Starting phenix.real_space_refine on Thu Sep 18 11:11:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxa_47283/09_2025/9dxa_47283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxa_47283/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dxa_47283/09_2025/9dxa_47283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxa_47283/09_2025/9dxa_47283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxa_47283/09_2025/9dxa_47283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxa_47283/09_2025/9dxa_47283.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.34, per 1000 atoms: 0.27 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: 1.34 Conformation dependent library (CDL) restraints added in 752.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 3.01 Time building geometry restraints manager: 1.80 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 902 or (resid 903 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 )))) selection = (chain 'C' and (resid 15 through 902 or (resid 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 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 C17 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: 7.250 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (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 ARG 0.002 0.000 ARG F 434 TYR 0.011 0.001 TYR F 377 PHE 0.010 0.001 PHE F 41 TRP 0.012 0.001 TRP C 24 HIS 0.003 0.001 HIS F 422 Details of bonding type rmsd covalent geometry : bond 0.00934 (16733) covalent geometry : angle 0.80296 (22530) SS BOND : bond 0.00176 ( 16) SS BOND : angle 0.51547 ( 32) hydrogen bonds : bond 0.11144 ( 1092) hydrogen bonds : angle 4.34007 ( 3216) *********************** 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 : 0.638 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: 0.8456 (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: 0.8101 (pt0) REVERT: B 406 ASN cc_start: 0.8586 (m-40) cc_final: 0.8354 (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: 0.8250 (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: 0.8505 (m-10) REVERT: D 153 LEU cc_start: 0.8173 (mt) cc_final: 0.7582 (tt) REVERT: D 332 TYR cc_start: 0.7920 (t80) cc_final: 0.7404 (t80) REVERT: D 374 PHE cc_start: 0.7784 (t80) cc_final: 0.7410 (t80) REVERT: D 385 LEU cc_start: 0.7222 (tp) cc_final: 0.6708 (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: 0.6651 (p90) REVERT: F 400 LYS cc_start: 0.7787 (mttt) cc_final: 0.7445 (mmtt) outliers start: 4 outliers final: 2 residues processed: 443 average time/residue: 0.1496 time to fit residues: 96.1406 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 : 0.616 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 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 406 ASN D 239 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 151 ASN F 312 GLN F 332 ASN F 453 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.166460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115829 restraints weight = 24902.354| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.40 r_work: 0.3410 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2209 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= 0.124 Angle : 0.483 12.084 22562 Z= 0.248 Chirality : 0.038 0.189 2417 Planarity : 0.003 0.034 2685 Dihedral : 15.147 169.928 2496 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.40 % Allowed : 11.36 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1844 helix: 2.02 (0.14), residues: 1341 sheet: 1.32 (0.52), residues: 105 loop : -0.42 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.019 0.001 TYR C 351 PHE 0.021 0.001 PHE E 419 TRP 0.016 0.001 TRP B 341 HIS 0.008 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00274 (16733) covalent geometry : angle 0.48279 (22530) SS BOND : bond 0.00221 ( 16) SS BOND : angle 0.60175 ( 32) hydrogen bonds : bond 0.03404 ( 1092) hydrogen bonds : angle 3.55745 ( 3216) *********************** 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 321 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.631 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: 0.8494 (ptt180) cc_final: 0.8268 (ptp-110) REVERT: A 143 TRP cc_start: 0.8340 (p-90) cc_final: 0.8047 (p90) REVERT: A 368 VAL cc_start: 0.7953 (m) cc_final: 0.7630 (p) REVERT: A 369 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7774 (pttt) REVERT: B 131 LEU cc_start: 0.8729 (tt) cc_final: 0.8447 (tp) REVERT: B 236 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8179 (pt0) REVERT: B 406 ASN cc_start: 0.8529 (m-40) cc_final: 0.8323 (m-40) REVERT: C 48 THR cc_start: 0.9031 (m) cc_final: 0.8810 (p) REVERT: C 171 ARG cc_start: 0.8051 (tpt170) cc_final: 0.7619 (ttm-80) REVERT: C 241 LYS cc_start: 0.8835 (tptp) cc_final: 0.8562 (tppt) REVERT: C 320 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8834 (mp) REVERT: C 343 MET cc_start: 0.8700 (mtp) cc_final: 0.8471 (mtp) REVERT: C 375 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7905 (mtt) REVERT: D 59 TRP cc_start: 0.7353 (m-90) cc_final: 0.6954 (m100) REVERT: D 153 LEU cc_start: 0.8112 (mt) cc_final: 0.7559 (tt) REVERT: D 332 TYR cc_start: 0.7842 (t80) cc_final: 0.7330 (t80) REVERT: D 374 PHE cc_start: 0.7740 (t80) cc_final: 0.7377 (t80) REVERT: E 321 ILE cc_start: 0.8028 (mm) cc_final: 0.7782 (pt) REVERT: E 359 MET cc_start: 0.7781 (tmm) cc_final: 0.7387 (ppp) REVERT: E 370 TYR cc_start: 0.7790 (t80) cc_final: 0.7221 (t80) REVERT: F 46 GLN cc_start: 0.8199 (tp40) cc_final: 0.7851 (mm-40) REVERT: F 296 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.4540 (ptp-170) REVERT: F 359 MET cc_start: 0.8080 (mmm) cc_final: 0.7756 (mmt) REVERT: F 400 LYS cc_start: 0.7775 (mttt) cc_final: 0.7340 (mmtt) outliers start: 42 outliers final: 27 residues processed: 308 average time/residue: 0.1420 time to fit residues: 65.3344 Evaluate side-chains 263 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 160 LEU 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 169 THR 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 293 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 296 ARG 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 28 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 381 GLN E 152 GLN E 312 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN F 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114834 restraints weight = 25070.012| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.19 r_work: 0.3358 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16749 Z= 0.207 Angle : 0.537 9.034 22562 Z= 0.281 Chirality : 0.040 0.204 2417 Planarity : 0.003 0.032 2685 Dihedral : 13.987 179.458 2494 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.37 % Allowed : 12.16 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.19), residues: 1844 helix: 1.94 (0.14), residues: 1333 sheet: 1.19 (0.50), residues: 104 loop : -0.51 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 296 TYR 0.018 0.002 TYR D 127 PHE 0.017 0.002 PHE B 250 TRP 0.021 0.001 TRP B 341 HIS 0.007 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00480 (16733) covalent geometry : angle 0.53626 (22530) SS BOND : bond 0.00438 ( 16) SS BOND : angle 0.85579 ( 32) hydrogen bonds : bond 0.03590 ( 1092) hydrogen bonds : angle 3.67054 ( 3216) *********************** 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 293 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8589 (ptt180) cc_final: 0.8380 (ptp-110) REVERT: A 143 TRP cc_start: 0.8603 (p-90) cc_final: 0.8305 (p90) REVERT: A 161 LEU cc_start: 0.8688 (mt) cc_final: 0.8438 (pp) REVERT: A 369 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8013 (pttt) REVERT: B 153 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 236 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7940 (tm-30) REVERT: B 343 MET cc_start: 0.7897 (mtm) cc_final: 0.7683 (mtm) REVERT: C 25 ASP cc_start: 0.8443 (t0) cc_final: 0.8228 (t70) REVERT: C 171 ARG cc_start: 0.8221 (tpt170) cc_final: 0.7744 (ttm-80) REVERT: C 241 LYS cc_start: 0.8818 (tptp) cc_final: 0.8531 (tppt) REVERT: C 284 TYR cc_start: 0.8691 (t80) cc_final: 0.8037 (t80) REVERT: C 320 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8966 (mp) REVERT: C 375 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: C 404 GLN cc_start: 0.7900 (tp40) cc_final: 0.7687 (tp-100) REVERT: D 25 ASP cc_start: 0.8516 (m-30) cc_final: 0.8252 (t70) REVERT: D 59 TRP cc_start: 0.7505 (m-90) cc_final: 0.7045 (m100) REVERT: D 153 LEU cc_start: 0.8104 (mt) cc_final: 0.7505 (tt) REVERT: D 332 TYR cc_start: 0.8019 (t80) cc_final: 0.7459 (t80) REVERT: D 343 MET cc_start: 0.6504 (ttm) cc_final: 0.5379 (ttm) REVERT: D 374 PHE cc_start: 0.7846 (t80) cc_final: 0.7491 (t80) REVERT: E 321 ILE cc_start: 0.8192 (mm) cc_final: 0.7951 (pt) REVERT: E 359 MET cc_start: 0.8124 (tmm) cc_final: 0.7602 (ppp) REVERT: F 400 LYS cc_start: 0.7789 (mttt) cc_final: 0.7414 (mmtt) outliers start: 59 outliers final: 41 residues processed: 276 average time/residue: 0.1431 time to fit residues: 59.2909 Evaluate side-chains 253 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 HIS 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 286 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 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 253 HIS 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 37 MET 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 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 Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 175 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 B 406 ASN E 312 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN F 429 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119787 restraints weight = 24925.364| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.84 r_work: 0.3366 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16749 Z= 0.122 Angle : 0.470 7.640 22562 Z= 0.245 Chirality : 0.037 0.140 2417 Planarity : 0.003 0.031 2685 Dihedral : 12.987 179.432 2494 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.08 % Allowed : 13.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 1844 helix: 2.05 (0.14), residues: 1330 sheet: 1.35 (0.51), residues: 104 loop : -0.42 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 296 TYR 0.015 0.001 TYR D 386 PHE 0.015 0.001 PHE E 419 TRP 0.020 0.001 TRP B 341 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00273 (16733) covalent geometry : angle 0.46920 (22530) SS BOND : bond 0.00299 ( 16) SS BOND : angle 0.66428 ( 32) hydrogen bonds : bond 0.03225 ( 1092) hydrogen bonds : angle 3.54582 ( 3216) *********************** 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 289 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.648 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: 0.8489 (ptt180) cc_final: 0.8269 (ptp-110) REVERT: A 143 TRP cc_start: 0.8329 (p-90) cc_final: 0.8034 (p90) REVERT: A 369 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7975 (ptmt) REVERT: B 236 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7901 (tm-30) REVERT: B 292 ASP cc_start: 0.8552 (p0) cc_final: 0.8282 (p0) REVERT: C 171 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7697 (ttm-80) REVERT: C 241 LYS cc_start: 0.8817 (tptp) cc_final: 0.8509 (tppt) REVERT: C 284 TYR cc_start: 0.8554 (t80) cc_final: 0.7931 (t80) REVERT: C 320 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8857 (mp) REVERT: C 343 MET cc_start: 0.8530 (mtp) cc_final: 0.8225 (mtp) REVERT: D 25 ASP cc_start: 0.8364 (m-30) cc_final: 0.8124 (t70) REVERT: D 59 TRP cc_start: 0.7336 (m-90) cc_final: 0.6934 (m100) REVERT: D 153 LEU cc_start: 0.8057 (mt) cc_final: 0.7483 (tt) REVERT: D 332 TYR cc_start: 0.7851 (t80) cc_final: 0.7239 (t80) REVERT: D 374 PHE cc_start: 0.7774 (t80) cc_final: 0.7447 (t80) REVERT: E 153 MET cc_start: 0.8587 (tpp) cc_final: 0.8374 (ttt) REVERT: E 321 ILE cc_start: 0.8165 (mm) cc_final: 0.7917 (pt) REVERT: E 359 MET cc_start: 0.8242 (tmm) cc_final: 0.7835 (ppp) REVERT: F 46 GLN cc_start: 0.8281 (tp40) cc_final: 0.7865 (mm-40) REVERT: F 375 CYS cc_start: 0.8202 (m) cc_final: 0.7539 (t) REVERT: F 400 LYS cc_start: 0.7715 (mttt) cc_final: 0.7345 (mmtt) outliers start: 54 outliers final: 40 residues processed: 274 average time/residue: 0.1426 time to fit residues: 58.1380 Evaluate side-chains 254 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 A residue 293 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 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 320 ILE Chi-restraints excluded: chain C residue 368 VAL 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 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 34 VAL 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 358 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 149 optimal weight: 20.0000 chunk 53 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 D 404 GLN E 312 GLN F 46 GLN F 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.165107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115785 restraints weight = 25030.490| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3373 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3160 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= 0.152 Angle : 0.495 11.910 22562 Z= 0.256 Chirality : 0.038 0.235 2417 Planarity : 0.003 0.042 2685 Dihedral : 12.656 179.279 2494 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.25 % Allowed : 13.07 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.19), residues: 1844 helix: 2.04 (0.14), residues: 1332 sheet: 1.31 (0.51), residues: 104 loop : -0.51 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 403 TYR 0.018 0.001 TYR F 427 PHE 0.017 0.001 PHE C 393 TRP 0.022 0.001 TRP B 341 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00349 (16733) covalent geometry : angle 0.49468 (22530) SS BOND : bond 0.00335 ( 16) SS BOND : angle 0.70874 ( 32) hydrogen bonds : bond 0.03300 ( 1092) hydrogen bonds : angle 3.54088 ( 3216) *********************** 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 281 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.664 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: 0.8558 (ptt180) cc_final: 0.8339 (ptp-110) REVERT: A 46 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: A 143 TRP cc_start: 0.8430 (p-90) cc_final: 0.8188 (p90) REVERT: A 161 LEU cc_start: 0.8663 (mt) cc_final: 0.8353 (pp) REVERT: A 369 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8042 (ptmt) REVERT: B 236 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7922 (tm-30) REVERT: B 292 ASP cc_start: 0.8802 (p0) cc_final: 0.8538 (p0) REVERT: C 171 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7486 (ttm-80) REVERT: C 241 LYS cc_start: 0.8847 (tptp) cc_final: 0.8541 (tppt) REVERT: C 284 TYR cc_start: 0.8794 (t80) cc_final: 0.8170 (t80) REVERT: C 320 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8905 (mp) REVERT: D 25 ASP cc_start: 0.8509 (m-30) cc_final: 0.8291 (t70) REVERT: D 59 TRP cc_start: 0.7488 (m-90) cc_final: 0.7017 (m100) REVERT: D 153 LEU cc_start: 0.8092 (mt) cc_final: 0.7501 (tt) REVERT: D 332 TYR cc_start: 0.8019 (t80) cc_final: 0.7398 (t80) REVERT: D 343 MET cc_start: 0.6628 (ttm) cc_final: 0.6155 (ttm) REVERT: D 374 PHE cc_start: 0.7864 (t80) cc_final: 0.7551 (t80) REVERT: E 153 MET cc_start: 0.8879 (tpp) cc_final: 0.8609 (ttt) REVERT: E 359 MET cc_start: 0.8516 (tmm) cc_final: 0.8076 (ppp) REVERT: F 375 CYS cc_start: 0.8280 (m) cc_final: 0.7621 (t) REVERT: F 400 LYS cc_start: 0.7785 (mttt) cc_final: 0.7393 (mmtt) outliers start: 57 outliers final: 42 residues processed: 267 average time/residue: 0.1409 time to fit residues: 56.2241 Evaluate side-chains 253 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 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 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 286 VAL Chi-restraints excluded: chain B residue 293 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 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 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 358 ASN Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 407 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 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 B 253 HIS C 404 GLN D 404 GLN F 46 GLN F 151 ASN F 152 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.165406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119475 restraints weight = 25002.332| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.75 r_work: 0.3362 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16749 Z= 0.132 Angle : 0.480 8.478 22562 Z= 0.250 Chirality : 0.038 0.140 2417 Planarity : 0.003 0.029 2685 Dihedral : 12.311 173.075 2494 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.71 % Allowed : 13.13 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 1844 helix: 2.05 (0.14), residues: 1330 sheet: 1.33 (0.50), residues: 104 loop : -0.43 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 434 TYR 0.019 0.001 TYR D 127 PHE 0.022 0.001 PHE C 393 TRP 0.026 0.001 TRP B 341 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00299 (16733) covalent geometry : angle 0.48017 (22530) SS BOND : bond 0.00294 ( 16) SS BOND : angle 0.65714 ( 32) hydrogen bonds : bond 0.03255 ( 1092) hydrogen bonds : angle 3.53581 ( 3216) *********************** 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 283 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.532 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: 0.8488 (ptt180) cc_final: 0.8240 (ptp-110) REVERT: A 46 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7613 (tp40) REVERT: A 143 TRP cc_start: 0.8269 (p-90) cc_final: 0.7968 (p90) REVERT: A 161 LEU cc_start: 0.8569 (mt) cc_final: 0.8307 (pp) REVERT: A 369 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7953 (ptmt) REVERT: B 236 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7900 (tm-30) REVERT: B 284 TYR cc_start: 0.8828 (t80) cc_final: 0.8152 (t80) REVERT: B 292 ASP cc_start: 0.8608 (p0) cc_final: 0.8323 (p0) REVERT: C 241 LYS cc_start: 0.8813 (tptp) cc_final: 0.8508 (tppt) REVERT: C 284 TYR cc_start: 0.8699 (t80) cc_final: 0.8049 (t80) REVERT: C 320 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8816 (mp) REVERT: D 25 ASP cc_start: 0.8346 (m-30) cc_final: 0.8121 (t70) REVERT: D 30 TYR cc_start: 0.7806 (m-10) cc_final: 0.7588 (m-80) REVERT: D 59 TRP cc_start: 0.7321 (m-90) cc_final: 0.6919 (m100) REVERT: D 153 LEU cc_start: 0.8154 (mt) cc_final: 0.7580 (tt) REVERT: D 232 LEU cc_start: 0.3178 (OUTLIER) cc_final: 0.1538 (pt) REVERT: D 236 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8332 (tm-30) REVERT: D 332 TYR cc_start: 0.7820 (t80) cc_final: 0.7186 (t80) REVERT: D 343 MET cc_start: 0.6641 (ttm) cc_final: 0.6180 (ttm) REVERT: D 374 PHE cc_start: 0.7826 (t80) cc_final: 0.7530 (t80) REVERT: E 359 MET cc_start: 0.8315 (tmm) cc_final: 0.7891 (ppp) REVERT: F 375 CYS cc_start: 0.8092 (m) cc_final: 0.7447 (t) REVERT: F 400 LYS cc_start: 0.7742 (mttt) cc_final: 0.7341 (mmtt) outliers start: 65 outliers final: 54 residues processed: 268 average time/residue: 0.1245 time to fit residues: 50.3986 Evaluate side-chains 268 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 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 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 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 232 LEU 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 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 46 GLN Chi-restraints excluded: chain F residue 172 ILE 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 388 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 149 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 155 HIS B 239 GLN C 49 GLN D 404 GLN F 46 GLN F 151 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 = 0.4141 r_free = 0.4141 target = 0.165761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117266 restraints weight = 24769.618| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3401 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16749 Z= 0.127 Angle : 0.496 14.141 22562 Z= 0.253 Chirality : 0.038 0.300 2417 Planarity : 0.003 0.030 2685 Dihedral : 12.240 178.506 2494 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.77 % Allowed : 13.58 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1844 helix: 2.03 (0.14), residues: 1332 sheet: 1.47 (0.51), residues: 103 loop : -0.48 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 309 TYR 0.026 0.001 TYR D 127 PHE 0.020 0.001 PHE E 419 TRP 0.028 0.001 TRP B 341 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00284 (16733) covalent geometry : angle 0.49609 (22530) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.63790 ( 32) hydrogen bonds : bond 0.03208 ( 1092) hydrogen bonds : angle 3.53325 ( 3216) *********************** 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 284 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.713 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: 0.8508 (ptt180) cc_final: 0.8288 (ptp-110) REVERT: A 46 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: A 143 TRP cc_start: 0.8291 (p-90) cc_final: 0.8050 (p90) REVERT: A 161 LEU cc_start: 0.8614 (mt) cc_final: 0.8391 (pp) REVERT: A 369 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8043 (ptmt) REVERT: B 236 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7933 (tm-30) REVERT: B 284 TYR cc_start: 0.8764 (t80) cc_final: 0.8312 (t80) REVERT: B 292 ASP cc_start: 0.8747 (p0) cc_final: 0.8476 (p0) REVERT: C 241 LYS cc_start: 0.8839 (tptp) cc_final: 0.8512 (tppt) REVERT: C 284 TYR cc_start: 0.8773 (t80) cc_final: 0.8128 (t80) REVERT: C 320 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8913 (mp) REVERT: C 404 GLN cc_start: 0.8110 (mp10) cc_final: 0.7746 (mp10) REVERT: D 25 ASP cc_start: 0.8505 (m-30) cc_final: 0.8239 (t70) REVERT: D 30 TYR cc_start: 0.7924 (m-10) cc_final: 0.7672 (m-80) REVERT: D 59 TRP cc_start: 0.7401 (m-90) cc_final: 0.6988 (m100) REVERT: D 144 PHE cc_start: 0.7149 (m-10) cc_final: 0.6888 (m-10) REVERT: D 153 LEU cc_start: 0.8131 (mt) cc_final: 0.7553 (tt) REVERT: D 232 LEU cc_start: 0.3206 (OUTLIER) cc_final: 0.1616 (pt) REVERT: D 236 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8268 (tm-30) REVERT: D 332 TYR cc_start: 0.8022 (t80) cc_final: 0.7407 (t80) REVERT: D 343 MET cc_start: 0.6765 (ttm) cc_final: 0.6321 (ttm) REVERT: D 374 PHE cc_start: 0.7884 (t80) cc_final: 0.7561 (t80) REVERT: E 153 MET cc_start: 0.8728 (tpp) cc_final: 0.8527 (ttt) REVERT: E 359 MET cc_start: 0.8494 (tmm) cc_final: 0.8104 (ppp) REVERT: F 46 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: F 375 CYS cc_start: 0.8172 (m) cc_final: 0.7520 (t) REVERT: F 400 LYS cc_start: 0.7761 (mttt) cc_final: 0.7343 (mmtt) outliers start: 66 outliers final: 55 residues processed: 269 average time/residue: 0.1239 time to fit residues: 50.6189 Evaluate side-chains 269 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 376 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 232 LEU 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 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 46 GLN Chi-restraints excluded: chain F residue 172 ILE 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 388 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 42 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 88 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 F 46 GLN F 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119593 restraints weight = 24835.542| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.16 r_work: 0.3432 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16749 Z= 0.096 Angle : 0.469 12.948 22562 Z= 0.241 Chirality : 0.037 0.178 2417 Planarity : 0.003 0.030 2685 Dihedral : 11.820 176.728 2494 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.74 % Allowed : 14.78 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.20), residues: 1844 helix: 2.12 (0.14), residues: 1330 sheet: 1.59 (0.51), residues: 103 loop : -0.36 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 309 TYR 0.022 0.001 TYR D 127 PHE 0.029 0.001 PHE C 393 TRP 0.029 0.001 TRP B 341 HIS 0.007 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00199 (16733) covalent geometry : angle 0.46866 (22530) SS BOND : bond 0.00214 ( 16) SS BOND : angle 0.54761 ( 32) hydrogen bonds : bond 0.03067 ( 1092) hydrogen bonds : angle 3.45681 ( 3216) *********************** 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 277 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.675 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: 0.8462 (ptt180) cc_final: 0.8235 (ptp-110) REVERT: A 46 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7607 (tp40) REVERT: A 143 TRP cc_start: 0.8168 (p-90) cc_final: 0.7923 (p90) REVERT: A 369 LYS cc_start: 0.8481 (mmtm) cc_final: 0.8051 (pttt) REVERT: B 153 LEU cc_start: 0.8409 (mm) cc_final: 0.8134 (mm) REVERT: B 236 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7926 (tm-30) REVERT: B 284 TYR cc_start: 0.8683 (t80) cc_final: 0.8267 (t80) REVERT: B 292 ASP cc_start: 0.8637 (p0) cc_final: 0.8396 (p0) REVERT: C 241 LYS cc_start: 0.8822 (tptp) cc_final: 0.8477 (tppt) REVERT: C 284 TYR cc_start: 0.8704 (t80) cc_final: 0.8124 (t80) REVERT: C 320 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8884 (mp) REVERT: C 404 GLN cc_start: 0.8285 (mp10) cc_final: 0.7946 (mp10) REVERT: D 25 ASP cc_start: 0.8467 (m-30) cc_final: 0.8198 (t70) REVERT: D 30 TYR cc_start: 0.7880 (m-10) cc_final: 0.7622 (m-80) REVERT: D 59 TRP cc_start: 0.7483 (m-90) cc_final: 0.7019 (m100) REVERT: D 144 PHE cc_start: 0.7215 (m-10) cc_final: 0.6936 (m-10) REVERT: D 153 LEU cc_start: 0.8109 (mt) cc_final: 0.7520 (tt) REVERT: D 332 TYR cc_start: 0.8012 (t80) cc_final: 0.7406 (t80) REVERT: D 334 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8003 (mt) REVERT: D 343 MET cc_start: 0.6633 (ttm) cc_final: 0.6237 (ttm) REVERT: D 374 PHE cc_start: 0.7876 (t80) cc_final: 0.7547 (t80) REVERT: E 359 MET cc_start: 0.8482 (tmm) cc_final: 0.8084 (ppp) REVERT: F 46 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: F 375 CYS cc_start: 0.8203 (m) cc_final: 0.7560 (t) REVERT: F 400 LYS cc_start: 0.7779 (mttt) cc_final: 0.7356 (mmtt) outliers start: 48 outliers final: 40 residues processed: 261 average time/residue: 0.1320 time to fit residues: 51.8162 Evaluate side-chains 259 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 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 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 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 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 326 TYR 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 46 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 92 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN F 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.164496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115347 restraints weight = 24908.375| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.27 r_work: 0.3361 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16749 Z= 0.168 Angle : 0.519 12.206 22562 Z= 0.268 Chirality : 0.039 0.184 2417 Planarity : 0.003 0.029 2685 Dihedral : 11.837 178.682 2494 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.37 % Allowed : 14.67 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1844 helix: 2.03 (0.14), residues: 1331 sheet: 1.38 (0.51), residues: 104 loop : -0.44 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 309 TYR 0.024 0.001 TYR D 127 PHE 0.025 0.001 PHE C 393 TRP 0.032 0.001 TRP B 341 HIS 0.007 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00387 (16733) covalent geometry : angle 0.51847 (22530) SS BOND : bond 0.00359 ( 16) SS BOND : angle 0.70044 ( 32) hydrogen bonds : bond 0.03285 ( 1092) hydrogen bonds : angle 3.53764 ( 3216) *********************** 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 271 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.655 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: 0.8593 (ptt180) cc_final: 0.8298 (ptp-110) REVERT: A 46 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7646 (tp40) REVERT: A 143 TRP cc_start: 0.8332 (p-90) cc_final: 0.8080 (p90) REVERT: A 369 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8012 (ptmt) REVERT: B 153 LEU cc_start: 0.8491 (mm) cc_final: 0.8209 (mm) REVERT: B 236 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7931 (tm-30) REVERT: B 284 TYR cc_start: 0.8858 (t80) cc_final: 0.8157 (t80) REVERT: B 292 ASP cc_start: 0.8836 (p0) cc_final: 0.8567 (p0) REVERT: C 241 LYS cc_start: 0.8806 (tptp) cc_final: 0.8491 (tppt) REVERT: C 246 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7901 (pttm) REVERT: C 284 TYR cc_start: 0.8870 (t80) cc_final: 0.8213 (t80) REVERT: C 320 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 25 ASP cc_start: 0.8525 (m-30) cc_final: 0.8231 (t70) REVERT: D 30 TYR cc_start: 0.7934 (m-10) cc_final: 0.7704 (m-80) REVERT: D 59 TRP cc_start: 0.7450 (m-90) cc_final: 0.6797 (m100) REVERT: D 153 LEU cc_start: 0.8011 (mt) cc_final: 0.7551 (tt) REVERT: D 232 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.1586 (pt) REVERT: D 236 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8310 (tm-30) REVERT: D 332 TYR cc_start: 0.7989 (t80) cc_final: 0.7354 (t80) REVERT: D 343 MET cc_start: 0.6765 (ttm) cc_final: 0.6310 (ttm) REVERT: D 374 PHE cc_start: 0.7883 (t80) cc_final: 0.7552 (t80) REVERT: E 359 MET cc_start: 0.8488 (tmm) cc_final: 0.8066 (ppp) REVERT: F 400 LYS cc_start: 0.7829 (mttt) cc_final: 0.7379 (mmtt) REVERT: F 423 MET cc_start: 0.5294 (ppp) cc_final: 0.5058 (ppp) outliers start: 59 outliers final: 49 residues processed: 258 average time/residue: 0.1340 time to fit residues: 52.2756 Evaluate side-chains 259 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 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 320 ILE Chi-restraints excluded: chain C residue 329 VAL 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 232 LEU 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 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 46 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 155 HIS D 49 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.165992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117613 restraints weight = 24524.506| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.19 r_work: 0.3395 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16749 Z= 0.121 Angle : 0.497 13.867 22562 Z= 0.256 Chirality : 0.038 0.182 2417 Planarity : 0.003 0.038 2685 Dihedral : 11.497 174.407 2494 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.97 % Allowed : 15.24 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.20), residues: 1844 helix: 2.03 (0.14), residues: 1332 sheet: 1.53 (0.51), residues: 103 loop : -0.48 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 434 TYR 0.020 0.001 TYR D 127 PHE 0.025 0.001 PHE E 419 TRP 0.030 0.001 TRP B 341 HIS 0.006 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00271 (16733) covalent geometry : angle 0.49649 (22530) SS BOND : bond 0.00267 ( 16) SS BOND : angle 0.61851 ( 32) hydrogen bonds : bond 0.03168 ( 1092) hydrogen bonds : angle 3.50053 ( 3216) ********************** 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 266 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8501 (ptt180) cc_final: 0.8208 (ptp-110) REVERT: A 46 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: A 143 TRP cc_start: 0.8271 (p-90) cc_final: 0.7980 (p90) REVERT: A 369 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8015 (ptmt) REVERT: B 153 LEU cc_start: 0.8546 (mm) cc_final: 0.8239 (mm) REVERT: B 236 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7964 (tm-30) REVERT: B 284 TYR cc_start: 0.8801 (t80) cc_final: 0.8326 (t80) REVERT: B 292 ASP cc_start: 0.8781 (p0) cc_final: 0.8514 (p0) REVERT: C 241 LYS cc_start: 0.8811 (tptp) cc_final: 0.8481 (tppt) REVERT: C 284 TYR cc_start: 0.8816 (t80) cc_final: 0.8152 (t80) REVERT: C 320 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 25 ASP cc_start: 0.8495 (m-30) cc_final: 0.8205 (t70) REVERT: D 30 TYR cc_start: 0.7892 (m-10) cc_final: 0.7659 (m-80) REVERT: D 59 TRP cc_start: 0.7474 (m-90) cc_final: 0.7018 (m100) REVERT: D 144 PHE cc_start: 0.7281 (m-10) cc_final: 0.7065 (m-10) REVERT: D 153 LEU cc_start: 0.7928 (mt) cc_final: 0.7458 (tt) REVERT: D 332 TYR cc_start: 0.7964 (t80) cc_final: 0.7349 (t80) REVERT: D 343 MET cc_start: 0.6684 (ttm) cc_final: 0.6304 (ttm) REVERT: D 374 PHE cc_start: 0.7896 (t80) cc_final: 0.7574 (t80) REVERT: E 359 MET cc_start: 0.8489 (tmm) cc_final: 0.8033 (ppp) REVERT: F 37 MET cc_start: 0.8428 (tpp) cc_final: 0.8197 (ttp) REVERT: F 400 LYS cc_start: 0.7862 (mttt) cc_final: 0.7396 (mmtt) REVERT: F 423 MET cc_start: 0.5218 (ppp) cc_final: 0.4995 (ppp) outliers start: 52 outliers final: 47 residues processed: 253 average time/residue: 0.1247 time to fit residues: 47.9314 Evaluate side-chains 256 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 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 320 ILE Chi-restraints excluded: chain C residue 329 VAL 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 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 326 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 138 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS F 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116970 restraints weight = 24900.306| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.17 r_work: 0.3391 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3699 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= 0.140 Angle : 0.510 13.244 22562 Z= 0.263 Chirality : 0.038 0.181 2417 Planarity : 0.003 0.037 2685 Dihedral : 11.340 169.686 2494 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 15.58 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.19), residues: 1844 helix: 2.06 (0.14), residues: 1322 sheet: 1.44 (0.51), residues: 103 loop : -0.34 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 434 TYR 0.021 0.001 TYR D 127 PHE 0.034 0.001 PHE C 324 TRP 0.031 0.001 TRP B 341 HIS 0.006 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00319 (16733) covalent geometry : angle 0.50961 (22530) SS BOND : bond 0.00320 ( 16) SS BOND : angle 0.66118 ( 32) hydrogen bonds : bond 0.03213 ( 1092) hydrogen bonds : angle 3.51905 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4827.08 seconds wall clock time: 83 minutes 26.99 seconds (5006.99 seconds total)