Starting phenix.real_space_refine on Tue Jan 21 06:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_28901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_28901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_28901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_28901.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_28901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7b_28901/01_2025/8f7b_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-5571/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: 10.34, per 1000 atoms: 0.64 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: 3.50 Conformation dependent library (CDL) restraints added in 1.6 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: 5.00 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4304 1.34 - 1.46: 3553 1.46 - 1.58: 8563 1.58 - 1.70: 7 1.70 - 1.82: 158 Bond restraints: 16585 Sorted by residual: bond pdb=" C10 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sigma weight residual 1.206 1.359 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.783 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" O4P PEE E 901 " pdb=" P PEE E 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" O4P PEE F 901 " pdb=" P PEE F 901 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 16580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 22059 2.78 - 5.55: 236 5.55 - 8.33: 58 8.33 - 11.11: 6 11.11 - 13.89: 7 Bond angle restraints: 22366 Sorted by residual: angle pdb=" N LEU A 344 " pdb=" CA LEU A 344 " pdb=" C LEU A 344 " ideal model delta sigma weight residual 111.69 118.08 -6.39 1.23e+00 6.61e-01 2.70e+01 angle pdb=" O1P PEE F 901 " pdb=" P PEE F 901 " pdb=" O2P PEE F 901 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.23 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.21 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 22361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 9496 35.76 - 71.52: 307 71.52 - 107.28: 28 107.28 - 143.04: 8 143.04 - 178.80: 9 Dihedral angle restraints: 9848 sinusoidal: 4159 harmonic: 5689 Sorted by residual: dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 295 " pdb=" CB CYS A 295 " ideal model delta sinusoidal sigma weight residual 93.00 36.75 56.25 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" C4 PEE B 901 " pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " pdb=" O3P PEE B 901 " ideal model delta sinusoidal sigma weight residual 171.78 -7.02 178.80 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2260 0.082 - 0.164: 145 0.164 - 0.246: 9 0.246 - 0.328: 0 0.328 - 0.410: 2 Chirality restraints: 2416 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE E 53 " pdb=" CA ILE E 53 " pdb=" CG1 ILE E 53 " pdb=" CG2 ILE E 53 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2413 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.026 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D 168 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 170 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP F 170 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 170 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 170 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 170 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 170 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 170 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 145 " -0.023 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP F 145 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 145 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 145 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 145 " 0.000 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3862 2.79 - 3.32: 15296 3.32 - 3.85: 28129 3.85 - 4.37: 32223 4.37 - 4.90: 55592 Nonbonded interactions: 135102 Sorted by model distance: nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR A 316 " pdb=" OE2 GLU B 115 " model vdw 2.303 3.040 nonbonded pdb=" OD1 ASP F 50 " pdb=" NE2 HIS F 310 " model vdw 2.308 3.120 nonbonded pdb=" OD2 ASP F 50 " pdb=" OH TYR F 116 " model vdw 2.314 3.040 ... (remaining 135097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 408 or resid 901 or (resid 902 and (name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 408 or (resid 901 and (name N or name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C2 or name C20 or name C4 or name C5 or name O1P or name O2 or name O2 \ P or name O3P or name O4 or name O4P or name P )) or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or (resid 901 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C4 or name C5 o \ r name O1P or name O2 or name O2P or name O3P or name O4 or name O4P or name P ) \ ) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or (resid 902 and (name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.320 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- 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 : 1.856 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: 0.2845 time to fit residues: 113.7374 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 : 1.836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.166710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119730 restraints weight = 20615.107| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.30 r_work: 0.3401 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7681 (t) cc_final: 0.7040 (p) REVERT: A 171 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: B 359 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6936 (mm-30) REVERT: C 30 TYR cc_start: 0.7984 (m-80) cc_final: 0.7756 (m-10) REVERT: C 364 ASP cc_start: 0.5088 (p0) cc_final: 0.4863 (p0) REVERT: D 287 HIS cc_start: 0.8230 (p90) cc_final: 0.8022 (p90) REVERT: E 47 VAL cc_start: 0.8598 (t) cc_final: 0.8241 (m) REVERT: F 300 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: F 392 LEU cc_start: 0.8106 (tp) cc_final: 0.7761 (tp) outliers start: 31 outliers final: 19 residues processed: 271 average time/residue: 0.2980 time to fit residues: 119.3681 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 : 1.881 ------------------------------------------------------------------------------- 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 154 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 129 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN C 46 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.168301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121843 restraints weight = 20451.691| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.29 r_work: 0.3432 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16585 Z= 0.158 Angle : 0.427 6.134 22366 Z= 0.233 Chirality : 0.036 0.168 2416 Planarity : 0.003 0.038 2701 Dihedral : 9.167 166.553 2315 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 17.74 % Favored : 80.27 % 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: 2.21 (0.14), residues: 1333 sheet: 0.51 (0.53), residues: 105 loop : -1.15 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 145 HIS 0.008 0.001 HIS A 253 PHE 0.011 0.001 PHE E 324 TYR 0.013 0.001 TYR C 338 ARG 0.005 0.000 ARG E 251 *********************** 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 286 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 TYR cc_start: 0.8810 (m-10) cc_final: 0.8435 (m-10) REVERT: B 171 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8338 (tpp-160) REVERT: B 359 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7058 (mm-30) REVERT: C 30 TYR cc_start: 0.8015 (m-80) cc_final: 0.7718 (m-10) REVERT: C 143 TRP cc_start: 0.8010 (t60) cc_final: 0.7634 (t60) REVERT: C 364 ASP cc_start: 0.5142 (p0) cc_final: 0.4915 (p0) REVERT: D 168 TRP cc_start: 0.6844 (t-100) cc_final: 0.6095 (t-100) REVERT: D 169 THR cc_start: 0.6401 (m) cc_final: 0.6138 (m) REVERT: E 275 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7968 (t80) REVERT: F 113 GLN cc_start: 0.8707 (mt0) cc_final: 0.8504 (mt0) REVERT: F 264 ARG cc_start: 0.6462 (mpt-90) cc_final: 0.4869 (ttp80) REVERT: F 300 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7454 (mtt) REVERT: F 392 LEU cc_start: 0.8086 (tp) cc_final: 0.7688 (tp) outliers start: 35 outliers final: 19 residues processed: 272 average time/residue: 0.2769 time to fit residues: 112.2681 Evaluate side-chains 257 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN C 155 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120190 restraints weight = 20463.621| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.30 r_work: 0.3376 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16585 Z= 0.195 Angle : 0.440 6.659 22366 Z= 0.239 Chirality : 0.037 0.142 2416 Planarity : 0.003 0.039 2701 Dihedral : 8.150 145.348 2313 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.33 % Allowed : 18.08 % Favored : 79.59 % 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: 2.16 (0.19), residues: 1858 helix: 2.26 (0.14), residues: 1332 sheet: 0.46 (0.54), residues: 105 loop : -1.09 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 145 HIS 0.008 0.001 HIS A 253 PHE 0.012 0.001 PHE B 374 TYR 0.013 0.001 TYR F 279 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 279 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7593 (t) cc_final: 0.6969 (p) REVERT: A 161 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7799 (mm) REVERT: B 17 TYR cc_start: 0.8845 (m-10) cc_final: 0.8467 (m-10) REVERT: B 171 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8330 (tpp-160) REVERT: B 359 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 30 TYR cc_start: 0.8020 (m-80) cc_final: 0.7718 (m-10) REVERT: C 143 TRP cc_start: 0.8058 (t60) cc_final: 0.7697 (t60) REVERT: C 245 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7324 (mp0) REVERT: C 364 ASP cc_start: 0.5126 (p0) cc_final: 0.4839 (p0) REVERT: C 375 MET cc_start: 0.7786 (mtm) cc_final: 0.7469 (mtm) REVERT: D 144 PHE cc_start: 0.7219 (m-10) cc_final: 0.6988 (m-10) REVERT: D 168 TRP cc_start: 0.6859 (t-100) cc_final: 0.6134 (t-100) REVERT: D 169 THR cc_start: 0.6368 (m) cc_final: 0.6108 (m) REVERT: E 275 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8032 (t80) REVERT: E 324 PHE cc_start: 0.7676 (t80) cc_final: 0.7418 (t80) REVERT: F 113 GLN cc_start: 0.8803 (mt0) cc_final: 0.8548 (mm-40) REVERT: F 146 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: F 264 ARG cc_start: 0.6468 (mpt-90) cc_final: 0.4777 (tmm160) REVERT: F 300 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7798 (mtp) REVERT: F 392 LEU cc_start: 0.8199 (tp) cc_final: 0.7794 (tp) outliers start: 41 outliers final: 23 residues processed: 269 average time/residue: 0.2664 time to fit residues: 109.1141 Evaluate side-chains 256 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 244 PHE 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 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 279 TYR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 51 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN C 155 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS F 134 HIS F 309 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120531 restraints weight = 20773.920| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.31 r_work: 0.3412 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16585 Z= 0.181 Angle : 0.434 7.917 22366 Z= 0.235 Chirality : 0.037 0.138 2416 Planarity : 0.003 0.037 2701 Dihedral : 6.934 83.204 2313 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.27 % Allowed : 18.59 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.31 (0.14), residues: 1337 sheet: 0.35 (0.53), residues: 105 loop : -1.14 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 145 HIS 0.009 0.001 HIS A 253 PHE 0.010 0.001 PHE D 250 TYR 0.021 0.001 TYR E 382 ARG 0.005 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 284 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 168 TRP cc_start: 0.7763 (t-100) cc_final: 0.7555 (t-100) REVERT: B 171 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8320 (tpp-160) REVERT: B 359 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7023 (mm-30) REVERT: C 245 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7305 (mp0) REVERT: C 364 ASP cc_start: 0.5269 (p0) cc_final: 0.4952 (p0) REVERT: C 403 ARG cc_start: 0.7834 (ptp-110) cc_final: 0.7243 (mtm110) REVERT: D 169 THR cc_start: 0.6471 (m) cc_final: 0.6193 (m) REVERT: D 284 TYR cc_start: 0.7932 (t80) cc_final: 0.7727 (t80) REVERT: E 275 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8073 (t80) REVERT: E 309 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7816 (ttt180) REVERT: E 324 PHE cc_start: 0.7537 (t80) cc_final: 0.7233 (t80) REVERT: E 381 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6782 (mm-40) REVERT: F 113 GLN cc_start: 0.8675 (mt0) cc_final: 0.8437 (mm-40) REVERT: F 146 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: F 264 ARG cc_start: 0.6458 (mpt-90) cc_final: 0.4762 (tmm160) REVERT: F 300 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7685 (mtp) outliers start: 40 outliers final: 24 residues processed: 271 average time/residue: 0.2754 time to fit residues: 113.0825 Evaluate side-chains 258 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 B residue 244 PHE Chi-restraints excluded: chain B residue 361 SER 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 C residue 281 TYR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET 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 267 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 C 155 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117081 restraints weight = 20780.220| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.29 r_work: 0.3354 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16585 Z= 0.314 Angle : 0.513 9.882 22366 Z= 0.275 Chirality : 0.040 0.142 2416 Planarity : 0.003 0.035 2701 Dihedral : 7.224 80.742 2313 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.73 % Allowed : 19.04 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.19), residues: 1858 helix: 2.15 (0.14), residues: 1336 sheet: 0.15 (0.55), residues: 100 loop : -1.26 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 170 HIS 0.009 0.001 HIS A 253 PHE 0.015 0.002 PHE D 250 TYR 0.014 0.002 TYR A 30 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 282 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7473 (t) cc_final: 0.6865 (p) REVERT: A 161 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 359 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 403 ARG cc_start: 0.8500 (ttm110) cc_final: 0.7921 (ptp90) REVERT: C 245 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6928 (mp0) REVERT: C 343 MET cc_start: 0.8599 (mmm) cc_final: 0.8310 (mtp) REVERT: C 364 ASP cc_start: 0.5335 (p0) cc_final: 0.5018 (p0) REVERT: C 403 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7400 (ptp-110) REVERT: D 168 TRP cc_start: 0.6990 (t-100) cc_final: 0.6775 (t60) REVERT: D 308 TYR cc_start: 0.9105 (m-80) cc_final: 0.8870 (m-80) REVERT: E 309 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.7733 (ttt180) REVERT: E 324 PHE cc_start: 0.7731 (t80) cc_final: 0.7454 (t80) REVERT: F 36 LEU cc_start: 0.8359 (tp) cc_final: 0.8110 (mp) REVERT: F 146 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: F 264 ARG cc_start: 0.6496 (mpt-90) cc_final: 0.4781 (ttp80) REVERT: F 300 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7827 (mtp) outliers start: 48 outliers final: 33 residues processed: 272 average time/residue: 0.2791 time to fit residues: 115.9845 Evaluate side-chains 261 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 293 VAL 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 144 PHE Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 267 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 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1478 > 50: distance: 34 - 61: 9.332 distance: 40 - 73: 7.182 distance: 44 - 49: 3.850 distance: 49 - 50: 3.008 distance: 50 - 51: 5.809 distance: 50 - 53: 7.318 distance: 51 - 52: 3.990 distance: 51 - 61: 3.813 distance: 53 - 54: 6.679 distance: 54 - 55: 4.366 distance: 54 - 56: 7.283 distance: 55 - 57: 7.300 distance: 56 - 58: 11.962 distance: 57 - 59: 6.601 distance: 58 - 59: 4.563 distance: 59 - 60: 3.220 distance: 61 - 62: 3.592 distance: 62 - 63: 4.727 distance: 62 - 65: 6.686 distance: 63 - 64: 5.895 distance: 63 - 73: 5.934 distance: 65 - 66: 7.162 distance: 66 - 67: 6.087 distance: 66 - 68: 3.106 distance: 67 - 69: 6.219 distance: 68 - 70: 12.295 distance: 70 - 71: 3.479 distance: 71 - 72: 7.109 distance: 73 - 74: 13.632 distance: 74 - 75: 9.230 distance: 74 - 77: 9.355 distance: 75 - 76: 6.254 distance: 75 - 80: 7.432 distance: 77 - 78: 18.913 distance: 77 - 79: 11.760 distance: 80 - 81: 3.414 distance: 81 - 82: 4.103 distance: 81 - 84: 5.957 distance: 82 - 83: 12.769 distance: 82 - 90: 8.954 distance: 84 - 85: 7.860 distance: 85 - 86: 3.325 distance: 85 - 87: 14.941 distance: 86 - 88: 5.092 distance: 87 - 89: 4.307 distance: 88 - 89: 8.890 distance: 90 - 91: 4.676 distance: 91 - 92: 10.234 distance: 91 - 94: 5.573 distance: 92 - 93: 12.646 distance: 92 - 98: 12.152 distance: 94 - 95: 3.989 distance: 95 - 96: 3.230 distance: 95 - 97: 8.172 distance: 98 - 99: 8.565 distance: 99 - 100: 16.940 distance: 99 - 102: 3.641 distance: 100 - 101: 7.252 distance: 100 - 106: 9.116 distance: 102 - 103: 5.277 distance: 102 - 104: 6.745 distance: 103 - 105: 3.135 distance: 106 - 107: 9.489 distance: 107 - 108: 6.459 distance: 107 - 110: 5.131 distance: 108 - 109: 8.185 distance: 108 - 115: 11.047 distance: 110 - 111: 10.035 distance: 111 - 112: 3.507 distance: 112 - 113: 3.117 distance: 113 - 114: 9.293 distance: 115 - 116: 6.661 distance: 116 - 117: 10.638 distance: 116 - 119: 7.140 distance: 117 - 118: 7.068 distance: 117 - 126: 8.709 distance: 119 - 120: 6.654 distance: 120 - 121: 7.705 distance: 120 - 122: 3.477 distance: 121 - 123: 4.679 distance: 122 - 124: 9.986 distance: 123 - 125: 11.982 distance: 124 - 125: 4.357 distance: 126 - 127: 20.642 distance: 127 - 128: 15.562 distance: 127 - 130: 23.652 distance: 128 - 129: 19.342 distance: 128 - 134: 35.778 distance: 130 - 131: 9.848 distance: 131 - 132: 13.833 distance: 131 - 133: 15.652 distance: 134 - 135: 3.885 distance: 134 - 167: 18.747 distance: 135 - 136: 16.055 distance: 135 - 138: 7.084 distance: 136 - 137: 8.935 distance: 136 - 141: 7.540 distance: 137 - 164: 15.168 distance: 138 - 139: 23.353 distance: 138 - 140: 17.906