Starting phenix.real_space_refine on Sat Jun 14 15:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxa_47283/06_2025/9dxa_47283.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 104 5.16 5 C 10845 2.51 5 N 2519 2.21 5 O 2814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16291 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2654 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain breaks: 2 Chain: "B" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2658 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2654 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2658 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2580 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 2 Chain: "F" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2580 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 104 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.83, per 1000 atoms: 0.60 Number of scatterers: 16291 At special positions: 0 Unit cell: (102.704, 104.8, 133.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 9 15.00 O 2814 8.00 N 2519 7.00 C 10845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 355 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 154 " - pdb=" SG CYS F 340 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 9 sheets defined 76.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.926A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.553A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.845A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.826A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 345 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.160A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.514A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 146 removed outlier: 5.556A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.451A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.861A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 removed outlier: 3.754A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 removed outlier: 4.130A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.175A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.624A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.094A pdb=" N ARG C 18 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.814A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.769A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 285 removed outlier: 3.797A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 removed outlier: 4.328A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.033A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.886A pdb=" N ARG D 18 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 5.243A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.439A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.730A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 285 removed outlier: 4.062A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.227A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 removed outlier: 3.506A pdb=" N PHE D 374 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.135A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.613A pdb=" N TRP D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.922A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 165 through 184 removed outlier: 4.476A pdb=" N TRP E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 207 Processing helix chain 'E' and resid 207 through 216 removed outlier: 4.035A pdb=" N THR E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 300 Processing helix chain 'E' and resid 303 through 329 removed outlier: 3.891A pdb=" N ASN E 329 " --> pdb=" O CYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 391 removed outlier: 3.835A pdb=" N ILE E 391 " --> pdb=" O TRP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 405 Processing helix chain 'E' and resid 415 through 428 Processing helix chain 'E' and resid 428 through 438 removed outlier: 4.062A pdb=" N SER E 432 " --> pdb=" O ASP E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 456 Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.908A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 187 removed outlier: 5.580A pdb=" N TRP F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 187 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 207 removed outlier: 3.791A pdb=" N LYS F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 216 removed outlier: 3.784A pdb=" N THR F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 300 removed outlier: 4.003A pdb=" N ALA F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 330 Processing helix chain 'F' and resid 344 through 349 Processing helix chain 'F' and resid 360 through 388 Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'F' and resid 414 through 428 removed outlier: 3.533A pdb=" N ALA F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 440 removed outlier: 3.555A pdb=" N SER F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.626A pdb=" N ILE A 53 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'E' and resid 395 through 396 removed outlier: 3.576A pdb=" N VAL E 413 " --> pdb=" O TYR E 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 52 through 56 1092 hydrogen bonds defined for protein. 3216 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: 4.50 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2607 1.32 - 1.45: 4741 1.45 - 1.57: 9217 1.57 - 1.69: 18 1.69 - 1.81: 150 Bond restraints: 16733 Sorted by residual: bond pdb=" C18 PEE E 901 " pdb=" C19 PEE E 901 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C38 PEE A 901 " pdb=" C39 PEE A 901 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C38 PEE F 903 " pdb=" C39 PEE F 903 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C38 PEE A 902 " pdb=" C39 PEE A 902 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 ... (remaining 16728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 22426 3.33 - 6.66: 43 6.66 - 9.99: 5 9.99 - 13.32: 42 13.32 - 16.65: 14 Bond angle restraints: 22530 Sorted by residual: angle pdb=" C38 PEE D 901 " pdb=" C39 PEE D 901 " pdb=" C40 PEE D 901 " ideal model delta sigma weight residual 112.47 129.12 -16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C38 PEE F 901 " pdb=" C39 PEE F 901 " pdb=" C40 PEE F 901 " ideal model delta sigma weight residual 112.47 128.08 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C18 PEE D 902 " pdb=" C19 PEE D 902 " pdb=" C20 PEE D 902 " ideal model delta sigma weight residual 113.02 127.90 -14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C17 PEE D 902 " pdb=" C18 PEE D 902 " pdb=" C19 PEE D 902 " ideal model delta sigma weight residual 113.68 128.51 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C18 PEE B 901 " pdb=" C19 PEE B 901 " pdb=" C20 PEE B 901 " ideal model delta sigma weight residual 113.02 127.76 -14.74 3.00e+00 1.11e-01 2.41e+01 ... (remaining 22525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.87: 9769 31.87 - 63.74: 180 63.74 - 95.61: 9 95.61 - 127.48: 27 127.48 - 159.35: 11 Dihedral angle restraints: 9996 sinusoidal: 4336 harmonic: 5660 Sorted by residual: dihedral pdb=" C12 PEE A 903 " pdb=" C10 PEE A 903 " pdb=" C11 PEE A 903 " pdb=" O4 PEE A 903 " ideal model delta sinusoidal sigma weight residual -19.47 -178.82 159.35 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C4 PEE A 901 " pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sinusoidal sigma weight residual -75.78 79.33 -155.11 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C32 PEE A 901 " pdb=" C30 PEE A 901 " pdb=" C31 PEE A 901 " pdb=" O3 PEE A 901 " ideal model delta sinusoidal sigma weight residual 161.16 6.79 154.37 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 9993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1692 0.034 - 0.068: 565 0.068 - 0.102: 114 0.102 - 0.136: 44 0.136 - 0.170: 2 Chirality restraints: 2417 Sorted by residual: chirality pdb=" C2 PEE F 903 " pdb=" C1 PEE F 903 " pdb=" C3 PEE F 903 " pdb=" O2 PEE F 903 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" C2 PEE B 903 " pdb=" C1 PEE B 903 " pdb=" C3 PEE B 903 " pdb=" O2 PEE B 903 " both_signs ideal model delta sigma weight residual False -2.33 -2.48 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.46 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 2414 not shown) Planarity restraints: 2685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 326 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C TYR E 326 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR E 326 " -0.024 2.00e-02 2.50e+03 pdb=" N THR E 327 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PEE D 901 " -0.025 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C11 PEE D 901 " 0.007 2.00e-02 2.50e+03 pdb=" O2 PEE D 901 " 0.008 2.00e-02 2.50e+03 pdb=" O4 PEE D 901 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 284 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C TYR A 284 " 0.022 2.00e-02 2.50e+03 pdb=" O TYR A 284 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 285 " -0.008 2.00e-02 2.50e+03 ... (remaining 2682 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4154 2.81 - 3.33: 15470 3.33 - 3.85: 27442 3.85 - 4.38: 30823 4.38 - 4.90: 54755 Nonbonded interactions: 132644 Sorted by model distance: nonbonded pdb=" O LEU B 302 " pdb=" OH TYR C 99 " model vdw 2.281 3.040 nonbonded pdb=" O GLY F 436 " pdb=" OG SER F 440 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 303 " pdb=" OH TYR B 308 " model vdw 2.293 3.040 nonbonded pdb=" O ILE E 323 " pdb=" OG1 THR E 327 " model vdw 2.297 3.040 nonbonded pdb=" O VAL A 47 " pdb=" NE2 GLN B 49 " model vdw 2.297 3.120 ... (remaining 132639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 411 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C21 or name O2 or name O4 )) or (resid 902 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name O2 or name O4 )) or re \ sid 903)) selection = (chain 'B' and (resid 15 through 68 or resid 94 through 411 or (resid 901 throug \ h 903 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 411 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C20 or name C21 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 68 or resid 94 through 411 or (resid 901 and (n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name O2 or name O \ 4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ O2 or name O4 )) or (resid 903 and (name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C20 or name C21 or name O2 or name O4 )))) } ncs_group { reference = (chain 'E' and (resid 15 through 456 or resid 901 or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 456 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C21 or name O2 or name O4 )) or resid 902)) } 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: 4.870 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: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.250 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.009 0.216 16749 Z= 0.470 Angle : 0.803 16.647 22562 Z= 0.336 Chirality : 0.037 0.170 2417 Planarity : 0.003 0.049 2685 Dihedral : 15.022 159.355 6276 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.23 % Allowed : 5.08 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 1844 helix: 1.90 (0.13), residues: 1307 sheet: 1.39 (0.52), residues: 105 loop : -0.48 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 24 HIS 0.003 0.001 HIS F 422 PHE 0.010 0.001 PHE F 41 TYR 0.011 0.001 TYR F 377 ARG 0.002 0.000 ARG F 434 Details of bonding type rmsd hydrogen bonds : bond 0.11144 ( 1092) hydrogen bonds : angle 4.34007 ( 3216) SS BOND : bond 0.00176 ( 16) SS BOND : angle 0.51547 ( 32) covalent geometry : bond 0.00934 (16733) covalent geometry : angle 0.80296 (22530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 440 time to evaluate : 1.894 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: B 131 LEU cc_start: 0.8914 (tt) cc_final: 0.8457 (mt) REVERT: B 155 HIS cc_start: 0.7884 (t-170) cc_final: 0.7645 (t70) REVERT: B 236 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8063 (tt0) REVERT: B 406 ASN cc_start: 0.8586 (m-40) cc_final: 0.8351 (m-40) REVERT: C 130 LEU cc_start: 0.8711 (tp) cc_final: 0.8388 (tt) REVERT: C 171 ARG cc_start: 0.7800 (tpt170) cc_final: 0.7540 (ttm-80) REVERT: C 379 ILE cc_start: 0.8475 (mm) cc_final: 0.8251 (mm) REVERT: D 59 TRP cc_start: 0.7318 (m-90) cc_final: 0.7018 (m100) REVERT: D 127 TYR cc_start: 0.8726 (m-80) cc_final: 0.8504 (m-10) REVERT: D 153 LEU cc_start: 0.8173 (mt) cc_final: 0.7584 (tt) REVERT: D 332 TYR cc_start: 0.7920 (t80) cc_final: 0.7405 (t80) REVERT: D 374 PHE cc_start: 0.7784 (t80) cc_final: 0.7411 (t80) REVERT: D 385 LEU cc_start: 0.7222 (tp) cc_final: 0.6709 (tp) REVERT: E 21 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7837 (mttm) REVERT: E 46 GLN cc_start: 0.7692 (tp40) cc_final: 0.7451 (tm-30) REVERT: E 321 ILE cc_start: 0.8106 (mm) cc_final: 0.7850 (pt) REVERT: E 370 TYR cc_start: 0.7789 (t80) cc_final: 0.7351 (t80) REVERT: E 377 TYR cc_start: 0.7451 (t80) cc_final: 0.7209 (t80) REVERT: F 21 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7907 (mttp) REVERT: F 205 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6652 (p90) REVERT: F 400 LYS cc_start: 0.7787 (mttt) cc_final: 0.7444 (mmtt) outliers start: 4 outliers final: 2 residues processed: 443 average time/residue: 0.3037 time to fit residues: 193.8670 Evaluate side-chains 261 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 205 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN F 141 ASN F 151 ASN F 312 GLN F 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112638 restraints weight = 25036.397| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.34 r_work: 0.3317 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16749 Z= 0.278 Angle : 0.610 12.012 22562 Z= 0.317 Chirality : 0.043 0.220 2417 Planarity : 0.003 0.034 2685 Dihedral : 15.567 164.253 2496 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.48 % Allowed : 11.13 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 1844 helix: 1.84 (0.14), residues: 1328 sheet: 1.04 (0.52), residues: 104 loop : -0.56 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 341 HIS 0.009 0.001 HIS B 119 PHE 0.022 0.002 PHE B 353 TYR 0.021 0.002 TYR C 351 ARG 0.006 0.001 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1092) hydrogen bonds : angle 3.81707 ( 3216) SS BOND : bond 0.00523 ( 16) SS BOND : angle 0.94962 ( 32) covalent geometry : bond 0.00650 (16733) covalent geometry : angle 0.60947 (22530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TRP cc_start: 0.8613 (p-90) cc_final: 0.8333 (p90) REVERT: A 369 LYS cc_start: 0.8482 (mmtm) cc_final: 0.7856 (pttt) REVERT: B 46 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 49 GLN cc_start: 0.8121 (mm110) cc_final: 0.7863 (mm110) REVERT: B 236 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8248 (pt0) REVERT: B 292 ASP cc_start: 0.9064 (p0) cc_final: 0.8762 (p0) REVERT: B 406 ASN cc_start: 0.8562 (m-40) cc_final: 0.8345 (m-40) REVERT: C 48 THR cc_start: 0.9131 (m) cc_final: 0.8906 (p) REVERT: C 171 ARG cc_start: 0.8391 (tpt170) cc_final: 0.7830 (ttm-80) REVERT: C 239 GLN cc_start: 0.8273 (pt0) cc_final: 0.8042 (pm20) REVERT: C 241 LYS cc_start: 0.8856 (tptp) cc_final: 0.8608 (tppt) REVERT: C 243 LEU cc_start: 0.8723 (tt) cc_final: 0.8349 (tp) REVERT: C 320 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (mp) REVERT: D 25 ASP cc_start: 0.8500 (m-30) cc_final: 0.8243 (t70) REVERT: D 46 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 59 TRP cc_start: 0.7528 (m-90) cc_final: 0.7072 (m100) REVERT: D 153 LEU cc_start: 0.8122 (mt) cc_final: 0.7401 (tp) REVERT: D 236 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 332 TYR cc_start: 0.7994 (t80) cc_final: 0.7420 (t80) REVERT: D 374 PHE cc_start: 0.7786 (t80) cc_final: 0.7464 (t80) REVERT: E 17 TYR cc_start: 0.6264 (m-10) cc_final: 0.5862 (m-10) REVERT: E 18 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7651 (mpt180) REVERT: E 37 MET cc_start: 0.8406 (ptm) cc_final: 0.8206 (ptm) REVERT: E 321 ILE cc_start: 0.8119 (mm) cc_final: 0.7879 (pt) REVERT: E 359 MET cc_start: 0.8034 (tmm) cc_final: 0.7701 (ppp) REVERT: F 400 LYS cc_start: 0.7721 (mttt) cc_final: 0.7382 (mmtt) outliers start: 61 outliers final: 38 residues processed: 301 average time/residue: 0.2818 time to fit residues: 125.8128 Evaluate side-chains 248 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 239 GLN B 253 HIS C 49 GLN C 404 GLN F 151 ASN F 332 ASN F 415 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118979 restraints weight = 24776.265| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.98 r_work: 0.3340 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16749 Z= 0.137 Angle : 0.483 10.240 22562 Z= 0.253 Chirality : 0.038 0.181 2417 Planarity : 0.003 0.031 2685 Dihedral : 13.761 175.421 2494 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.80 % Allowed : 13.30 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 1844 helix: 1.95 (0.14), residues: 1332 sheet: 1.10 (0.51), residues: 105 loop : -0.48 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 341 HIS 0.006 0.001 HIS B 119 PHE 0.014 0.001 PHE E 419 TYR 0.014 0.001 TYR E 427 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 1092) hydrogen bonds : angle 3.62706 ( 3216) SS BOND : bond 0.00326 ( 16) SS BOND : angle 0.69446 ( 32) covalent geometry : bond 0.00310 (16733) covalent geometry : angle 0.48240 (22530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 1.685 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: A 143 TRP cc_start: 0.8381 (p-90) cc_final: 0.8133 (p90) REVERT: A 369 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7886 (pttt) REVERT: B 236 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7910 (tm-30) REVERT: C 171 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7792 (ttm-80) REVERT: C 241 LYS cc_start: 0.8828 (tptp) cc_final: 0.8527 (tppt) REVERT: C 284 TYR cc_start: 0.8589 (t80) cc_final: 0.7911 (t80) REVERT: C 320 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (mp) REVERT: D 25 ASP cc_start: 0.8357 (m-30) cc_final: 0.8104 (t70) REVERT: D 46 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8058 (tm-30) REVERT: D 59 TRP cc_start: 0.7347 (m-90) cc_final: 0.6910 (m100) REVERT: D 153 LEU cc_start: 0.8081 (mt) cc_final: 0.7488 (tt) REVERT: D 332 TYR cc_start: 0.7812 (t80) cc_final: 0.7187 (t80) REVERT: D 374 PHE cc_start: 0.7778 (t80) cc_final: 0.7462 (t80) REVERT: E 153 MET cc_start: 0.8638 (tpp) cc_final: 0.8381 (ttt) REVERT: E 321 ILE cc_start: 0.8138 (mm) cc_final: 0.7889 (pt) REVERT: E 359 MET cc_start: 0.7855 (tmm) cc_final: 0.7295 (ppp) REVERT: F 400 LYS cc_start: 0.7710 (mttt) cc_final: 0.7352 (mmtt) outliers start: 49 outliers final: 35 residues processed: 287 average time/residue: 0.2736 time to fit residues: 116.5496 Evaluate side-chains 247 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 67 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 140 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 103 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: A 49 GLN B 239 GLN B 406 ASN E 312 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN F 152 GLN F 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.165868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116878 restraints weight = 24844.679| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.23 r_work: 0.3390 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16749 Z= 0.120 Angle : 0.467 8.005 22562 Z= 0.244 Chirality : 0.037 0.143 2417 Planarity : 0.003 0.030 2685 Dihedral : 12.576 177.874 2494 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.97 % Allowed : 13.76 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.20), residues: 1844 helix: 2.04 (0.14), residues: 1330 sheet: 1.24 (0.51), residues: 105 loop : -0.43 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 341 HIS 0.005 0.001 HIS B 119 PHE 0.015 0.001 PHE E 419 TYR 0.017 0.001 TYR D 127 ARG 0.005 0.000 ARG E 296 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 1092) hydrogen bonds : angle 3.54245 ( 3216) SS BOND : bond 0.00274 ( 16) SS BOND : angle 0.64930 ( 32) covalent geometry : bond 0.00267 (16733) covalent geometry : angle 0.46665 (22530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8549 (ptt180) cc_final: 0.8310 (ptp-110) REVERT: A 46 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7681 (tp40) REVERT: A 143 TRP cc_start: 0.8468 (p-90) cc_final: 0.8220 (p90) REVERT: A 161 LEU cc_start: 0.8615 (mt) cc_final: 0.8359 (pp) REVERT: A 369 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8054 (pttt) REVERT: B 46 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 236 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7962 (tm-30) REVERT: B 292 ASP cc_start: 0.8749 (p0) cc_final: 0.8495 (p0) REVERT: C 171 ARG cc_start: 0.8199 (tpt170) cc_final: 0.7756 (ttm-80) REVERT: C 241 LYS cc_start: 0.8858 (tptp) cc_final: 0.8511 (tppt) REVERT: C 284 TYR cc_start: 0.8681 (t80) cc_final: 0.8026 (t80) REVERT: C 320 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8937 (mp) REVERT: C 400 ASN cc_start: 0.8761 (m-40) cc_final: 0.8494 (m-40) REVERT: C 404 GLN cc_start: 0.8171 (mp10) cc_final: 0.7894 (mp10) REVERT: D 25 ASP cc_start: 0.8502 (m-30) cc_final: 0.8250 (t70) REVERT: D 46 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 59 TRP cc_start: 0.7471 (m-90) cc_final: 0.7016 (m100) REVERT: D 153 LEU cc_start: 0.8092 (mt) cc_final: 0.7500 (tt) REVERT: D 332 TYR cc_start: 0.8031 (t80) cc_final: 0.7434 (t80) REVERT: D 374 PHE cc_start: 0.7877 (t80) cc_final: 0.7538 (t80) REVERT: E 359 MET cc_start: 0.8473 (tmm) cc_final: 0.8071 (ppp) REVERT: F 209 TRP cc_start: 0.5034 (m100) cc_final: 0.4754 (m100) REVERT: F 400 LYS cc_start: 0.7722 (mttt) cc_final: 0.7349 (mmtt) outliers start: 52 outliers final: 42 residues processed: 271 average time/residue: 0.2860 time to fit residues: 115.6821 Evaluate side-chains 254 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 173 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 142 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114904 restraints weight = 25279.853| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.33 r_work: 0.3343 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16749 Z= 0.151 Angle : 0.494 12.332 22562 Z= 0.256 Chirality : 0.038 0.159 2417 Planarity : 0.003 0.030 2685 Dihedral : 12.207 177.202 2494 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.48 % Allowed : 14.44 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1844 helix: 2.05 (0.14), residues: 1330 sheet: 1.27 (0.51), residues: 104 loop : -0.48 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 341 HIS 0.005 0.001 HIS B 119 PHE 0.017 0.001 PHE E 419 TYR 0.020 0.001 TYR D 127 ARG 0.012 0.000 ARG D 403 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 1092) hydrogen bonds : angle 3.56320 ( 3216) SS BOND : bond 0.00332 ( 16) SS BOND : angle 0.70359 ( 32) covalent geometry : bond 0.00347 (16733) covalent geometry : angle 0.49337 (22530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8610 (ptt180) cc_final: 0.8336 (ptp-110) REVERT: A 46 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: A 143 TRP cc_start: 0.8467 (p-90) cc_final: 0.8157 (p90) REVERT: A 161 LEU cc_start: 0.8608 (mt) cc_final: 0.8368 (pp) REVERT: A 369 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8036 (pttt) REVERT: B 46 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 236 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7924 (tm-30) REVERT: B 292 ASP cc_start: 0.8834 (p0) cc_final: 0.8568 (p0) REVERT: C 25 ASP cc_start: 0.8492 (t0) cc_final: 0.8286 (t70) REVERT: C 171 ARG cc_start: 0.8219 (tpt170) cc_final: 0.7784 (ttm170) REVERT: C 241 LYS cc_start: 0.8812 (tptp) cc_final: 0.8483 (tppt) REVERT: C 284 TYR cc_start: 0.8775 (t80) cc_final: 0.8089 (t80) REVERT: C 320 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8938 (mp) REVERT: C 400 ASN cc_start: 0.8774 (m-40) cc_final: 0.8474 (m-40) REVERT: D 25 ASP cc_start: 0.8510 (m-30) cc_final: 0.8289 (t70) REVERT: D 46 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8185 (tm-30) REVERT: D 59 TRP cc_start: 0.7447 (m-90) cc_final: 0.6794 (m100) REVERT: D 153 LEU cc_start: 0.8103 (mt) cc_final: 0.7500 (tt) REVERT: D 332 TYR cc_start: 0.8034 (t80) cc_final: 0.7410 (t80) REVERT: D 343 MET cc_start: 0.6771 (ttm) cc_final: 0.6048 (ttm) REVERT: D 374 PHE cc_start: 0.7895 (t80) cc_final: 0.7571 (t80) REVERT: E 153 MET cc_start: 0.8825 (tpp) cc_final: 0.8568 (ttt) REVERT: E 359 MET cc_start: 0.8520 (tmm) cc_final: 0.8228 (tmm) REVERT: F 51 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: F 209 TRP cc_start: 0.5070 (m100) cc_final: 0.4767 (m100) REVERT: F 375 CYS cc_start: 0.8187 (m) cc_final: 0.7526 (t) REVERT: F 400 LYS cc_start: 0.7759 (mttt) cc_final: 0.7351 (mmtt) outliers start: 61 outliers final: 49 residues processed: 267 average time/residue: 0.2841 time to fit residues: 114.2573 Evaluate side-chains 261 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 388 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 107 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 253 HIS C 49 GLN D 404 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.165484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116333 restraints weight = 25057.175| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.27 r_work: 0.3384 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16749 Z= 0.122 Angle : 0.472 10.517 22562 Z= 0.244 Chirality : 0.038 0.154 2417 Planarity : 0.003 0.030 2685 Dihedral : 11.679 174.977 2494 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.60 % Allowed : 14.38 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.20), residues: 1844 helix: 2.11 (0.14), residues: 1328 sheet: 1.29 (0.51), residues: 105 loop : -0.44 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 341 HIS 0.005 0.001 HIS B 119 PHE 0.018 0.001 PHE E 419 TYR 0.026 0.001 TYR D 127 ARG 0.006 0.000 ARG D 403 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 1092) hydrogen bonds : angle 3.51475 ( 3216) SS BOND : bond 0.00280 ( 16) SS BOND : angle 0.63733 ( 32) covalent geometry : bond 0.00273 (16733) covalent geometry : angle 0.47152 (22530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8564 (ptt180) cc_final: 0.8325 (ptp-110) REVERT: A 46 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: A 143 TRP cc_start: 0.8374 (p-90) cc_final: 0.8093 (p90) REVERT: A 161 LEU cc_start: 0.8622 (mt) cc_final: 0.8419 (pp) REVERT: A 369 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8112 (pttt) REVERT: B 46 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 236 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7909 (tm-30) REVERT: B 284 TYR cc_start: 0.8834 (t80) cc_final: 0.8368 (t80) REVERT: B 292 ASP cc_start: 0.8758 (p0) cc_final: 0.8490 (p0) REVERT: C 25 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (t70) REVERT: C 171 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7771 (ttm170) REVERT: C 241 LYS cc_start: 0.8847 (tptp) cc_final: 0.8493 (tppt) REVERT: C 284 TYR cc_start: 0.8784 (t80) cc_final: 0.8158 (t80) REVERT: C 320 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8948 (mp) REVERT: C 404 GLN cc_start: 0.8229 (mp10) cc_final: 0.7848 (mp10) REVERT: D 25 ASP cc_start: 0.8511 (m-30) cc_final: 0.8293 (t70) REVERT: D 59 TRP cc_start: 0.7447 (m-90) cc_final: 0.7002 (m100) REVERT: D 153 LEU cc_start: 0.8060 (mt) cc_final: 0.7454 (tt) REVERT: D 265 MET cc_start: 0.7959 (mmm) cc_final: 0.7683 (mmm) REVERT: D 332 TYR cc_start: 0.8024 (t80) cc_final: 0.7422 (t80) REVERT: D 343 MET cc_start: 0.6821 (ttm) cc_final: 0.6204 (ttm) REVERT: D 374 PHE cc_start: 0.7901 (t80) cc_final: 0.7583 (t80) REVERT: E 153 MET cc_start: 0.8817 (tpp) cc_final: 0.8599 (ttt) REVERT: E 359 MET cc_start: 0.8504 (tmm) cc_final: 0.8248 (tmm) REVERT: F 46 GLN cc_start: 0.8162 (tp40) cc_final: 0.7914 (mm-40) REVERT: F 51 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: F 209 TRP cc_start: 0.4965 (m100) cc_final: 0.4693 (m100) REVERT: F 375 CYS cc_start: 0.8189 (m) cc_final: 0.7531 (t) REVERT: F 400 LYS cc_start: 0.7787 (mttt) cc_final: 0.7363 (mmtt) outliers start: 63 outliers final: 50 residues processed: 282 average time/residue: 0.2676 time to fit residues: 114.6587 Evaluate side-chains 270 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 388 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 239 GLN C 49 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116367 restraints weight = 24949.228| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.24 r_work: 0.3384 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16749 Z= 0.131 Angle : 0.495 12.398 22562 Z= 0.255 Chirality : 0.038 0.228 2417 Planarity : 0.003 0.030 2685 Dihedral : 11.538 171.199 2494 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 14.73 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.20), residues: 1844 helix: 2.11 (0.14), residues: 1331 sheet: 1.32 (0.51), residues: 105 loop : -0.42 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 341 HIS 0.007 0.001 HIS D 132 PHE 0.020 0.001 PHE E 419 TYR 0.024 0.001 TYR D 127 ARG 0.004 0.000 ARG E 296 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 1092) hydrogen bonds : angle 3.52168 ( 3216) SS BOND : bond 0.00305 ( 16) SS BOND : angle 0.64958 ( 32) covalent geometry : bond 0.00298 (16733) covalent geometry : angle 0.49505 (22530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8495 (ptt180) cc_final: 0.8289 (ptp-110) REVERT: A 46 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7676 (tp40) REVERT: A 143 TRP cc_start: 0.8364 (p-90) cc_final: 0.8070 (p90) REVERT: A 369 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8109 (pttt) REVERT: B 236 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7924 (tm-30) REVERT: B 284 TYR cc_start: 0.8769 (t80) cc_final: 0.8306 (t80) REVERT: B 292 ASP cc_start: 0.8752 (p0) cc_final: 0.8481 (p0) REVERT: C 25 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8239 (t70) REVERT: C 171 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7728 (ttm-80) REVERT: C 241 LYS cc_start: 0.8829 (tptp) cc_final: 0.8467 (tppt) REVERT: C 243 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 284 TYR cc_start: 0.8775 (t80) cc_final: 0.8196 (t80) REVERT: C 320 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 404 GLN cc_start: 0.8450 (mp10) cc_final: 0.8148 (mp10) REVERT: D 25 ASP cc_start: 0.8527 (m-30) cc_final: 0.8285 (t70) REVERT: D 59 TRP cc_start: 0.7426 (m-90) cc_final: 0.6792 (m100) REVERT: D 153 LEU cc_start: 0.8106 (mt) cc_final: 0.7508 (tt) REVERT: D 265 MET cc_start: 0.7964 (mmm) cc_final: 0.7670 (mmm) REVERT: D 332 TYR cc_start: 0.8036 (t80) cc_final: 0.7425 (t80) REVERT: D 343 MET cc_start: 0.6829 (ttm) cc_final: 0.6187 (ttm) REVERT: D 374 PHE cc_start: 0.7926 (t80) cc_final: 0.7619 (t80) REVERT: E 153 MET cc_start: 0.8829 (tpp) cc_final: 0.8580 (ttt) REVERT: E 359 MET cc_start: 0.8511 (tmm) cc_final: 0.8264 (tmm) REVERT: F 46 GLN cc_start: 0.8152 (tp40) cc_final: 0.7931 (mm-40) REVERT: F 51 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: F 209 TRP cc_start: 0.5019 (m100) cc_final: 0.4770 (m100) REVERT: F 375 CYS cc_start: 0.8182 (m) cc_final: 0.7539 (t) REVERT: F 400 LYS cc_start: 0.7807 (mttt) cc_final: 0.7394 (mmtt) outliers start: 68 outliers final: 57 residues processed: 274 average time/residue: 0.2899 time to fit residues: 119.5925 Evaluate side-chains 275 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 388 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 66 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 75 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: B 49 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.165181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116173 restraints weight = 24961.141| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.26 r_work: 0.3382 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16749 Z= 0.133 Angle : 0.502 11.061 22562 Z= 0.260 Chirality : 0.038 0.182 2417 Planarity : 0.003 0.028 2685 Dihedral : 11.391 166.018 2494 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.77 % Allowed : 14.90 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.20), residues: 1844 helix: 2.09 (0.14), residues: 1330 sheet: 1.33 (0.51), residues: 105 loop : -0.39 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 341 HIS 0.006 0.001 HIS D 132 PHE 0.022 0.001 PHE E 419 TYR 0.024 0.001 TYR D 127 ARG 0.004 0.000 ARG E 296 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 1092) hydrogen bonds : angle 3.52361 ( 3216) SS BOND : bond 0.00310 ( 16) SS BOND : angle 0.65692 ( 32) covalent geometry : bond 0.00302 (16733) covalent geometry : angle 0.50138 (22530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 220 time to evaluate : 1.676 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: A 18 ARG cc_start: 0.8519 (ptt180) cc_final: 0.8300 (ptp-110) REVERT: A 46 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7683 (tp40) REVERT: A 143 TRP cc_start: 0.8358 (p-90) cc_final: 0.8062 (p90) REVERT: A 369 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8109 (pttt) REVERT: B 236 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7937 (tm-30) REVERT: B 284 TYR cc_start: 0.8766 (t80) cc_final: 0.8321 (t80) REVERT: B 292 ASP cc_start: 0.8762 (p0) cc_final: 0.8490 (p0) REVERT: C 25 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8259 (t70) REVERT: C 143 TRP cc_start: 0.8888 (p-90) cc_final: 0.8578 (p-90) REVERT: C 171 ARG cc_start: 0.8217 (tpt170) cc_final: 0.7743 (ttm-80) REVERT: C 241 LYS cc_start: 0.8826 (tptp) cc_final: 0.8462 (tppt) REVERT: C 243 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8691 (tp) REVERT: C 284 TYR cc_start: 0.8779 (t80) cc_final: 0.8196 (t80) REVERT: C 320 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 404 GLN cc_start: 0.8437 (mp10) cc_final: 0.8124 (mp10) REVERT: D 25 ASP cc_start: 0.8528 (m-30) cc_final: 0.8271 (t70) REVERT: D 59 TRP cc_start: 0.7441 (m-90) cc_final: 0.6802 (m100) REVERT: D 144 PHE cc_start: 0.7385 (m-10) cc_final: 0.7147 (m-10) REVERT: D 153 LEU cc_start: 0.8186 (mt) cc_final: 0.7612 (tt) REVERT: D 265 MET cc_start: 0.7950 (mmm) cc_final: 0.7642 (mmm) REVERT: D 332 TYR cc_start: 0.8026 (t80) cc_final: 0.7420 (t80) REVERT: D 343 MET cc_start: 0.6811 (ttm) cc_final: 0.6147 (ttm) REVERT: D 374 PHE cc_start: 0.7928 (t80) cc_final: 0.7620 (t80) REVERT: E 153 MET cc_start: 0.8857 (tpp) cc_final: 0.8588 (ttt) REVERT: E 359 MET cc_start: 0.8493 (tmm) cc_final: 0.8175 (tmm) REVERT: F 46 GLN cc_start: 0.7934 (tp40) cc_final: 0.7690 (tm-30) REVERT: F 51 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: F 209 TRP cc_start: 0.5010 (m100) cc_final: 0.4775 (m100) REVERT: F 375 CYS cc_start: 0.8165 (m) cc_final: 0.7515 (t) REVERT: F 400 LYS cc_start: 0.7874 (mttt) cc_final: 0.7436 (mmtt) outliers start: 66 outliers final: 57 residues processed: 271 average time/residue: 0.2805 time to fit residues: 114.4811 Evaluate side-chains 276 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 388 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 239 GLN B 253 HIS C 155 HIS D 49 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116936 restraints weight = 24996.013| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.25 r_work: 0.3386 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16749 Z= 0.119 Angle : 0.493 10.890 22562 Z= 0.254 Chirality : 0.038 0.178 2417 Planarity : 0.003 0.028 2685 Dihedral : 11.050 153.865 2494 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.77 % Allowed : 14.67 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1844 helix: 2.13 (0.14), residues: 1329 sheet: 1.42 (0.51), residues: 105 loop : -0.38 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 341 HIS 0.005 0.001 HIS D 132 PHE 0.023 0.001 PHE E 419 TYR 0.023 0.001 TYR D 127 ARG 0.004 0.000 ARG F 434 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1092) hydrogen bonds : angle 3.47804 ( 3216) SS BOND : bond 0.00281 ( 16) SS BOND : angle 0.62919 ( 32) covalent geometry : bond 0.00265 (16733) covalent geometry : angle 0.49259 (22530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 2.128 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: A 18 ARG cc_start: 0.8535 (ptt180) cc_final: 0.8289 (ptp-110) REVERT: A 46 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7679 (tp40) REVERT: A 143 TRP cc_start: 0.8292 (p-90) cc_final: 0.8027 (p90) REVERT: A 369 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8127 (pttt) REVERT: B 236 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7909 (tm-30) REVERT: B 284 TYR cc_start: 0.8756 (t80) cc_final: 0.8340 (t80) REVERT: B 292 ASP cc_start: 0.8711 (p0) cc_final: 0.8437 (p0) REVERT: C 25 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8260 (t70) REVERT: C 171 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7698 (ttm-80) REVERT: C 241 LYS cc_start: 0.8823 (tptp) cc_final: 0.8469 (tppt) REVERT: C 284 TYR cc_start: 0.8777 (t80) cc_final: 0.8187 (t80) REVERT: C 320 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8899 (mp) REVERT: D 25 ASP cc_start: 0.8517 (m-30) cc_final: 0.8258 (t70) REVERT: D 59 TRP cc_start: 0.7397 (m-90) cc_final: 0.6953 (m100) REVERT: D 144 PHE cc_start: 0.7454 (m-10) cc_final: 0.7176 (m-10) REVERT: D 153 LEU cc_start: 0.8194 (mt) cc_final: 0.7616 (tt) REVERT: D 265 MET cc_start: 0.7905 (mmm) cc_final: 0.7581 (mmm) REVERT: D 332 TYR cc_start: 0.8012 (t80) cc_final: 0.7417 (t80) REVERT: D 343 MET cc_start: 0.6752 (ttm) cc_final: 0.6099 (ttm) REVERT: D 374 PHE cc_start: 0.7910 (t80) cc_final: 0.7595 (t80) REVERT: E 153 MET cc_start: 0.8833 (tpp) cc_final: 0.8564 (ttt) REVERT: E 359 MET cc_start: 0.8507 (tmm) cc_final: 0.8245 (tmm) REVERT: E 390 ARG cc_start: 0.5626 (ttt90) cc_final: 0.5409 (ttm170) REVERT: F 359 MET cc_start: 0.8390 (mmp) cc_final: 0.8133 (mmt) REVERT: F 400 LYS cc_start: 0.7849 (mttt) cc_final: 0.7396 (mmtt) REVERT: F 410 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.3338 (mp) outliers start: 66 outliers final: 56 residues processed: 273 average time/residue: 0.2849 time to fit residues: 117.4695 Evaluate side-chains 276 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 388 LEU Chi-restraints excluded: chain F residue 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS B 239 GLN C 155 HIS ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117387 restraints weight = 24918.060| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.21 r_work: 0.3386 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16749 Z= 0.122 Angle : 0.504 10.493 22562 Z= 0.260 Chirality : 0.038 0.184 2417 Planarity : 0.003 0.028 2685 Dihedral : 10.901 139.638 2494 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.42 % Allowed : 15.01 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1844 helix: 2.14 (0.14), residues: 1326 sheet: 1.43 (0.52), residues: 105 loop : -0.42 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 143 HIS 0.005 0.001 HIS D 132 PHE 0.025 0.001 PHE E 419 TYR 0.022 0.001 TYR D 127 ARG 0.003 0.000 ARG F 434 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 1092) hydrogen bonds : angle 3.48024 ( 3216) SS BOND : bond 0.00281 ( 16) SS BOND : angle 0.62520 ( 32) covalent geometry : bond 0.00275 (16733) covalent geometry : angle 0.50380 (22530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8540 (ptt180) cc_final: 0.8221 (ptp-110) REVERT: A 46 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: A 143 TRP cc_start: 0.8276 (p-90) cc_final: 0.7972 (p90) REVERT: A 369 LYS cc_start: 0.8542 (mmtm) cc_final: 0.7983 (pttp) REVERT: B 236 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7969 (tm-30) REVERT: B 284 TYR cc_start: 0.8789 (t80) cc_final: 0.8330 (t80) REVERT: B 292 ASP cc_start: 0.8734 (p0) cc_final: 0.8459 (p0) REVERT: C 25 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8186 (t70) REVERT: C 171 ARG cc_start: 0.8199 (tpt170) cc_final: 0.7713 (ttm-80) REVERT: C 241 LYS cc_start: 0.8793 (tptp) cc_final: 0.8451 (tppt) REVERT: C 284 TYR cc_start: 0.8825 (t80) cc_final: 0.8176 (t80) REVERT: C 320 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8847 (mp) REVERT: D 25 ASP cc_start: 0.8488 (m-30) cc_final: 0.8206 (t70) REVERT: D 59 TRP cc_start: 0.7419 (m-90) cc_final: 0.6944 (m100) REVERT: D 144 PHE cc_start: 0.7446 (m-10) cc_final: 0.7155 (m-10) REVERT: D 153 LEU cc_start: 0.8009 (mt) cc_final: 0.7556 (tt) REVERT: D 265 MET cc_start: 0.7822 (mmm) cc_final: 0.7519 (mmm) REVERT: D 332 TYR cc_start: 0.7948 (t80) cc_final: 0.7340 (t80) REVERT: D 343 MET cc_start: 0.6735 (ttm) cc_final: 0.6104 (ttm) REVERT: D 374 PHE cc_start: 0.7873 (t80) cc_final: 0.7559 (t80) REVERT: E 153 MET cc_start: 0.8859 (tpp) cc_final: 0.8599 (ttt) REVERT: E 359 MET cc_start: 0.8499 (tmm) cc_final: 0.8185 (tmm) REVERT: F 45 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7403 (ttt) REVERT: F 400 LYS cc_start: 0.7838 (mttt) cc_final: 0.7372 (mmtt) REVERT: F 410 ILE cc_start: 0.3601 (OUTLIER) cc_final: 0.3325 (mp) outliers start: 60 outliers final: 54 residues processed: 268 average time/residue: 0.2743 time to fit residues: 109.9070 Evaluate side-chains 274 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 326 TYR Chi-restraints excluded: chain F residue 388 LEU Chi-restraints excluded: chain F residue 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS F 151 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.165323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116720 restraints weight = 25111.406| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.24 r_work: 0.3380 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16749 Z= 0.136 Angle : 0.529 11.512 22562 Z= 0.277 Chirality : 0.039 0.186 2417 Planarity : 0.003 0.038 2685 Dihedral : 10.737 136.099 2494 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.48 % Allowed : 15.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.20), residues: 1844 helix: 2.06 (0.14), residues: 1327 sheet: 1.41 (0.52), residues: 105 loop : -0.42 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 143 HIS 0.005 0.001 HIS D 132 PHE 0.024 0.001 PHE E 419 TYR 0.020 0.001 TYR D 127 ARG 0.010 0.000 ARG E 434 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1092) hydrogen bonds : angle 3.59760 ( 3216) SS BOND : bond 0.00301 ( 16) SS BOND : angle 0.64924 ( 32) covalent geometry : bond 0.00308 (16733) covalent geometry : angle 0.52902 (22530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10230.48 seconds wall clock time: 175 minutes 54.59 seconds (10554.59 seconds total)