Starting phenix.real_space_refine on Fri Jul 3 14:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.map" model { file = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ud3_20731/07_2026/6ud3_20731.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9350 2.51 5 N 2315 2.21 5 O 2581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14346 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2846 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2846 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2846 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2846 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2846 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'RI5': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.21 Number of scatterers: 14346 At special positions: 0 Unit cell: (91.16, 90.1, 131.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2581 8.00 N 2315 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 567.2 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 38.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 251 through 269 removed outlier: 4.118A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 294 Processing helix chain 'A' and resid 306 through 339 removed outlier: 3.970A pdb=" N ALA A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 441 removed outlier: 3.638A pdb=" N ARG A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.882A pdb=" N PHE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 251 through 269 removed outlier: 4.119A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 306 through 339 removed outlier: 3.971A pdb=" N ALA C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 441 removed outlier: 3.638A pdb=" N ARG C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.881A pdb=" N PHE C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 251 through 269 removed outlier: 4.118A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 294 Processing helix chain 'E' and resid 306 through 339 removed outlier: 3.970A pdb=" N ALA E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 441 removed outlier: 3.638A pdb=" N ARG E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.881A pdb=" N PHE E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE E 436 " --> pdb=" O THR E 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 251 through 269 removed outlier: 4.119A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 294 Processing helix chain 'D' and resid 306 through 339 removed outlier: 3.970A pdb=" N ALA D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 441 removed outlier: 3.637A pdb=" N ARG D 415 " --> pdb=" O ASP D 411 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.881A pdb=" N PHE D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 251 through 269 removed outlier: 4.118A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 294 Processing helix chain 'B' and resid 306 through 339 removed outlier: 3.970A pdb=" N ALA B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 441 removed outlier: 3.638A pdb=" N ARG B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.881A pdb=" N PHE B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.751A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 8.331A pdb=" N GLN A 201 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 86 removed outlier: 3.841A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 124 removed outlier: 4.182A pdb=" N GLU A 241 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 124 removed outlier: 4.081A pdb=" N CYS A 233 " --> pdb=" O CYS A 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 removed outlier: 5.750A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 8.332A pdb=" N GLN C 201 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 81 through 86 removed outlier: 3.841A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124 removed outlier: 4.182A pdb=" N GLU C 241 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 123 through 124 removed outlier: 4.080A pdb=" N CYS C 233 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.751A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 89 through 91 removed outlier: 8.330A pdb=" N GLN E 201 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE E 67 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 81 through 86 removed outlier: 3.841A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'E' and resid 123 through 124 removed outlier: 4.182A pdb=" N GLU E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 123 through 124 removed outlier: 4.081A pdb=" N CYS E 233 " --> pdb=" O CYS E 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.751A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 89 through 91 removed outlier: 8.331A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 81 through 86 removed outlier: 3.841A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124 removed outlier: 4.182A pdb=" N GLU D 241 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124 removed outlier: 4.081A pdb=" N CYS D 233 " --> pdb=" O CYS D 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.750A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 89 through 91 removed outlier: 8.331A pdb=" N GLN B 201 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 67 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 81 through 86 removed outlier: 3.842A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'B' and resid 123 through 124 removed outlier: 4.182A pdb=" N GLU B 241 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 123 through 124 removed outlier: 4.081A pdb=" N CYS B 233 " --> pdb=" O CYS B 222 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2010 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: 1.95 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.58 - 0.84: 1 0.84 - 1.10: 1 1.10 - 1.36: 4521 1.36 - 1.62: 10001 1.62 - 1.88: 176 Bond restraints: 14700 Sorted by residual: bond pdb=" C08 RI5 A 503 " pdb=" C13 RI5 A 503 " ideal model delta sigma weight residual 1.554 0.584 0.970 2.00e-02 2.50e+03 2.35e+03 bond pdb=" C07 RI5 A 503 " pdb=" C15 RI5 A 503 " ideal model delta sigma weight residual 1.508 1.009 0.499 2.00e-02 2.50e+03 6.23e+02 bond pdb=" C08 RI5 A 503 " pdb=" C09 RI5 A 503 " ideal model delta sigma weight residual 1.551 1.167 0.384 2.00e-02 2.50e+03 3.69e+02 bond pdb=" C07 RI5 A 503 " pdb=" C08 RI5 A 503 " ideal model delta sigma weight residual 1.571 1.883 -0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C05 RI5 A 503 " pdb=" O12 RI5 A 503 " ideal model delta sigma weight residual 1.440 1.728 -0.288 2.00e-02 2.50e+03 2.08e+02 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.70: 19779 6.70 - 13.41: 153 13.41 - 20.11: 12 20.11 - 26.82: 0 26.82 - 33.52: 2 Bond angle restraints: 19946 Sorted by residual: angle pdb=" C07 RI5 A 503 " pdb=" C15 RI5 A 503 " pdb=" O16 RI5 A 503 " ideal model delta sigma weight residual 118.77 152.29 -33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C13 RI5 A 503 " pdb=" C14 RI5 A 503 " pdb=" O16 RI5 A 503 " ideal model delta sigma weight residual 113.55 145.85 -32.30 3.00e+00 1.11e-01 1.16e+02 angle pdb=" NE ARG B 89 " pdb=" CZ ARG B 89 " pdb=" NH2 ARG B 89 " ideal model delta sigma weight residual 119.20 126.33 -7.13 9.00e-01 1.23e+00 6.28e+01 angle pdb=" NE ARG A 89 " pdb=" CZ ARG A 89 " pdb=" NH2 ARG A 89 " ideal model delta sigma weight residual 119.20 126.33 -7.13 9.00e-01 1.23e+00 6.27e+01 angle pdb=" NE ARG E 89 " pdb=" CZ ARG E 89 " pdb=" NH2 ARG E 89 " ideal model delta sigma weight residual 119.20 126.31 -7.11 9.00e-01 1.23e+00 6.25e+01 ... (remaining 19941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 7928 15.43 - 30.85: 661 30.85 - 46.28: 106 46.28 - 61.71: 20 61.71 - 77.13: 10 Dihedral angle restraints: 8725 sinusoidal: 3520 harmonic: 5205 Sorted by residual: dihedral pdb=" CA THR D 137 " pdb=" C THR D 137 " pdb=" N ASP D 138 " pdb=" CA ASP D 138 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA THR B 137 " pdb=" C THR B 137 " pdb=" N ASP B 138 " pdb=" CA ASP B 138 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA THR C 137 " pdb=" C THR C 137 " pdb=" N ASP C 138 " pdb=" CA ASP C 138 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.440: 2243 0.440 - 0.879: 12 0.879 - 1.319: 1 1.319 - 1.759: 0 1.759 - 2.198: 1 Chirality restraints: 2257 Sorted by residual: chirality pdb=" C08 RI5 A 503 " pdb=" C07 RI5 A 503 " pdb=" C09 RI5 A 503 " pdb=" C13 RI5 A 503 " both_signs ideal model delta sigma weight residual False 2.99 0.79 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" C14 RI5 A 503 " pdb=" C13 RI5 A 503 " pdb=" C15 RI5 A 503 " pdb=" O16 RI5 A 503 " both_signs ideal model delta sigma weight residual True 2.42 1.19 1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB ILE B 424 " pdb=" CA ILE B 424 " pdb=" CG1 ILE B 424 " pdb=" CG2 ILE B 424 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 2254 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 502 " -0.032 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C GLY A 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLY A 502 " -0.038 2.00e-02 2.50e+03 pdb=" OXT GLY A 502 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 501 " -0.032 2.00e-02 2.50e+03 6.18e-02 3.82e+01 pdb=" C GLY D 501 " 0.107 2.00e-02 2.50e+03 pdb=" O GLY D 501 " -0.038 2.00e-02 2.50e+03 pdb=" OXT GLY D 501 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 502 " -0.032 2.00e-02 2.50e+03 6.17e-02 3.81e+01 pdb=" C GLY C 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLY C 502 " -0.038 2.00e-02 2.50e+03 pdb=" OXT GLY C 502 " -0.037 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3770 2.81 - 3.34: 12890 3.34 - 3.86: 23604 3.86 - 4.38: 25383 4.38 - 4.90: 45243 Nonbonded interactions: 110890 Sorted by model distance: nonbonded pdb=" O LEU A 279 " pdb=" OG1 THR A 283 " model vdw 2.293 3.040 nonbonded pdb=" O LEU D 279 " pdb=" OG1 THR D 283 " model vdw 2.293 3.040 nonbonded pdb=" O LEU E 279 " pdb=" OG1 THR E 283 " model vdw 2.293 3.040 nonbonded pdb=" O LEU C 279 " pdb=" OG1 THR C 283 " model vdw 2.294 3.040 nonbonded pdb=" O LEU B 279 " pdb=" OG1 THR B 283 " model vdw 2.294 3.040 ... (remaining 110885 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 31 through 441 or resid 502)) selection = (chain 'B' and resid 31 through 501) selection = (chain 'C' and (resid 31 through 441 or resid 502)) selection = (chain 'D' and resid 31 through 501) selection = (chain 'E' and (resid 31 through 441 or resid 502)) } 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 group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.170 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.018 0.970 14700 Z= 0.801 Angle : 1.600 33.524 19946 Z= 0.888 Chirality : 0.112 2.198 2257 Planarity : 0.011 0.062 2483 Dihedral : 11.857 77.132 5345 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.19), residues: 1740 helix: 0.11 (0.21), residues: 640 sheet: -2.11 (0.27), residues: 340 loop : -2.00 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.053 0.006 TYR A 325 PHE 0.081 0.005 PHE A 169 TRP 0.022 0.004 TRP E 263 HIS 0.006 0.002 HIS E 335 Details of bonding type rmsd/Z covalent geometry : bond 0.01779 / 0.80 (14700) covalent geometry : angle 1.60028 / 0.89 (19946) hydrogen bonds : bond 0.16487 / 10.54 ( 635) hydrogen bonds : angle 7.27235 / 4.95 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.8418 (m) cc_final: 0.7936 (m) REVERT: A 263 TRP cc_start: 0.8433 (m-10) cc_final: 0.7736 (m-10) REVERT: C 176 CYS cc_start: 0.8377 (m) cc_final: 0.8084 (m) REVERT: C 263 TRP cc_start: 0.8431 (m-10) cc_final: 0.7771 (m-10) REVERT: E 114 LEU cc_start: 0.8239 (mt) cc_final: 0.7672 (pt) REVERT: D 114 LEU cc_start: 0.8269 (mt) cc_final: 0.7718 (pt) REVERT: D 179 GLN cc_start: 0.8623 (mt0) cc_final: 0.8366 (mt0) REVERT: D 263 TRP cc_start: 0.8411 (m-10) cc_final: 0.7804 (m-10) REVERT: B 114 LEU cc_start: 0.8301 (mt) cc_final: 0.7720 (pt) REVERT: B 187 MET cc_start: 0.7905 (tpp) cc_final: 0.7091 (mmt) REVERT: B 256 LEU cc_start: 0.9053 (tp) cc_final: 0.8746 (tt) REVERT: B 263 TRP cc_start: 0.8424 (m-10) cc_final: 0.7751 (m-10) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1085 time to fit residues: 65.2200 Evaluate side-chains 216 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN C 290 GLN E 335 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 335 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078619 restraints weight = 45709.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081443 restraints weight = 23135.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.083306 restraints weight = 14264.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084576 restraints weight = 10024.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.085413 restraints weight = 7706.072| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14700 Z= 0.141 Angle : 0.675 9.309 19946 Z= 0.338 Chirality : 0.045 0.192 2257 Planarity : 0.004 0.039 2483 Dihedral : 4.649 17.731 1915 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 15.17 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 1740 helix: 1.38 (0.19), residues: 660 sheet: -1.33 (0.24), residues: 460 loop : -1.97 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 295 TYR 0.014 0.001 TYR B 429 PHE 0.018 0.001 PHE D 169 TRP 0.020 0.002 TRP A 118 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14700) covalent geometry : angle 0.67520 / 0.34 (19946) hydrogen bonds : bond 0.04033 / 2.66 ( 635) hydrogen bonds : angle 4.24999 / 2.95 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.7959 (mpp) cc_final: 0.7693 (mpp) REVERT: A 174 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6729 (mm110) REVERT: A 263 TRP cc_start: 0.7995 (m-10) cc_final: 0.7323 (m100) REVERT: A 319 PHE cc_start: 0.7894 (t80) cc_final: 0.7660 (t80) REVERT: C 263 TRP cc_start: 0.8076 (m-10) cc_final: 0.7537 (m-10) REVERT: C 311 MET cc_start: 0.8346 (mtm) cc_final: 0.8129 (ttm) REVERT: E 171 MET cc_start: 0.8042 (mpp) cc_final: 0.7822 (mpp) REVERT: E 187 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7394 (tpp) REVERT: E 287 MET cc_start: 0.9118 (mmm) cc_final: 0.8822 (tpp) REVERT: E 311 MET cc_start: 0.8174 (mmm) cc_final: 0.7897 (ttm) REVERT: D 250 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8038 (tp40) REVERT: D 263 TRP cc_start: 0.7918 (m-10) cc_final: 0.7411 (m-10) REVERT: B 256 LEU cc_start: 0.9068 (tp) cc_final: 0.8731 (tt) REVERT: B 263 TRP cc_start: 0.8090 (m-10) cc_final: 0.7809 (m-10) REVERT: B 287 MET cc_start: 0.8930 (mmm) cc_final: 0.8694 (tpp) outliers start: 34 outliers final: 17 residues processed: 243 average time/residue: 0.0903 time to fit residues: 34.1121 Evaluate side-chains 188 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 431 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 0.0030 chunk 152 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 66 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN A 335 HIS C 335 HIS ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.088875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074922 restraints weight = 46184.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.077648 restraints weight = 23836.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079444 restraints weight = 14897.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.080661 restraints weight = 10615.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081444 restraints weight = 8257.906| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14700 Z= 0.117 Angle : 0.616 7.264 19946 Z= 0.304 Chirality : 0.043 0.143 2257 Planarity : 0.003 0.035 2483 Dihedral : 4.400 18.161 1915 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.86 % Allowed : 16.38 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1740 helix: 2.05 (0.19), residues: 660 sheet: -0.86 (0.26), residues: 415 loop : -1.87 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 437 TYR 0.014 0.001 TYR E 429 PHE 0.012 0.001 PHE D 169 TRP 0.009 0.001 TRP A 118 HIS 0.004 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14700) covalent geometry : angle 0.61607 / 0.30 (19946) hydrogen bonds : bond 0.03464 / 2.28 ( 635) hydrogen bonds : angle 3.77352 / 2.63 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7360 (pmm) cc_final: 0.7143 (pmm) REVERT: A 174 GLN cc_start: 0.6630 (mm-40) cc_final: 0.6301 (mm110) REVERT: A 263 TRP cc_start: 0.8038 (m-10) cc_final: 0.7792 (m-10) REVERT: A 289 THR cc_start: 0.8904 (m) cc_final: 0.8601 (p) REVERT: C 187 MET cc_start: 0.8747 (mmm) cc_final: 0.8383 (mmm) REVERT: C 263 TRP cc_start: 0.8096 (m-10) cc_final: 0.7567 (m-10) REVERT: E 287 MET cc_start: 0.9154 (mmm) cc_final: 0.8940 (tpp) REVERT: E 437 ARG cc_start: 0.5192 (mtm180) cc_final: 0.4936 (ptp-170) REVERT: D 250 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: D 263 TRP cc_start: 0.8040 (m-10) cc_final: 0.7632 (m-10) REVERT: D 437 ARG cc_start: 0.5342 (mtt180) cc_final: 0.5085 (ptt-90) REVERT: B 187 MET cc_start: 0.8448 (tpp) cc_final: 0.8238 (mmm) REVERT: B 256 LEU cc_start: 0.9079 (tp) cc_final: 0.8726 (tt) REVERT: B 263 TRP cc_start: 0.8092 (m-10) cc_final: 0.7873 (m-10) REVERT: B 437 ARG cc_start: 0.5218 (mtt180) cc_final: 0.4929 (mtm-85) outliers start: 45 outliers final: 20 residues processed: 226 average time/residue: 0.0971 time to fit residues: 33.6120 Evaluate side-chains 184 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 431 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067201 restraints weight = 47123.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069759 restraints weight = 24281.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071485 restraints weight = 15342.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072653 restraints weight = 11085.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073460 restraints weight = 8752.412| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14700 Z= 0.216 Angle : 0.695 8.537 19946 Z= 0.354 Chirality : 0.045 0.144 2257 Planarity : 0.004 0.080 2483 Dihedral : 5.045 22.075 1915 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.30 % Allowed : 17.21 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1740 helix: 2.33 (0.19), residues: 660 sheet: -0.44 (0.27), residues: 395 loop : -1.85 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.021 0.002 TYR A 429 PHE 0.018 0.002 PHE D 169 TRP 0.010 0.002 TRP D 267 HIS 0.002 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (14700) covalent geometry : angle 0.69470 / 0.35 (19946) hydrogen bonds : bond 0.03863 / 2.50 ( 635) hydrogen bonds : angle 3.80712 / 2.64 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7752 (pmm) cc_final: 0.7513 (pmm) REVERT: A 263 TRP cc_start: 0.8106 (m-10) cc_final: 0.7889 (m-10) REVERT: C 32 MET cc_start: 0.7868 (pmm) cc_final: 0.7602 (pmm) REVERT: C 256 LEU cc_start: 0.9236 (tp) cc_final: 0.8818 (tt) REVERT: C 263 TRP cc_start: 0.8133 (m-10) cc_final: 0.7876 (m-10) REVERT: E 206 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7713 (pp) REVERT: E 263 TRP cc_start: 0.8267 (m-10) cc_final: 0.7821 (m-10) REVERT: E 308 ASP cc_start: 0.8511 (m-30) cc_final: 0.8226 (m-30) REVERT: D 250 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: D 263 TRP cc_start: 0.8111 (m-10) cc_final: 0.7703 (m-10) REVERT: D 287 MET cc_start: 0.9096 (mmm) cc_final: 0.8835 (tpp) REVERT: D 400 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7197 (ptp90) REVERT: D 437 ARG cc_start: 0.5852 (mtt180) cc_final: 0.5642 (ptp-170) REVERT: B 256 LEU cc_start: 0.9153 (tp) cc_final: 0.8838 (tt) REVERT: B 263 TRP cc_start: 0.8198 (m-10) cc_final: 0.7876 (m-10) REVERT: B 400 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7012 (ptp90) outliers start: 52 outliers final: 24 residues processed: 189 average time/residue: 0.1033 time to fit residues: 29.8514 Evaluate side-chains 166 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 400 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.076340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061871 restraints weight = 46854.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064407 restraints weight = 24097.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066098 restraints weight = 15347.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067245 restraints weight = 11165.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068037 restraints weight = 8857.931| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14700 Z= 0.220 Angle : 0.690 8.655 19946 Z= 0.350 Chirality : 0.044 0.148 2257 Planarity : 0.004 0.050 2483 Dihedral : 5.445 40.547 1915 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.81 % Allowed : 17.40 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1740 helix: 2.40 (0.19), residues: 660 sheet: -0.30 (0.27), residues: 405 loop : -1.95 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.015 0.002 TYR B 429 PHE 0.015 0.002 PHE D 169 TRP 0.008 0.001 TRP A 263 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (14700) covalent geometry : angle 0.69008 / 0.35 (19946) hydrogen bonds : bond 0.03795 / 2.47 ( 635) hydrogen bonds : angle 3.80919 / 2.65 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7914 (pmm) cc_final: 0.7650 (pmm) REVERT: A 187 MET cc_start: 0.8646 (tpp) cc_final: 0.8434 (tpp) REVERT: A 212 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (pt) REVERT: A 263 TRP cc_start: 0.8073 (m-10) cc_final: 0.7799 (m-10) REVERT: C 187 MET cc_start: 0.8644 (mmm) cc_final: 0.8283 (tpt) REVERT: C 256 LEU cc_start: 0.9190 (tp) cc_final: 0.8839 (tt) REVERT: C 263 TRP cc_start: 0.8138 (m-10) cc_final: 0.7721 (m-10) REVERT: C 308 ASP cc_start: 0.8636 (m-30) cc_final: 0.8341 (m-30) REVERT: E 206 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7840 (pp) REVERT: E 263 TRP cc_start: 0.8227 (m-10) cc_final: 0.7834 (m-10) REVERT: E 287 MET cc_start: 0.9250 (tpp) cc_final: 0.9031 (tpp) REVERT: E 308 ASP cc_start: 0.8655 (m-30) cc_final: 0.8331 (m-30) REVERT: E 400 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7178 (ptp90) REVERT: D 180 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9119 (mt) REVERT: D 250 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8389 (tp40) REVERT: D 263 TRP cc_start: 0.8140 (m-10) cc_final: 0.7690 (m-10) REVERT: D 400 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7196 (ptp90) REVERT: D 437 ARG cc_start: 0.5275 (mtt180) cc_final: 0.4526 (ptp-170) REVERT: B 80 MET cc_start: 0.9233 (mmm) cc_final: 0.8777 (mmm) REVERT: B 256 LEU cc_start: 0.9103 (tp) cc_final: 0.8799 (tt) REVERT: B 263 TRP cc_start: 0.8117 (m-10) cc_final: 0.7767 (m-10) REVERT: B 400 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (ptp90) outliers start: 60 outliers final: 37 residues processed: 191 average time/residue: 0.1027 time to fit residues: 30.0631 Evaluate side-chains 182 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 400 ARG Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 400 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.063218 restraints weight = 47005.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065730 restraints weight = 24716.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067386 restraints weight = 15813.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068535 restraints weight = 11507.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069331 restraints weight = 9118.780| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14700 Z= 0.159 Angle : 0.656 9.709 19946 Z= 0.328 Chirality : 0.043 0.159 2257 Planarity : 0.003 0.049 2483 Dihedral : 5.339 47.054 1915 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.43 % Allowed : 19.43 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1740 helix: 2.52 (0.19), residues: 660 sheet: -0.08 (0.28), residues: 395 loop : -1.91 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.013 0.002 TYR D 246 PHE 0.011 0.001 PHE D 169 TRP 0.005 0.001 TRP A 92 HIS 0.003 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (14700) covalent geometry : angle 0.65556 / 0.33 (19946) hydrogen bonds : bond 0.03529 / 2.31 ( 635) hydrogen bonds : angle 3.68340 / 2.57 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7816 (t0) cc_final: 0.7533 (t0) REVERT: A 212 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8818 (pt) REVERT: A 263 TRP cc_start: 0.8017 (m-10) cc_final: 0.7786 (m-10) REVERT: C 187 MET cc_start: 0.8510 (mmm) cc_final: 0.8227 (tpt) REVERT: C 251 MET cc_start: 0.8569 (mpp) cc_final: 0.8263 (mpp) REVERT: C 263 TRP cc_start: 0.8102 (m-10) cc_final: 0.7832 (m-10) REVERT: C 308 ASP cc_start: 0.8555 (m-30) cc_final: 0.8289 (m-30) REVERT: E 206 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7869 (pp) REVERT: E 251 MET cc_start: 0.8623 (mpp) cc_final: 0.8301 (mpp) REVERT: E 263 TRP cc_start: 0.8177 (m-10) cc_final: 0.7772 (m-10) REVERT: E 308 ASP cc_start: 0.8525 (m-30) cc_final: 0.8239 (m-30) REVERT: E 400 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7271 (ptp90) REVERT: D 180 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9142 (mt) REVERT: D 250 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (tp40) REVERT: D 263 TRP cc_start: 0.8082 (m-10) cc_final: 0.7613 (m-10) REVERT: D 285 LEU cc_start: 0.9186 (mt) cc_final: 0.8848 (tt) REVERT: B 80 MET cc_start: 0.9144 (mmm) cc_final: 0.8746 (mmm) REVERT: B 256 LEU cc_start: 0.9099 (tp) cc_final: 0.8800 (tt) REVERT: B 263 TRP cc_start: 0.8076 (m-10) cc_final: 0.7740 (m-10) REVERT: B 311 MET cc_start: 0.8360 (mtp) cc_final: 0.7708 (ttm) outliers start: 54 outliers final: 37 residues processed: 188 average time/residue: 0.1031 time to fit residues: 29.5769 Evaluate side-chains 180 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2372 > 50: distance: 81 - 122: 9.723 distance: 84 - 119: 8.995 distance: 111 - 112: 4.828 distance: 111 - 254: 4.311 distance: 112 - 113: 3.654 distance: 112 - 115: 4.898 distance: 113 - 114: 3.540 distance: 113 - 119: 7.317 distance: 114 - 251: 4.254 distance: 115 - 116: 6.592 distance: 116 - 117: 21.793 distance: 116 - 118: 8.089 distance: 120 - 121: 4.112 distance: 120 - 123: 11.401 distance: 121 - 122: 14.914 distance: 121 - 128: 10.932 distance: 123 - 124: 4.649 distance: 124 - 125: 4.516 distance: 125 - 126: 11.583 distance: 125 - 127: 6.593 distance: 128 - 129: 13.672 distance: 129 - 130: 7.314 distance: 129 - 132: 8.164 distance: 130 - 131: 3.819 distance: 130 - 134: 3.475 distance: 132 - 133: 5.742 distance: 135 - 136: 9.330 distance: 135 - 138: 12.108 distance: 136 - 137: 14.232 distance: 136 - 145: 12.707 distance: 139 - 140: 5.720 distance: 139 - 141: 3.882 distance: 140 - 142: 4.065 distance: 141 - 143: 5.711 distance: 142 - 144: 13.966 distance: 143 - 144: 5.198 distance: 145 - 146: 7.843 distance: 146 - 147: 11.343 distance: 147 - 148: 3.433 distance: 147 - 149: 5.104 distance: 149 - 150: 6.512 distance: 150 - 151: 7.183 distance: 150 - 153: 14.733 distance: 151 - 152: 7.053 distance: 151 - 161: 5.562 distance: 153 - 154: 9.070 distance: 154 - 155: 4.464 distance: 155 - 157: 3.687 distance: 158 - 159: 3.777 distance: 159 - 160: 6.075 distance: 161 - 162: 7.814 distance: 162 - 163: 9.133 distance: 162 - 165: 9.503 distance: 163 - 164: 10.301 distance: 163 - 168: 5.148 distance: 165 - 166: 15.870 distance: 165 - 167: 20.755 distance: 168 - 169: 20.553 distance: 169 - 170: 16.111 distance: 169 - 172: 11.810 distance: 170 - 171: 15.490 distance: 170 - 176: 32.208 distance: 172 - 173: 7.171 distance: 173 - 174: 40.551 distance: 174 - 175: 28.229 distance: 176 - 177: 6.207 distance: 177 - 178: 25.870 distance: 177 - 180: 21.048 distance: 178 - 179: 9.427 distance: 178 - 184: 18.131 distance: 180 - 181: 7.399 distance: 181 - 182: 5.325 distance: 181 - 183: 5.715 distance: 184 - 185: 27.533 distance: 185 - 186: 7.299 distance: 185 - 188: 29.510 distance: 186 - 187: 3.049 distance: 186 - 192: 4.159 distance: 188 - 189: 12.030 distance: 189 - 190: 30.507 distance: 189 - 191: 19.171