Starting phenix.real_space_refine on Sun Aug 24 02:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7b_28901/08_2025/8f7b_28901.cif" } resolution = 3.15 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= 0.003 sd= 0.073 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 6 5.49 5 S 106 5.16 5 C 10678 2.51 5 N 2547 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16166 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2672 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2668 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2654 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "D" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2648 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 64 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.19 Number of scatterers: 16166 At special positions: 0 Unit cell: (96.416, 106.896, 134.144, 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 106 16.00 P 6 15.00 O 2829 8.00 N 2547 7.00 C 10678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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=2.04 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 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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: 1.12 Conformation dependent library (CDL) restraints added in 707.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 76.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.188A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.966A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.944A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.581A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.920A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 3.887A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) 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: 4.141A 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 410 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.983A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.569A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.544A pdb=" N CYS B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.251A 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 410 removed outlier: 3.529A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 22 through 50 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.619A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.870A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 345 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: 4.117A 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 410 Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.639A pdb=" N ASP D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.602A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.896A 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 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 315 through 346 removed outlier: 4.261A 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 369 through 383 removed outlier: 3.617A pdb=" N ALA D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 removed outlier: 4.262A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.542A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.831A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.498A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.545A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 317 through 345 removed outlier: 3.577A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.566A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.263A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.689A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.022A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.531A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 Processing helix chain 'F' and resid 169 through 179 Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 256 through 284 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 351 through 356 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.333A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 393 through 408 removed outlier: 3.982A pdb=" N GLU F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.601A pdb=" N VAL A 293 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.784A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.636A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'F' and resid 52 through 56 1102 hydrogen bonds defined for protein. 3261 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: 2.34 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4304 1.34 - 1.46: 3553 1.46 - 1.58: 8563 1.58 - 1.70: 7 1.70 - 1.82: 158 Bond restraints: 16585 Sorted by residual: bond pdb=" C10 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sigma weight residual 1.206 1.359 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.783 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" O4P PEE E 901 " pdb=" P PEE E 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" O4P PEE F 901 " pdb=" P PEE F 901 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 16580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 22059 2.78 - 5.55: 236 5.55 - 8.33: 58 8.33 - 11.11: 6 11.11 - 13.89: 7 Bond angle restraints: 22366 Sorted by residual: angle pdb=" N LEU A 344 " pdb=" CA LEU A 344 " pdb=" C LEU A 344 " ideal model delta sigma weight residual 111.69 118.08 -6.39 1.23e+00 6.61e-01 2.70e+01 angle pdb=" O1P PEE F 901 " pdb=" P PEE F 901 " pdb=" O2P PEE F 901 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.23 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.21 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 22361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 9496 35.76 - 71.52: 307 71.52 - 107.28: 28 107.28 - 143.04: 8 143.04 - 178.80: 9 Dihedral angle restraints: 9848 sinusoidal: 4159 harmonic: 5689 Sorted by residual: dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 295 " pdb=" CB CYS A 295 " ideal model delta sinusoidal sigma weight residual 93.00 36.75 56.25 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" C4 PEE B 901 " pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " pdb=" O3P PEE B 901 " ideal model delta sinusoidal sigma weight residual 171.78 -7.02 178.80 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2260 0.082 - 0.164: 145 0.164 - 0.246: 9 0.246 - 0.328: 0 0.328 - 0.410: 2 Chirality restraints: 2416 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.21e+00 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 -2.73 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE E 53 " pdb=" CA ILE E 53 " pdb=" CG1 ILE E 53 " pdb=" CG2 ILE E 53 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2413 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.026 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D 168 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 170 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP F 170 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 170 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 170 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 170 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 170 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 170 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 145 " -0.023 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP F 145 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 145 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 145 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 145 " 0.000 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3862 2.79 - 3.32: 15296 3.32 - 3.85: 28129 3.85 - 4.37: 32223 4.37 - 4.90: 55592 Nonbonded interactions: 135102 Sorted by model distance: nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR A 316 " pdb=" OE2 GLU B 115 " model vdw 2.303 3.040 nonbonded pdb=" OD1 ASP F 50 " pdb=" NE2 HIS F 310 " model vdw 2.308 3.120 nonbonded pdb=" OD2 ASP F 50 " pdb=" OH TYR F 116 " model vdw 2.314 3.040 ... (remaining 135097 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 68 or resid 93 through 175 or resid 232 through \ 408 or resid 901 or (resid 902 and (name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 408 or (resid 901 and (name N or name C1 or 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 C1 \ 9 or name C2 or name C20 or name C4 or name C5 or name O1P or name O2 or name O2 \ P or name O3P or name O4 or name O4P or name P )) 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 O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or (resid 901 and (name N or name C1 or nam \ e 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 C2 or name C20 or name C4 or name C5 o \ r name O1P or name O2 or name O2P or name O3P or name O4 or name O4P or name P ) \ ) 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 O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or (resid 902 and (name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.005 0.153 16602 Z= 0.268 Angle : 0.788 13.885 22400 Z= 0.424 Chirality : 0.044 0.410 2416 Planarity : 0.005 0.080 2701 Dihedral : 18.683 178.800 6113 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.23 % Allowed : 17.51 % Favored : 82.26 % 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: 1.06 (0.19), residues: 1858 helix: 1.33 (0.13), residues: 1308 sheet: 0.62 (0.56), residues: 105 loop : -1.08 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.024 0.001 TYR C 284 PHE 0.044 0.002 PHE D 390 TRP 0.055 0.002 TRP F 170 HIS 0.013 0.001 HIS C 155 Details of bonding type rmsd covalent geometry : bond 0.00509 (16585) covalent geometry : angle 0.78690 (22366) SS BOND : bond 0.00308 ( 17) SS BOND : angle 1.43486 ( 34) hydrogen bonds : bond 0.12380 ( 1102) hydrogen bonds : angle 5.72917 ( 3261) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 265 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 MET cc_start: 0.7380 (tpt) cc_final: 0.7070 (tpt) REVERT: B 359 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 143 TRP cc_start: 0.7822 (t60) cc_final: 0.7459 (t60) REVERT: C 308 TYR cc_start: 0.9028 (m-80) cc_final: 0.8543 (m-80) REVERT: C 364 ASP cc_start: 0.5105 (p0) cc_final: 0.4800 (t0) REVERT: D 168 TRP cc_start: 0.6694 (t-100) cc_final: 0.6429 (t-100) REVERT: E 308 TYR cc_start: 0.9135 (m-80) cc_final: 0.8907 (m-80) REVERT: E 393 PHE cc_start: 0.7082 (m-80) cc_final: 0.6332 (m-80) REVERT: F 348 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6297 (tm-30) REVERT: F 387 ARG cc_start: 0.6728 (tmm160) cc_final: 0.6234 (tmm160) REVERT: F 392 LEU cc_start: 0.8295 (tp) cc_final: 0.8005 (tp) outliers start: 4 outliers final: 3 residues processed: 269 average time/residue: 0.1191 time to fit residues: 47.2837 Evaluate side-chains 249 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS A 406 ASN B 105 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.164648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119600 restraints weight = 20356.028| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.21 r_work: 0.3381 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16602 Z= 0.189 Angle : 0.499 6.395 22400 Z= 0.270 Chirality : 0.039 0.132 2416 Planarity : 0.004 0.037 2701 Dihedral : 11.983 172.013 2319 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.99 % Allowed : 17.00 % Favored : 81.01 % 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: 1.71 (0.19), residues: 1858 helix: 1.93 (0.14), residues: 1331 sheet: 0.32 (0.54), residues: 105 loop : -1.25 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.016 0.002 TYR C 338 PHE 0.015 0.001 PHE E 324 TRP 0.026 0.002 TRP F 145 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00441 (16585) covalent geometry : angle 0.49684 (22366) SS BOND : bond 0.00342 ( 17) SS BOND : angle 1.16913 ( 34) hydrogen bonds : bond 0.03715 ( 1102) hydrogen bonds : angle 4.28304 ( 3261) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7703 (t) cc_final: 0.7066 (p) REVERT: A 171 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8308 (ttm-80) REVERT: B 359 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6946 (mm-30) REVERT: C 30 TYR cc_start: 0.8006 (m-80) cc_final: 0.7783 (m-10) REVERT: C 364 ASP cc_start: 0.5197 (p0) cc_final: 0.4976 (p0) REVERT: C 404 GLN cc_start: 0.7290 (mm110) cc_final: 0.7011 (mm110) REVERT: D 99 TYR cc_start: 0.8818 (m-10) cc_final: 0.8609 (m-10) REVERT: F 113 GLN cc_start: 0.8798 (mt0) cc_final: 0.8544 (mt0) REVERT: F 300 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: F 392 LEU cc_start: 0.8127 (tp) cc_final: 0.7770 (tp) outliers start: 35 outliers final: 19 residues processed: 277 average time/residue: 0.1095 time to fit residues: 45.9234 Evaluate side-chains 254 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 253 HIS A 406 ASN B 105 GLN C 46 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS F 134 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.166779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119969 restraints weight = 20863.665| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.31 r_work: 0.3402 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16602 Z= 0.139 Angle : 0.448 6.098 22400 Z= 0.244 Chirality : 0.037 0.122 2416 Planarity : 0.003 0.038 2701 Dihedral : 9.109 155.043 2315 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 17.74 % Favored : 79.93 % 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: 1858 helix: 2.14 (0.14), residues: 1332 sheet: 0.41 (0.53), residues: 105 loop : -1.21 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 387 TYR 0.013 0.001 TYR C 338 PHE 0.011 0.001 PHE B 374 TRP 0.021 0.001 TRP D 168 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00321 (16585) covalent geometry : angle 0.44665 (22366) SS BOND : bond 0.00273 ( 17) SS BOND : angle 1.11730 ( 34) hydrogen bonds : bond 0.03400 ( 1102) hydrogen bonds : angle 4.08431 ( 3261) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7675 (t) cc_final: 0.7050 (p) REVERT: A 161 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7889 (mp) REVERT: B 359 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6939 (mm-30) REVERT: C 30 TYR cc_start: 0.7980 (m-80) cc_final: 0.7747 (m-10) REVERT: C 143 TRP cc_start: 0.8134 (t60) cc_final: 0.7793 (t60) REVERT: C 364 ASP cc_start: 0.5121 (p0) cc_final: 0.4848 (p0) REVERT: D 99 TYR cc_start: 0.8810 (m-10) cc_final: 0.8592 (m-10) REVERT: D 169 THR cc_start: 0.6464 (m) cc_final: 0.6172 (m) REVERT: D 250 PHE cc_start: 0.6569 (t80) cc_final: 0.6367 (t80) REVERT: D 284 TYR cc_start: 0.7927 (t80) cc_final: 0.7657 (t80) REVERT: E 275 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8087 (t80) REVERT: E 324 PHE cc_start: 0.7774 (t80) cc_final: 0.7529 (t80) REVERT: F 300 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7553 (mtt) REVERT: F 392 LEU cc_start: 0.8126 (tp) cc_final: 0.7710 (tp) outliers start: 41 outliers final: 19 residues processed: 270 average time/residue: 0.1349 time to fit residues: 54.7048 Evaluate side-chains 251 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN B 105 GLN C 46 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 288 ASN F 309 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.165249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118431 restraints weight = 20837.454| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.30 r_work: 0.3379 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16602 Z= 0.167 Angle : 0.464 6.404 22400 Z= 0.252 Chirality : 0.038 0.182 2416 Planarity : 0.003 0.037 2701 Dihedral : 7.945 107.186 2313 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.50 % Allowed : 18.36 % Favored : 79.14 % 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: 1.94 (0.19), residues: 1858 helix: 2.11 (0.14), residues: 1336 sheet: 0.31 (0.55), residues: 100 loop : -1.22 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 387 TYR 0.012 0.001 TYR A 338 PHE 0.013 0.001 PHE B 374 TRP 0.024 0.001 TRP D 168 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00389 (16585) covalent geometry : angle 0.46204 (22366) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.19627 ( 34) hydrogen bonds : bond 0.03439 ( 1102) hydrogen bonds : angle 4.07520 ( 3261) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7441 (t) cc_final: 0.6832 (p) REVERT: A 161 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 17 TYR cc_start: 0.8853 (m-10) cc_final: 0.8488 (m-10) REVERT: B 359 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6923 (mm-30) REVERT: C 46 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: C 245 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7380 (mp0) REVERT: C 364 ASP cc_start: 0.5292 (p0) cc_final: 0.4995 (p0) REVERT: C 375 MET cc_start: 0.7727 (mtm) cc_final: 0.7515 (mtm) REVERT: D 99 TYR cc_start: 0.8819 (m-10) cc_final: 0.8581 (m-10) REVERT: D 144 PHE cc_start: 0.7275 (m-10) cc_final: 0.7059 (m-10) REVERT: D 249 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7845 (tptt) REVERT: D 250 PHE cc_start: 0.6661 (t80) cc_final: 0.6386 (t80) REVERT: D 284 TYR cc_start: 0.7904 (t80) cc_final: 0.7660 (t80) REVERT: E 275 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8145 (t80) REVERT: E 309 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8011 (ttt180) REVERT: E 324 PHE cc_start: 0.7765 (t80) cc_final: 0.7515 (t80) REVERT: F 300 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7678 (mtp) REVERT: F 392 LEU cc_start: 0.8265 (tp) cc_final: 0.7858 (tp) outliers start: 44 outliers final: 24 residues processed: 263 average time/residue: 0.1273 time to fit residues: 51.6090 Evaluate side-chains 253 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS C 46 GLN C 155 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119037 restraints weight = 20706.776| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.31 r_work: 0.3387 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16602 Z= 0.143 Angle : 0.450 7.760 22400 Z= 0.243 Chirality : 0.037 0.121 2416 Planarity : 0.003 0.038 2701 Dihedral : 7.212 78.590 2313 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.62 % Allowed : 18.25 % Favored : 79.14 % 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: 2.00 (0.19), residues: 1858 helix: 2.18 (0.14), residues: 1337 sheet: 0.29 (0.55), residues: 100 loop : -1.28 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 387 TYR 0.013 0.001 TYR A 338 PHE 0.011 0.001 PHE B 374 TRP 0.026 0.001 TRP D 168 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00330 (16585) covalent geometry : angle 0.44789 (22366) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.16029 ( 34) hydrogen bonds : bond 0.03314 ( 1102) hydrogen bonds : angle 4.01092 ( 3261) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7422 (t) cc_final: 0.6814 (p) REVERT: A 161 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7916 (mp) REVERT: B 17 TYR cc_start: 0.8858 (m-10) cc_final: 0.8475 (m-10) REVERT: B 359 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6912 (mm-30) REVERT: C 245 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7350 (mp0) REVERT: C 364 ASP cc_start: 0.5210 (p0) cc_final: 0.4894 (p0) REVERT: C 403 ARG cc_start: 0.7845 (ptp-110) cc_final: 0.7242 (mtm110) REVERT: D 99 TYR cc_start: 0.8815 (m-10) cc_final: 0.8581 (m-10) REVERT: D 250 PHE cc_start: 0.6735 (t80) cc_final: 0.6486 (t80) REVERT: D 284 TYR cc_start: 0.7766 (t80) cc_final: 0.7563 (t80) REVERT: E 275 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8060 (t80) REVERT: E 309 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7938 (ttt180) REVERT: E 324 PHE cc_start: 0.7731 (t80) cc_final: 0.7449 (t80) REVERT: F 300 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7670 (mtp) REVERT: F 392 LEU cc_start: 0.8319 (tp) cc_final: 0.7876 (tp) outliers start: 46 outliers final: 32 residues processed: 271 average time/residue: 0.1275 time to fit residues: 52.9753 Evaluate side-chains 262 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.163947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119135 restraints weight = 20327.229| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.21 r_work: 0.3379 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16602 Z= 0.167 Angle : 0.467 6.961 22400 Z= 0.252 Chirality : 0.038 0.143 2416 Planarity : 0.003 0.036 2701 Dihedral : 6.990 78.264 2313 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.90 % Allowed : 18.87 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.19), residues: 1858 helix: 2.15 (0.14), residues: 1336 sheet: 0.21 (0.54), residues: 100 loop : -1.26 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 387 TYR 0.013 0.001 TYR A 338 PHE 0.013 0.001 PHE B 374 TRP 0.028 0.002 TRP D 168 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00391 (16585) covalent geometry : angle 0.46470 (22366) SS BOND : bond 0.00298 ( 17) SS BOND : angle 1.20456 ( 34) hydrogen bonds : bond 0.03393 ( 1102) hydrogen bonds : angle 4.03718 ( 3261) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7436 (t) cc_final: 0.6835 (p) REVERT: A 161 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 343 MET cc_start: 0.9084 (mtm) cc_final: 0.8788 (mtm) REVERT: B 168 TRP cc_start: 0.7831 (t-100) cc_final: 0.7465 (t-100) REVERT: B 359 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7074 (mm-30) REVERT: C 245 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7303 (mp0) REVERT: C 364 ASP cc_start: 0.5220 (p0) cc_final: 0.4899 (p0) REVERT: C 403 ARG cc_start: 0.7784 (ptp-110) cc_final: 0.7139 (mtm110) REVERT: D 99 TYR cc_start: 0.8774 (m-10) cc_final: 0.8518 (m-10) REVERT: D 249 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7889 (tptt) REVERT: D 250 PHE cc_start: 0.6742 (t80) cc_final: 0.6439 (t80) REVERT: D 284 TYR cc_start: 0.7825 (t80) cc_final: 0.7604 (t80) REVERT: E 309 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8038 (ttt180) REVERT: E 324 PHE cc_start: 0.7726 (t80) cc_final: 0.7418 (t80) REVERT: E 381 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7224 (mm-40) REVERT: F 36 LEU cc_start: 0.8369 (tp) cc_final: 0.8144 (mp) REVERT: F 113 GLN cc_start: 0.8806 (mt0) cc_final: 0.8402 (mt0) REVERT: F 300 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7728 (mtp) outliers start: 51 outliers final: 35 residues processed: 269 average time/residue: 0.1261 time to fit residues: 52.2341 Evaluate side-chains 261 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 32 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.166371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121857 restraints weight = 20214.151| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.22 r_work: 0.3418 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16602 Z= 0.116 Angle : 0.437 7.601 22400 Z= 0.235 Chirality : 0.037 0.125 2416 Planarity : 0.003 0.039 2701 Dihedral : 6.493 81.233 2313 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 19.95 % Favored : 77.89 % 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: 2.16 (0.19), residues: 1858 helix: 2.29 (0.14), residues: 1336 sheet: 0.41 (0.53), residues: 104 loop : -1.23 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 387 TYR 0.013 0.001 TYR A 338 PHE 0.015 0.001 PHE D 144 TRP 0.031 0.002 TRP F 170 HIS 0.009 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00260 (16585) covalent geometry : angle 0.43490 (22366) SS BOND : bond 0.00263 ( 17) SS BOND : angle 1.10205 ( 34) hydrogen bonds : bond 0.03125 ( 1102) hydrogen bonds : angle 3.89471 ( 3261) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7469 (t) cc_final: 0.6877 (p) REVERT: A 161 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 17 TYR cc_start: 0.8736 (m-10) cc_final: 0.8384 (m-10) REVERT: B 168 TRP cc_start: 0.7805 (t-100) cc_final: 0.7525 (t-100) REVERT: B 359 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7054 (mm-30) REVERT: C 245 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6958 (mp0) REVERT: C 364 ASP cc_start: 0.5192 (p0) cc_final: 0.4875 (p0) REVERT: C 403 ARG cc_start: 0.7817 (ptp-110) cc_final: 0.7205 (mtm110) REVERT: D 99 TYR cc_start: 0.8759 (m-10) cc_final: 0.8532 (m-10) REVERT: D 144 PHE cc_start: 0.7211 (m-10) cc_final: 0.6925 (m-10) REVERT: D 164 PHE cc_start: 0.5851 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: D 168 TRP cc_start: 0.6764 (t-100) cc_final: 0.6339 (t-100) REVERT: E 309 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.7924 (ttt180) REVERT: E 324 PHE cc_start: 0.7621 (t80) cc_final: 0.7323 (t80) REVERT: E 381 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7157 (mm-40) REVERT: F 36 LEU cc_start: 0.8352 (tp) cc_final: 0.8112 (mp) REVERT: F 300 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7668 (mtt) REVERT: F 373 MET cc_start: 0.7652 (mtp) cc_final: 0.7313 (ttt) outliers start: 38 outliers final: 26 residues processed: 274 average time/residue: 0.1211 time to fit residues: 50.5658 Evaluate side-chains 258 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 154 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121971 restraints weight = 20712.672| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.52 r_work: 0.3406 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16602 Z= 0.130 Angle : 0.457 7.876 22400 Z= 0.246 Chirality : 0.037 0.145 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.415 82.877 2313 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.05 % Allowed : 20.30 % Favored : 77.66 % 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: 1858 helix: 2.31 (0.14), residues: 1336 sheet: 0.51 (0.54), residues: 104 loop : -1.26 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 387 TYR 0.013 0.001 TYR A 338 PHE 0.018 0.001 PHE D 250 TRP 0.036 0.002 TRP F 170 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00296 (16585) covalent geometry : angle 0.45491 (22366) SS BOND : bond 0.00232 ( 17) SS BOND : angle 1.13417 ( 34) hydrogen bonds : bond 0.03182 ( 1102) hydrogen bonds : angle 3.89298 ( 3261) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7367 (t) cc_final: 0.6774 (p) REVERT: A 161 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7900 (mp) REVERT: B 17 TYR cc_start: 0.8747 (m-10) cc_final: 0.8434 (m-10) REVERT: B 168 TRP cc_start: 0.7742 (t-100) cc_final: 0.7446 (t-100) REVERT: B 359 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 245 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6969 (mp0) REVERT: C 364 ASP cc_start: 0.5201 (p0) cc_final: 0.4879 (p0) REVERT: C 403 ARG cc_start: 0.7755 (ptp-110) cc_final: 0.7384 (ptp-110) REVERT: D 99 TYR cc_start: 0.8788 (m-10) cc_final: 0.8555 (m-10) REVERT: D 144 PHE cc_start: 0.7226 (m-10) cc_final: 0.7004 (m-10) REVERT: D 168 TRP cc_start: 0.6770 (t-100) cc_final: 0.6499 (t60) REVERT: D 390 PHE cc_start: 0.7226 (t80) cc_final: 0.6411 (t80) REVERT: E 37 MET cc_start: 0.8348 (ttp) cc_final: 0.8090 (ttt) REVERT: E 154 GLU cc_start: 0.7874 (tp30) cc_final: 0.7018 (pt0) REVERT: E 309 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7928 (ttt180) REVERT: E 324 PHE cc_start: 0.7553 (t80) cc_final: 0.7246 (t80) REVERT: E 381 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6879 (mm-40) REVERT: F 36 LEU cc_start: 0.8228 (tp) cc_final: 0.7979 (mp) REVERT: F 264 ARG cc_start: 0.6451 (mpt-90) cc_final: 0.4795 (ttp80) REVERT: F 300 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7806 (mtt) outliers start: 36 outliers final: 31 residues processed: 260 average time/residue: 0.1305 time to fit residues: 51.5437 Evaluate side-chains 260 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120853 restraints weight = 20400.991| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.24 r_work: 0.3403 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16602 Z= 0.136 Angle : 0.465 7.968 22400 Z= 0.250 Chirality : 0.038 0.143 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.375 84.948 2313 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.44 % Allowed : 19.84 % Favored : 77.71 % 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: 1858 helix: 2.33 (0.14), residues: 1335 sheet: 0.44 (0.54), residues: 105 loop : -1.20 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 387 TYR 0.013 0.001 TYR D 351 PHE 0.015 0.001 PHE D 250 TRP 0.041 0.002 TRP F 170 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (16585) covalent geometry : angle 0.46306 (22366) SS BOND : bond 0.00252 ( 17) SS BOND : angle 1.12305 ( 34) hydrogen bonds : bond 0.03202 ( 1102) hydrogen bonds : angle 3.89316 ( 3261) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7384 (t) cc_final: 0.6796 (p) REVERT: A 161 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 17 TYR cc_start: 0.8735 (m-10) cc_final: 0.8495 (m-10) REVERT: B 168 TRP cc_start: 0.7793 (t-100) cc_final: 0.7489 (t-100) REVERT: B 171 ARG cc_start: 0.8810 (tpp-160) cc_final: 0.8592 (tpp80) REVERT: B 265 MET cc_start: 0.7779 (tpt) cc_final: 0.7482 (tpt) REVERT: B 359 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 245 GLU cc_start: 0.7797 (mm-30) cc_final: 0.6962 (mp0) REVERT: C 309 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: C 364 ASP cc_start: 0.5198 (p0) cc_final: 0.4869 (p0) REVERT: C 403 ARG cc_start: 0.7736 (ptp-110) cc_final: 0.7376 (ptp-110) REVERT: C 404 GLN cc_start: 0.7293 (mm110) cc_final: 0.7034 (mm110) REVERT: D 99 TYR cc_start: 0.8793 (m-10) cc_final: 0.8549 (m-10) REVERT: D 144 PHE cc_start: 0.7368 (m-10) cc_final: 0.7139 (m-10) REVERT: D 168 TRP cc_start: 0.6746 (t-100) cc_final: 0.6499 (t60) REVERT: D 390 PHE cc_start: 0.7252 (t80) cc_final: 0.6401 (t80) REVERT: E 154 GLU cc_start: 0.7891 (tp30) cc_final: 0.7040 (pt0) REVERT: E 309 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.7869 (ttt180) REVERT: E 324 PHE cc_start: 0.7614 (t80) cc_final: 0.7302 (t80) REVERT: E 381 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7075 (mm-40) REVERT: F 36 LEU cc_start: 0.8264 (tp) cc_final: 0.8026 (mp) REVERT: F 113 GLN cc_start: 0.8753 (mt0) cc_final: 0.8522 (mt0) REVERT: F 264 ARG cc_start: 0.6378 (mpt-90) cc_final: 0.4649 (ttp80) REVERT: F 300 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7819 (mtt) outliers start: 43 outliers final: 32 residues processed: 260 average time/residue: 0.1193 time to fit residues: 47.6328 Evaluate side-chains 260 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 165 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 161 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121862 restraints weight = 20629.762| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.33 r_work: 0.3434 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16602 Z= 0.107 Angle : 0.449 8.339 22400 Z= 0.241 Chirality : 0.037 0.136 2416 Planarity : 0.003 0.038 2701 Dihedral : 6.120 88.340 2313 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 20.64 % Favored : 77.49 % 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: 2.38 (0.19), residues: 1858 helix: 2.44 (0.14), residues: 1332 sheet: 0.63 (0.54), residues: 104 loop : -1.11 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 387 TYR 0.013 0.001 TYR A 338 PHE 0.016 0.001 PHE D 250 TRP 0.046 0.002 TRP F 170 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00236 (16585) covalent geometry : angle 0.44700 (22366) SS BOND : bond 0.00294 ( 17) SS BOND : angle 1.06021 ( 34) hydrogen bonds : bond 0.03017 ( 1102) hydrogen bonds : angle 3.80152 ( 3261) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7454 (t) cc_final: 0.6855 (p) REVERT: A 161 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 17 TYR cc_start: 0.8715 (m-10) cc_final: 0.8479 (m-10) REVERT: B 168 TRP cc_start: 0.7754 (t-100) cc_final: 0.7419 (t-100) REVERT: B 171 ARG cc_start: 0.8837 (tpp-160) cc_final: 0.8626 (tpp80) REVERT: B 265 MET cc_start: 0.7739 (tpt) cc_final: 0.7494 (tpt) REVERT: C 245 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6986 (mp0) REVERT: C 364 ASP cc_start: 0.5190 (p0) cc_final: 0.4870 (p0) REVERT: C 404 GLN cc_start: 0.7290 (mm110) cc_final: 0.7038 (mm110) REVERT: D 99 TYR cc_start: 0.8768 (m-10) cc_final: 0.8517 (m-10) REVERT: D 144 PHE cc_start: 0.7334 (m-10) cc_final: 0.7078 (m-10) REVERT: D 168 TRP cc_start: 0.6711 (t-100) cc_final: 0.6489 (t60) REVERT: E 17 TYR cc_start: 0.7898 (m-10) cc_final: 0.7184 (p90) REVERT: E 154 GLU cc_start: 0.7918 (tp30) cc_final: 0.7164 (pt0) REVERT: E 155 HIS cc_start: 0.7949 (t-170) cc_final: 0.7733 (t-170) REVERT: E 309 ARG cc_start: 0.8344 (ttp-170) cc_final: 0.7766 (ttt180) REVERT: E 324 PHE cc_start: 0.7484 (t80) cc_final: 0.7200 (t80) REVERT: F 36 LEU cc_start: 0.8164 (tp) cc_final: 0.7897 (mp) REVERT: F 113 GLN cc_start: 0.8719 (mt0) cc_final: 0.8503 (mt0) REVERT: F 264 ARG cc_start: 0.6351 (mpt-90) cc_final: 0.4746 (ttp80) REVERT: F 300 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7797 (mtt) outliers start: 33 outliers final: 28 residues processed: 264 average time/residue: 0.1308 time to fit residues: 52.4232 Evaluate side-chains 258 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 97 optimal weight: 0.0030 chunk 152 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 160 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS E 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121422 restraints weight = 20670.736| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.30 r_work: 0.3429 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16602 Z= 0.115 Angle : 0.466 14.491 22400 Z= 0.248 Chirality : 0.037 0.136 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.129 89.786 2313 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 20.52 % Favored : 77.54 % 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: 2.33 (0.19), residues: 1858 helix: 2.40 (0.14), residues: 1339 sheet: 0.65 (0.53), residues: 104 loop : -1.19 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 118 TYR 0.012 0.001 TYR F 279 PHE 0.015 0.001 PHE D 250 TRP 0.045 0.001 TRP F 170 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00259 (16585) covalent geometry : angle 0.46400 (22366) SS BOND : bond 0.00236 ( 17) SS BOND : angle 1.09662 ( 34) hydrogen bonds : bond 0.03045 ( 1102) hydrogen bonds : angle 3.79319 ( 3261) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.15 seconds wall clock time: 79 minutes 40.30 seconds (4780.30 seconds total)