Starting phenix.real_space_refine on Tue Dec 31 18:36:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7b_28901/12_2024/8f7b_28901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7b_28901/12_2024/8f7b_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_28901/12_2024/8f7b_28901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7b_28901/12_2024/8f7b_28901.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7b_28901/12_2024/8f7b_28901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7b_28901/12_2024/8f7b_28901.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.69, per 1000 atoms: 0.66 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: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.38 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: 4.56 Time building geometry restraints manager: 4.61 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: 0.010 Normalize map: mean=0, sd=1: 8.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.540 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- 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 16585 Z= 0.326 Angle : 0.787 13.885 22366 Z= 0.423 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 : 5.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (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 TRP 0.055 0.002 TRP F 170 HIS 0.013 0.001 HIS C 155 PHE 0.044 0.002 PHE D 390 TYR 0.024 0.001 TYR C 284 ARG 0.012 0.001 ARG B 18 *********************** 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 : 1.824 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: 0.2922 time to fit residues: 116.3905 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 : 1.904 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 105 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16585 Z= 0.239 Angle : 0.479 6.589 22366 Z= 0.260 Chirality : 0.038 0.129 2416 Planarity : 0.003 0.037 2701 Dihedral : 12.031 175.070 2319 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.76 % Allowed : 16.77 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 1858 helix: 1.96 (0.14), residues: 1330 sheet: 0.38 (0.54), residues: 105 loop : -1.23 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 145 HIS 0.010 0.001 HIS A 253 PHE 0.014 0.001 PHE E 324 TYR 0.015 0.001 TYR C 338 ARG 0.005 0.000 ARG B 18 *********************** 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 282 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7768 (t) cc_final: 0.7110 (p) REVERT: A 171 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8070 (ttm-80) REVERT: B 359 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6915 (mm-30) REVERT: C 364 ASP cc_start: 0.4980 (p0) cc_final: 0.4736 (p0) REVERT: E 47 VAL cc_start: 0.8972 (t) cc_final: 0.8685 (m) REVERT: F 300 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7479 (mtt) REVERT: F 392 LEU cc_start: 0.8213 (tp) cc_final: 0.7960 (tp) outliers start: 31 outliers final: 19 residues processed: 271 average time/residue: 0.2884 time to fit residues: 116.0507 Evaluate side-chains 252 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU 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 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 Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 B 267 GLN C 46 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 288 ASN E 370 ASN F 112 ASN F 134 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16585 Z= 0.449 Angle : 0.574 6.674 22366 Z= 0.311 Chirality : 0.042 0.189 2416 Planarity : 0.004 0.035 2701 Dihedral : 9.982 144.600 2315 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.96 % Allowed : 18.02 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1858 helix: 1.79 (0.14), residues: 1339 sheet: 0.11 (0.53), residues: 105 loop : -1.50 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 168 HIS 0.012 0.001 HIS C 155 PHE 0.020 0.002 PHE D 374 TYR 0.020 0.002 TYR A 30 ARG 0.006 0.000 ARG F 387 *********************** 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 283 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7612 (t) cc_final: 0.6997 (p) REVERT: B 243 LEU cc_start: 0.7892 (tp) cc_final: 0.7652 (tt) REVERT: B 403 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8217 (ttm110) REVERT: C 364 ASP cc_start: 0.5156 (p0) cc_final: 0.4827 (p0) REVERT: D 386 TYR cc_start: 0.7989 (m-80) cc_final: 0.7648 (m-80) REVERT: E 53 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8911 (mp) REVERT: E 381 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7341 (mp10) REVERT: F 113 GLN cc_start: 0.8538 (mt0) cc_final: 0.8181 (mt0) REVERT: F 145 TRP cc_start: 0.6556 (p-90) cc_final: 0.6230 (p-90) REVERT: F 146 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: F 300 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7777 (mtp) REVERT: F 392 LEU cc_start: 0.8297 (tp) cc_final: 0.7934 (tp) outliers start: 52 outliers final: 30 residues processed: 266 average time/residue: 0.2839 time to fit residues: 113.1148 Evaluate side-chains 249 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 279 ILE 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 379 ILE 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 377 HIS 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 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 309 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 385 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E 377 HIS F 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16585 Z= 0.202 Angle : 0.447 6.182 22366 Z= 0.244 Chirality : 0.037 0.121 2416 Planarity : 0.003 0.036 2701 Dihedral : 8.042 108.572 2315 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.27 % Allowed : 19.10 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1858 helix: 2.08 (0.14), residues: 1329 sheet: 0.23 (0.55), residues: 100 loop : -1.34 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 168 HIS 0.008 0.001 HIS A 253 PHE 0.012 0.001 PHE D 144 TYR 0.014 0.001 TYR D 382 ARG 0.006 0.000 ARG F 387 *********************** 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 276 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7566 (t) cc_final: 0.6958 (p) REVERT: A 161 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 171 ARG cc_start: 0.8455 (tpp80) cc_final: 0.8221 (tpp-160) REVERT: B 359 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6892 (mm-30) REVERT: B 403 ARG cc_start: 0.8477 (ttm110) cc_final: 0.7888 (ptp90) REVERT: C 46 GLN cc_start: 0.8500 (tt0) cc_final: 0.8122 (tt0) REVERT: C 245 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7240 (mp0) REVERT: C 364 ASP cc_start: 0.5094 (p0) cc_final: 0.4775 (p0) REVERT: C 403 ARG cc_start: 0.7714 (ptp-110) cc_final: 0.7482 (mtm110) REVERT: D 386 TYR cc_start: 0.7830 (m-80) cc_final: 0.7581 (m-80) REVERT: E 309 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7581 (ttt180) REVERT: E 381 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7221 (mp10) REVERT: F 145 TRP cc_start: 0.6366 (p-90) cc_final: 0.6043 (p-90) REVERT: F 146 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: F 300 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7531 (mtp) REVERT: F 391 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: F 392 LEU cc_start: 0.8375 (tp) cc_final: 0.8071 (tp) outliers start: 40 outliers final: 24 residues processed: 265 average time/residue: 0.2820 time to fit residues: 112.0340 Evaluate side-chains 249 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 392 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE 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 330 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 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 383 LEU Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS C 49 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS D 287 HIS F 309 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16585 Z= 0.151 Angle : 0.425 8.317 22366 Z= 0.230 Chirality : 0.037 0.123 2416 Planarity : 0.003 0.038 2701 Dihedral : 6.873 81.136 2313 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 19.39 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.19), residues: 1858 helix: 2.23 (0.14), residues: 1337 sheet: 0.40 (0.54), residues: 104 loop : -1.25 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 170 HIS 0.011 0.001 HIS C 155 PHE 0.010 0.001 PHE D 372 TYR 0.013 0.001 TYR C 338 ARG 0.006 0.000 ARG F 387 *********************** 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 281 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7520 (t) cc_final: 0.6925 (p) REVERT: A 161 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 343 MET cc_start: 0.8797 (mtp) cc_final: 0.8548 (mtm) REVERT: B 17 TYR cc_start: 0.8861 (m-10) cc_final: 0.8545 (m-10) REVERT: B 168 TRP cc_start: 0.7827 (t-100) cc_final: 0.7626 (t-100) REVERT: B 171 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8206 (tpp-160) REVERT: B 359 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 143 TRP cc_start: 0.7979 (t60) cc_final: 0.7778 (t60) REVERT: C 245 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6782 (mp0) REVERT: C 364 ASP cc_start: 0.5078 (p0) cc_final: 0.4767 (p0) REVERT: D 168 TRP cc_start: 0.6843 (t-100) cc_final: 0.6311 (t-100) REVERT: E 308 TYR cc_start: 0.9205 (m-80) cc_final: 0.8839 (m-80) REVERT: E 309 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7531 (ttt180) REVERT: F 114 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8255 (mmt) REVERT: F 145 TRP cc_start: 0.6300 (p-90) cc_final: 0.6001 (p-90) REVERT: F 146 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: F 300 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7564 (mtt) REVERT: F 391 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6579 (m-80) outliers start: 41 outliers final: 23 residues processed: 269 average time/residue: 0.2724 time to fit residues: 111.5083 Evaluate side-chains 254 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 104 HIS 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 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 378 LEU 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 114 MET 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 383 LEU Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 105 GLN D 287 HIS E 370 ASN F 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16585 Z= 0.192 Angle : 0.452 9.435 22366 Z= 0.242 Chirality : 0.037 0.119 2416 Planarity : 0.003 0.036 2701 Dihedral : 6.660 83.286 2313 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.44 % Allowed : 19.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1858 helix: 2.26 (0.14), residues: 1336 sheet: 0.25 (0.53), residues: 104 loop : -1.25 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 170 HIS 0.010 0.001 HIS C 155 PHE 0.014 0.001 PHE D 144 TYR 0.013 0.001 TYR A 338 ARG 0.006 0.000 ARG F 387 *********************** 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 274 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7542 (t) cc_final: 0.6941 (p) REVERT: A 161 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8005 (mp) REVERT: B 17 TYR cc_start: 0.8861 (m-10) cc_final: 0.8515 (m-10) REVERT: B 168 TRP cc_start: 0.7829 (t-100) cc_final: 0.7573 (t-100) REVERT: B 359 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 238 GLU cc_start: 0.7363 (pt0) cc_final: 0.7149 (pp20) REVERT: C 364 ASP cc_start: 0.5092 (p0) cc_final: 0.4773 (p0) REVERT: C 403 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7877 (ptp-110) REVERT: E 309 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7562 (ttt180) REVERT: F 145 TRP cc_start: 0.6330 (p-90) cc_final: 0.6087 (p-90) REVERT: F 146 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: F 300 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7741 (mtt) REVERT: F 391 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6633 (m-80) outliers start: 43 outliers final: 28 residues processed: 261 average time/residue: 0.2755 time to fit residues: 109.8446 Evaluate side-chains 257 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 403 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU 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 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 Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16585 Z= 0.173 Angle : 0.446 8.489 22366 Z= 0.240 Chirality : 0.037 0.142 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.425 86.247 2313 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.62 % Allowed : 19.95 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1858 helix: 2.30 (0.14), residues: 1336 sheet: 0.41 (0.54), residues: 104 loop : -1.24 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 170 HIS 0.010 0.001 HIS A 253 PHE 0.013 0.001 PHE D 250 TYR 0.013 0.001 TYR A 338 ARG 0.006 0.000 ARG F 387 *********************** 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: 46 poor density : 235 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7509 (t) cc_final: 0.6919 (p) REVERT: A 161 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 17 TYR cc_start: 0.8854 (m-10) cc_final: 0.8559 (m-10) REVERT: B 359 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 238 GLU cc_start: 0.7446 (pt0) cc_final: 0.7191 (pp20) REVERT: C 364 ASP cc_start: 0.5087 (p0) cc_final: 0.4767 (p0) REVERT: C 403 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8001 (ptp-110) REVERT: E 309 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7579 (ttt180) REVERT: E 381 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7080 (mm-40) REVERT: F 145 TRP cc_start: 0.6416 (p-90) cc_final: 0.6111 (p-90) REVERT: F 146 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6013 (m-80) REVERT: F 300 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7720 (mtt) REVERT: F 391 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6521 (m-80) outliers start: 46 outliers final: 31 residues processed: 270 average time/residue: 0.2670 time to fit residues: 109.4997 Evaluate side-chains 263 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 104 HIS Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE 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 403 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU 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 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 Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE 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 71 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 0.0050 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16585 Z= 0.164 Angle : 0.450 8.293 22366 Z= 0.240 Chirality : 0.037 0.136 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.264 89.382 2313 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.50 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1858 helix: 2.33 (0.14), residues: 1336 sheet: 0.57 (0.55), residues: 104 loop : -1.23 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 170 HIS 0.010 0.001 HIS A 253 PHE 0.020 0.001 PHE D 144 TYR 0.013 0.001 TYR A 338 ARG 0.007 0.000 ARG F 387 *********************** 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 281 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7518 (t) cc_final: 0.6923 (p) REVERT: A 161 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 17 TYR cc_start: 0.8838 (m-10) cc_final: 0.8536 (m-10) REVERT: B 168 TRP cc_start: 0.7776 (t-100) cc_final: 0.7416 (t-100) REVERT: B 359 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7002 (mm-30) REVERT: C 238 GLU cc_start: 0.7435 (pt0) cc_final: 0.7178 (pp20) REVERT: C 364 ASP cc_start: 0.5110 (p0) cc_final: 0.4783 (p0) REVERT: C 403 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7971 (ptp-110) REVERT: D 164 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.6057 (m-80) REVERT: D 168 TRP cc_start: 0.6856 (t-100) cc_final: 0.6559 (t-100) REVERT: E 154 GLU cc_start: 0.7721 (tp30) cc_final: 0.7274 (pt0) REVERT: E 309 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7577 (ttt180) REVERT: E 381 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7055 (mm-40) REVERT: F 145 TRP cc_start: 0.6435 (p-90) cc_final: 0.6132 (p-90) REVERT: F 146 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: F 300 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7760 (mtt) REVERT: F 391 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6414 (m-80) outliers start: 44 outliers final: 32 residues processed: 270 average time/residue: 0.2828 time to fit residues: 115.0771 Evaluate side-chains 265 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 104 HIS 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 281 TYR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE 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 403 ARG Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU 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 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 309 ASN 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 391 PHE 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 170 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 404 GLN D 105 GLN D 287 HIS E 155 HIS F 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16585 Z= 0.187 Angle : 0.466 8.024 22366 Z= 0.248 Chirality : 0.038 0.134 2416 Planarity : 0.003 0.036 2701 Dihedral : 6.233 87.908 2313 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.27 % Allowed : 20.58 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1858 helix: 2.32 (0.14), residues: 1336 sheet: 0.54 (0.55), residues: 104 loop : -1.24 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 170 HIS 0.010 0.001 HIS A 253 PHE 0.014 0.001 PHE F 158 TYR 0.013 0.001 TYR F 279 ARG 0.007 0.000 ARG F 387 *********************** 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 271 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7517 (t) cc_final: 0.6929 (p) REVERT: A 161 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 17 TYR cc_start: 0.8828 (m-10) cc_final: 0.8570 (m-10) REVERT: B 168 TRP cc_start: 0.7787 (t-100) cc_final: 0.7487 (t-100) REVERT: B 359 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6995 (mm-30) REVERT: C 238 GLU cc_start: 0.7494 (pt0) cc_final: 0.7188 (pp20) REVERT: C 309 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7675 (ttm-80) REVERT: C 364 ASP cc_start: 0.5123 (p0) cc_final: 0.4793 (p0) REVERT: C 403 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8043 (ptp-110) REVERT: E 154 GLU cc_start: 0.7811 (tp30) cc_final: 0.7248 (pt0) REVERT: E 309 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7582 (ttt180) REVERT: E 381 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7029 (mm-40) REVERT: F 145 TRP cc_start: 0.6430 (p-90) cc_final: 0.6137 (p-90) REVERT: F 146 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: F 300 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: F 391 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6445 (m-80) outliers start: 40 outliers final: 32 residues processed: 259 average time/residue: 0.2840 time to fit residues: 111.2509 Evaluate side-chains 267 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 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 C residue 403 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU 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 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 309 ASN 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 374 LEU Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 0.0870 chunk 184 optimal weight: 0.3980 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 404 GLN D 105 GLN F 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16585 Z= 0.133 Angle : 0.448 7.847 22366 Z= 0.239 Chirality : 0.037 0.128 2416 Planarity : 0.003 0.039 2701 Dihedral : 5.848 83.031 2313 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.10 % Allowed : 20.86 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 1858 helix: 2.40 (0.14), residues: 1340 sheet: 0.75 (0.53), residues: 104 loop : -1.20 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 170 HIS 0.014 0.001 HIS A 253 PHE 0.027 0.001 PHE D 390 TYR 0.013 0.001 TYR F 279 ARG 0.005 0.000 ARG F 387 ********************** 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 286 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7499 (t) cc_final: 0.6912 (p) REVERT: A 161 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 17 TYR cc_start: 0.8774 (m-10) cc_final: 0.8522 (m-10) REVERT: B 168 TRP cc_start: 0.7754 (t-100) cc_final: 0.7421 (t-100) REVERT: B 171 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8476 (tpp80) REVERT: C 238 GLU cc_start: 0.7439 (pt0) cc_final: 0.7195 (pp20) REVERT: C 245 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6849 (mp0) REVERT: C 309 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: C 364 ASP cc_start: 0.5265 (p0) cc_final: 0.4975 (p0) REVERT: C 403 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8054 (ptp-110) REVERT: E 154 GLU cc_start: 0.7845 (tp30) cc_final: 0.7382 (pt0) REVERT: E 308 TYR cc_start: 0.9195 (m-80) cc_final: 0.8847 (m-80) REVERT: E 309 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7521 (ttt180) REVERT: F 145 TRP cc_start: 0.6405 (p-90) cc_final: 0.6095 (p-90) REVERT: F 146 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: F 264 ARG cc_start: 0.6173 (mpt-90) cc_final: 0.4786 (ttp80) REVERT: F 300 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: F 387 ARG cc_start: 0.6656 (tmm160) cc_final: 0.6416 (tmm160) REVERT: F 391 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6392 (m-80) outliers start: 37 outliers final: 26 residues processed: 275 average time/residue: 0.2810 time to fit residues: 116.4849 Evaluate side-chains 265 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 281 TYR 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 C residue 281 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU 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 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 374 LEU Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.166790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122097 restraints weight = 20342.672| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.23 r_work: 0.3422 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16585 Z= 0.170 Angle : 0.462 7.918 22366 Z= 0.248 Chirality : 0.038 0.138 2416 Planarity : 0.003 0.037 2701 Dihedral : 5.870 81.887 2313 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.99 % Allowed : 21.21 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.19), residues: 1858 helix: 2.39 (0.14), residues: 1337 sheet: 0.69 (0.52), residues: 104 loop : -1.16 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 170 HIS 0.013 0.001 HIS A 253 PHE 0.027 0.001 PHE D 390 TYR 0.014 0.001 TYR A 338 ARG 0.005 0.000 ARG F 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3619.06 seconds wall clock time: 67 minutes 45.16 seconds (4065.16 seconds total)