.3151 (OUTLIER) cc_final: 0.2871 (t) REVERT: L 545 TYR cc_start: 0.5674 (OUTLIER) cc_final: 0.5470 (m-80) REVERT: L 547 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7454 (mmmm) REVERT: M 45 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5377 (mp10) REVERT: M 65 SER cc_start: 0.6944 (OUTLIER) cc_final: 0.6469 (m) REVERT: M 146 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5685 (ppp) REVERT: M 203 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.6136 (m-10) REVERT: M 374 MET cc_start: 0.5040 (OUTLIER) cc_final: 0.4412 (pmt) REVERT: M 460 MET cc_start: 0.3257 (OUTLIER) cc_final: 0.2435 (pmt) REVERT: M 493 ILE cc_start: 0.7125 (mt) cc_final: 0.6873 (mm) REVERT: N 1 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5424 (ttm) REVERT: N 43 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6547 (mp) REVERT: N 100 ASP cc_start: 0.6010 (t0) cc_final: 0.5778 (t0) REVERT: N 200 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: N 211 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7681 (mt) REVERT: N 388 MET cc_start: 0.6937 (mtm) cc_final: 0.6497 (pp-130) REVERT: B 45 MET cc_start: 0.8725 (ttp) cc_final: 0.7944 (mmp) REVERT: B 170 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7905 (mpt) REVERT: B 200 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 219 GLU cc_start: 0.5387 (mm-30) cc_final: 0.4968 (mm-30) REVERT: H 13 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8461 (tt) REVERT: H 16 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8136 (tm) REVERT: H 148 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.7024 (ppp80) REVERT: H 209 ARG cc_start: 0.6743 (mmm-85) cc_final: 0.5856 (mmm-85) REVERT: H 228 GLU cc_start: 0.8280 (tp30) cc_final: 0.7975 (tp30) REVERT: H 229 TYR cc_start: 0.8222 (m-80) cc_final: 0.8010 (m-80) REVERT: H 241 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7290 (mp0) REVERT: H 281 MET cc_start: 0.6876 (ppp) cc_final: 0.6611 (ppp) REVERT: H 323 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7197 (mt0) REVERT: A 68 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: A 88 TRP cc_start: 0.7678 (t60) cc_final: 0.6788 (t60) REVERT: A 94 GLU cc_start: 0.8616 (mp0) cc_final: 0.8370 (mp0) REVERT: A 98 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7396 (p) REVERT: A 108 PHE cc_start: 0.7036 (t80) cc_final: 0.6698 (t80) outliers start: 175 outliers final: 102 residues processed: 617 average time/residue: 0.6073 time to fit residues: 475.1401 Evaluate side-chains 604 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 467 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 478 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 414 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN F 377 GLN F 409 GLN G 151 ASN G 490 GLN G 574 HIS G 901 HIS J 115 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 HIS L 566 ASN L 570 ASN ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.193007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158843 restraints weight = 56965.577| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.98 r_work: 0.3849 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38707 Z= 0.397 Angle : 2.521 50.677 52475 Z= 1.442 Chirality : 0.441 6.407 5797 Planarity : 0.004 0.051 6536 Dihedral : 10.351 127.477 5946 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 4.36 % Allowed : 29.12 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.55 (0.12), residues: 4683 helix: 1.25 (0.10), residues: 2567 sheet: -0.17 (0.31), residues: 289 loop : -0.78 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 64 TYR 0.035 0.002 TYR L 264 PHE 0.036 0.002 PHE C 63 TRP 0.039 0.002 TRP H 302 HIS 0.013 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.40 (38671) covalent geometry : angle 2.20715 / 1.44 (52382) hydrogen bonds : bond 0.04114 / 2.73 ( 2008) hydrogen bonds : angle 4.63219 / 3.25 ( 5796) metal coordination : bond 0.03177 / 2.04 ( 36) metal coordination : angle 29.00524 / 19.97 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 491 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6769 (tpp) REVERT: C 135 ASN cc_start: 0.5655 (OUTLIER) cc_final: 0.4908 (t0) REVERT: C 216 MET cc_start: 0.4381 (mmm) cc_final: 0.4118 (mtt) REVERT: C 317 ASN cc_start: 0.8321 (t0) cc_final: 0.7901 (t0) REVERT: C 333 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.4014 (ppp) REVERT: C 394 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.5729 (m-80) REVERT: C 399 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6723 (pt) REVERT: C 528 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6332 (mmt) REVERT: C 592 ASP cc_start: 0.6844 (t0) cc_final: 0.5890 (p0) REVERT: E 143 MET cc_start: 0.8060 (ttp) cc_final: 0.7520 (tmm) REVERT: F 73 TRP cc_start: 0.8128 (m-10) cc_final: 0.6799 (m-10) REVERT: F 94 MET cc_start: 0.6248 (ttt) cc_final: 0.5934 (ttt) REVERT: F 132 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5182 (tp) REVERT: F 217 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7398 (t0) REVERT: F 221 THR cc_start: 0.7612 (m) cc_final: 0.7392 (p) REVERT: F 281 MET cc_start: 0.6852 (pmm) cc_final: 0.6625 (mpp) REVERT: F 312 GLU cc_start: 0.8160 (pm20) cc_final: 0.7516 (mp0) REVERT: F 344 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7365 (tp30) REVERT: F 377 GLN cc_start: 0.6739 (mt0) cc_final: 0.6196 (mt0) REVERT: F 427 PHE cc_start: 0.5550 (t80) cc_final: 0.5265 (t80) REVERT: G 247 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 287 ARG cc_start: 0.6807 (tmm160) cc_final: 0.5749 (ttp80) REVERT: G 298 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: G 306 ASP cc_start: 0.7234 (t0) cc_final: 0.6592 (t0) REVERT: G 478 GLU cc_start: 0.6601 (mp0) cc_final: 0.6239 (mp0) REVERT: G 482 GLN cc_start: 0.7405 (tp40) cc_final: 0.7030 (tp-100) REVERT: G 496 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7659 (mtpp) REVERT: G 497 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7018 (tttt) REVERT: G 608 LEU cc_start: 0.8264 (tp) cc_final: 0.7667 (mp) REVERT: G 722 SER cc_start: 0.8525 (t) cc_final: 0.7957 (m) REVERT: G 740 MET cc_start: 0.8015 (ppp) cc_final: 0.7788 (tmt) REVERT: G 804 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7776 (tpp80) REVERT: G 874 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: I 153 MET cc_start: 0.7220 (mpt) cc_final: 0.6887 (mpt) REVERT: J 75 ASN cc_start: 0.8333 (t0) cc_final: 0.8077 (t0) REVERT: K 46 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7667 (t80) REVERT: L 1 MET cc_start: 0.5391 (tpp) cc_final: 0.5037 (tpt) REVERT: L 10 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7573 (tt) REVERT: L 68 MET cc_start: 0.4977 (mpt) cc_final: 0.4578 (mpt) REVERT: L 88 MET cc_start: 0.0763 (ptt) cc_final: 0.0191 (ptm) REVERT: L 135 ASN cc_start: 0.3163 (OUTLIER) cc_final: 0.2409 (m110) REVERT: L 140 TYR cc_start: 0.6450 (t80) cc_final: 0.5908 (t80) REVERT: L 152 LEU cc_start: 0.5139 (mt) cc_final: 0.4652 (mt) REVERT: L 399 LYS cc_start: 0.6638 (mmtm) cc_final: 0.6067 (tmtt) REVERT: L 424 MET cc_start: 0.7155 (pmm) cc_final: 0.6702 (pmm) REVERT: L 432 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6423 (mtt) REVERT: L 483 THR cc_start: 0.3070 (OUTLIER) cc_final: 0.2816 (t) REVERT: L 545 TYR cc_start: 0.5706 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: L 563 ASP cc_start: 0.4872 (t0) cc_final: 0.3600 (p0) REVERT: L 581 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7143 (mmpt) REVERT: M 146 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5929 (ppp) REVERT: M 203 TRP cc_start: 0.6571 (OUTLIER) cc_final: 0.6197 (m-10) REVERT: M 374 MET cc_start: 0.5060 (pmt) cc_final: 0.4669 (pmt) REVERT: N 43 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6799 (mp) REVERT: N 100 ASP cc_start: 0.6074 (t0) cc_final: 0.5833 (t0) REVERT: N 200 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: N 211 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7685 (mt) REVERT: N 388 MET cc_start: 0.6918 (mtm) cc_final: 0.6479 (pp-130) REVERT: B 45 MET cc_start: 0.8729 (ttp) cc_final: 0.7909 (mmp) REVERT: B 170 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7988 (mpt) REVERT: B 197 MET cc_start: 0.7798 (mmp) cc_final: 0.7169 (mmm) REVERT: B 200 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 219 GLU cc_start: 0.5506 (mm-30) cc_final: 0.5101 (mm-30) REVERT: H 13 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8558 (tt) REVERT: H 16 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8216 (tm) REVERT: H 148 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7133 (ppp80) REVERT: H 209 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6071 (mmm-85) REVERT: H 228 GLU cc_start: 0.8255 (tp30) cc_final: 0.7987 (tp30) REVERT: H 241 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7377 (mp0) REVERT: H 323 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7245 (mt0) REVERT: A 68 PHE cc_start: 0.7547 (m-10) cc_final: 0.7313 (m-10) REVERT: A 88 TRP cc_start: 0.7799 (t60) cc_final: 0.7069 (t60) REVERT: A 94 GLU cc_start: 0.8611 (mp0) cc_final: 0.8398 (mp0) REVERT: A 108 PHE cc_start: 0.7205 (t80) cc_final: 0.6905 (t80) outliers start: 168 outliers final: 96 residues processed: 613 average time/residue: 0.6001 time to fit residues: 466.3936 Evaluate side-chains 588 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 465 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 MET Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 476 SER Chi-restraints excluded: chain N residue 478 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 22 optimal weight: 5.9990 chunk 331 optimal weight: 0.0270 chunk 87 optimal weight: 0.8980 chunk 433 optimal weight: 0.5980 chunk 258 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 308 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN E 142 ASN F 409 GLN G 151 ASN G 299 GLN G 465 HIS G 490 GLN G 574 HIS J 115 ASN K 82 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 566 ASN L 570 ASN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.194307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.160955 restraints weight = 56961.668| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.93 r_work: 0.3873 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38707 Z= 0.390 Angle : 2.518 50.625 52475 Z= 1.440 Chirality : 0.441 6.396 5797 Planarity : 0.004 0.048 6536 Dihedral : 10.199 121.402 5946 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 3.42 % Allowed : 29.93 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.62 (0.12), residues: 4683 helix: 1.30 (0.10), residues: 2576 sheet: -0.02 (0.32), residues: 279 loop : -0.76 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 64 TYR 0.036 0.002 TYR A 116 PHE 0.028 0.002 PHE G 78 TRP 0.048 0.001 TRP H 302 HIS 0.013 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.39 (38671) covalent geometry : angle 2.20397 / 1.44 (52382) hydrogen bonds : bond 0.03868 / 2.57 ( 2008) hydrogen bonds : angle 4.57005 / 3.20 ( 5796) metal coordination : bond 0.02687 / 1.72 ( 36) metal coordination : angle 29.02347 / 20.01 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 494 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6733 (tpp) REVERT: C 135 ASN cc_start: 0.5550 (OUTLIER) cc_final: 0.4927 (t0) REVERT: C 216 MET cc_start: 0.4440 (mmm) cc_final: 0.4182 (mtt) REVERT: C 317 ASN cc_start: 0.8246 (t0) cc_final: 0.7842 (t0) REVERT: C 333 MET cc_start: 0.4199 (OUTLIER) cc_final: 0.3914 (ppp) REVERT: C 390 ARG cc_start: 0.5476 (tpt-90) cc_final: 0.4553 (ttt-90) REVERT: C 394 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.5638 (m-80) REVERT: C 399 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6710 (pt) REVERT: C 528 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6330 (mmt) REVERT: C 592 ASP cc_start: 0.6842 (t0) cc_final: 0.5955 (p0) REVERT: E 143 MET cc_start: 0.8011 (ttp) cc_final: 0.7559 (tmm) REVERT: F 52 ASN cc_start: 0.8189 (m-40) cc_final: 0.7914 (t160) REVERT: F 73 TRP cc_start: 0.8103 (m-10) cc_final: 0.6837 (m-10) REVERT: F 132 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5145 (tp) REVERT: F 217 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (t0) REVERT: F 221 THR cc_start: 0.7605 (m) cc_final: 0.7374 (p) REVERT: F 281 MET cc_start: 0.6775 (pmm) cc_final: 0.6523 (mpp) REVERT: F 312 GLU cc_start: 0.8160 (pm20) cc_final: 0.7521 (mp0) REVERT: F 333 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5430 (tp) REVERT: F 344 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7312 (tp30) REVERT: F 377 GLN cc_start: 0.6770 (mt0) cc_final: 0.6539 (mt0) REVERT: F 427 PHE cc_start: 0.5550 (t80) cc_final: 0.5313 (t80) REVERT: G 247 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7715 (mt-10) REVERT: G 287 ARG cc_start: 0.6707 (tmm160) cc_final: 0.5631 (ttp80) REVERT: G 298 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: G 306 ASP cc_start: 0.7115 (t0) cc_final: 0.6420 (t70) REVERT: G 478 GLU cc_start: 0.6602 (mp0) cc_final: 0.6261 (mp0) REVERT: G 482 GLN cc_start: 0.7392 (tp40) cc_final: 0.7042 (tp-100) REVERT: G 496 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7668 (mtpp) REVERT: G 608 LEU cc_start: 0.8262 (tp) cc_final: 0.7658 (mp) REVERT: G 722 SER cc_start: 0.8501 (t) cc_final: 0.7896 (m) REVERT: G 804 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7796 (tpp80) REVERT: I 153 MET cc_start: 0.7183 (mpt) cc_final: 0.6833 (mpt) REVERT: J 2 GLU cc_start: 0.6516 (mp0) cc_final: 0.6189 (mt-10) REVERT: J 75 ASN cc_start: 0.8321 (t0) cc_final: 0.8075 (t0) REVERT: J 86 GLN cc_start: 0.6818 (mt0) cc_final: 0.6021 (pm20) REVERT: K 46 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7472 (t80) REVERT: K 99 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: L 10 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7629 (tt) REVERT: L 68 MET cc_start: 0.4825 (mpt) cc_final: 0.4402 (mpt) REVERT: L 88 MET cc_start: 0.0736 (ptt) cc_final: 0.0128 (ptm) REVERT: L 113 TYR cc_start: 0.4153 (p90) cc_final: 0.3801 (p90) REVERT: L 135 ASN cc_start: 0.3111 (OUTLIER) cc_final: 0.2449 (m110) REVERT: L 140 TYR cc_start: 0.6354 (t80) cc_final: 0.5805 (t80) REVERT: L 163 ASN cc_start: 0.6198 (m-40) cc_final: 0.5828 (t0) REVERT: L 357 HIS cc_start: 0.6863 (m-70) cc_final: 0.5961 (p-80) REVERT: L 399 LYS cc_start: 0.6701 (mmtm) cc_final: 0.6112 (tmtt) REVERT: L 432 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6550 (mtt) REVERT: L 545 TYR cc_start: 0.5674 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: L 563 ASP cc_start: 0.4545 (t0) cc_final: 0.3590 (p0) REVERT: L 581 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7194 (mmpt) REVERT: M 146 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5566 (ppp) REVERT: M 203 TRP cc_start: 0.6560 (OUTLIER) cc_final: 0.6192 (m-10) REVERT: M 374 MET cc_start: 0.4945 (pmt) cc_final: 0.4600 (pmt) REVERT: N 43 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6784 (mp) REVERT: N 100 ASP cc_start: 0.6028 (t0) cc_final: 0.5823 (t0) REVERT: N 211 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (mt) REVERT: N 388 MET cc_start: 0.6900 (mtm) cc_final: 0.6511 (pp-130) REVERT: B 45 MET cc_start: 0.8699 (ttp) cc_final: 0.7901 (mmp) REVERT: B 170 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7955 (mpt) REVERT: B 197 MET cc_start: 0.7736 (mmp) cc_final: 0.7159 (mmm) REVERT: B 200 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 219 GLU cc_start: 0.5461 (mm-30) cc_final: 0.5063 (mm-30) REVERT: H 13 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (tt) REVERT: H 148 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7109 (ppp80) REVERT: H 209 ARG cc_start: 0.6912 (mmm-85) cc_final: 0.6096 (mmm-85) REVERT: H 228 GLU cc_start: 0.8248 (tp30) cc_final: 0.8001 (tp30) REVERT: H 241 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7344 (mp0) REVERT: H 323 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7267 (mt0) REVERT: A 68 PHE cc_start: 0.7404 (m-10) cc_final: 0.7160 (m-10) REVERT: A 88 TRP cc_start: 0.7765 (t60) cc_final: 0.7058 (t60) REVERT: A 98 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7472 (p) REVERT: A 102 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6482 (mt-10) REVERT: A 108 PHE cc_start: 0.7231 (t80) cc_final: 0.6926 (t80) outliers start: 132 outliers final: 76 residues processed: 590 average time/residue: 0.6081 time to fit residues: 454.6895 Evaluate side-chains 571 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 470 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 MET Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 545 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 203 TRP Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 476 SER Chi-restraints excluded: chain N residue 478 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 173 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 429 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN E 142 ASN F 409 GLN G 151 ASN G 490 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.191411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160593 restraints weight = 56934.997| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.75 r_work: 0.3848 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38707 Z= 0.407 Angle : 2.536 50.732 52475 Z= 1.447 Chirality : 0.442 6.460 5797 Planarity : 0.005 0.048 6536 Dihedral : 10.499 112.574 5946 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 3.55 % Allowed : 29.90 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % 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: 0.37 (0.12), residues: 4683 helix: 1.10 (0.10), residues: 2577 sheet: -0.01 (0.32), residues: 275 loop : -0.91 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 64 TYR 0.041 0.002 TYR A 116 PHE 0.038 0.002 PHE C 63 TRP 0.050 0.002 TRP H 302 HIS 0.012 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01169 / 0.41 (38671) covalent geometry : angle 2.22388 / 1.44 (52382) hydrogen bonds : bond 0.04393 / 2.92 ( 2008) hydrogen bonds : angle 4.75817 / 3.34 ( 5796) metal coordination : bond 0.03813 / 2.47 ( 36) metal coordination : angle 29.01664 / 19.96 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19104.75 seconds wall clock time: 325 minutes 4.94 seconds (19504.94 seconds total)