Starting phenix.real_space_refine on Sat Sep 12 07:49:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ud3_20731/09_2026/6ud3_20731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ud3_20731/09_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_20731/09_2026/6ud3_20731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ud3_20731/09_2026/6ud3_20731.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ud3_20731/09_2026/6ud3_20731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ud3_20731/09_2026/6ud3_20731.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ud3_20731/09_2026/6ud3_20731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ud3_20731/09_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-2.2.1-6174/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: 3.44, per 1000 atoms: 0.24 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: 1.16 Conformation dependent library (CDL) restraints added in 728.3 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: 0.57 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: 2.84 Time building geometry restraints manager: 1.63 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.400 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- 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 : 0.522 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: 0.1239 time to fit residues: 74.5263 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 : 0.513 ------------------------------------------------------------------------------- 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 : 0.594 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: 0.1056 time to fit residues: 39.9037 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 : 0.565 ------------------------------------------------------------------------------- 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 : 0.578 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: 0.1102 time to fit residues: 38.2729 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 : 0.590 ------------------------------------------------------------------------------- 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 : 0.525 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: 0.1117 time to fit residues: 32.2374 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 : 0.510 ------------------------------------------------------------------------------- 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 : 0.588 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: 0.1113 time to fit residues: 32.8663 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 : 1.003 ------------------------------------------------------------------------------- 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 : 0.380 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: 0.1152 time to fit residues: 32.9836 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 : 0.553 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 175 random chunks: chunk 142 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 85 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.2372 > 50:) chunk 90 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.078140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064187 restraints weight = 46762.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066772 restraints weight = 23900.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068467 restraints weight = 15101.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069625 restraints weight = 10861.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070400 restraints weight = 8559.328| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14700 Z= 0.144 Angle : 0.658 8.875 19946 Z= 0.324 Chirality : 0.043 0.179 2257 Planarity : 0.003 0.046 2483 Dihedral : 5.172 45.997 1915 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.05 % Allowed : 20.70 % Favored : 76.25 % 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: 0.44 (0.21), residues: 1740 helix: 2.58 (0.19), residues: 660 sheet: -0.03 (0.28), residues: 400 loop : -1.95 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 437 TYR 0.014 0.001 TYR D 246 PHE 0.013 0.001 PHE D 169 TRP 0.009 0.001 TRP E 194 HIS 0.003 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14700) covalent geometry : angle 0.65801 / 0.32 (19946) hydrogen bonds : bond 0.03399 / 2.22 ( 635) hydrogen bonds : angle 3.60093 / 2.51 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 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 197 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7893 (t0) cc_final: 0.7632 (t70) REVERT: A 212 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8754 (pt) REVERT: A 263 TRP cc_start: 0.8022 (m-10) cc_final: 0.7783 (m-10) REVERT: C 32 MET cc_start: 0.7976 (pmm) cc_final: 0.7662 (pmm) REVERT: C 187 MET cc_start: 0.8549 (mmm) cc_final: 0.8273 (tpt) REVERT: C 257 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8881 (tp) REVERT: C 263 TRP cc_start: 0.8098 (m-10) cc_final: 0.7842 (m-10) REVERT: C 308 ASP cc_start: 0.8602 (m-30) cc_final: 0.8323 (m-30) REVERT: C 311 MET cc_start: 0.7850 (mtp) cc_final: 0.7629 (ttm) REVERT: E 206 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7840 (pp) REVERT: E 251 MET cc_start: 0.8652 (mpp) cc_final: 0.8419 (mpp) REVERT: E 263 TRP cc_start: 0.8143 (m-10) cc_final: 0.7742 (m-10) REVERT: E 308 ASP cc_start: 0.8594 (m-30) cc_final: 0.8261 (m-30) REVERT: E 311 MET cc_start: 0.8133 (mtp) cc_final: 0.7626 (ttm) REVERT: E 400 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7148 (ptp90) REVERT: D 250 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8307 (tp40) REVERT: D 263 TRP cc_start: 0.8128 (m-10) cc_final: 0.7663 (m-10) REVERT: D 285 LEU cc_start: 0.9131 (mt) cc_final: 0.8812 (tt) REVERT: B 80 MET cc_start: 0.9179 (mmm) cc_final: 0.8953 (mmm) REVERT: B 256 LEU cc_start: 0.9054 (tp) cc_final: 0.8764 (tt) REVERT: B 263 TRP cc_start: 0.8101 (m-10) cc_final: 0.7764 (m-10) outliers start: 48 outliers final: 34 residues processed: 186 average time/residue: 0.0997 time to fit residues: 28.6710 Evaluate side-chains 182 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 164 MET 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 258 ILE Chi-restraints excluded: chain C residue 288 THR 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 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 128 LYS 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 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 316 LEU Chi-restraints excluded: chain B residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 84 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 61 optimal weight: 0.0570 chunk 58 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068289 restraints weight = 46978.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070818 restraints weight = 24485.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072579 restraints weight = 15879.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073773 restraints weight = 11543.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074589 restraints weight = 9155.051| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6268 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= 0.124 Angle : 0.652 9.218 19946 Z= 0.318 Chirality : 0.042 0.161 2257 Planarity : 0.003 0.046 2483 Dihedral : 4.950 42.551 1915 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.43 % Allowed : 20.57 % Favored : 76.00 % 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: 0.52 (0.21), residues: 1740 helix: 2.63 (0.19), residues: 660 sheet: 0.09 (0.28), residues: 400 loop : -1.92 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 295 TYR 0.010 0.001 TYR D 429 PHE 0.008 0.001 PHE C 266 TRP 0.005 0.001 TRP E 263 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14700) covalent geometry : angle 0.65183 / 0.32 (19946) hydrogen bonds : bond 0.03210 / 2.10 ( 635) hydrogen bonds : angle 3.51660 / 2.45 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 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 202 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7831 (t0) cc_final: 0.7490 (t0) REVERT: A 212 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8781 (pt) REVERT: A 263 TRP cc_start: 0.8006 (m-10) cc_final: 0.7772 (m-10) REVERT: A 311 MET cc_start: 0.7888 (mtp) cc_final: 0.7589 (ttm) REVERT: C 32 MET cc_start: 0.7936 (pmm) cc_final: 0.7663 (pmm) REVERT: C 187 MET cc_start: 0.8431 (mmm) cc_final: 0.8201 (mmm) REVERT: C 257 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8835 (tp) REVERT: C 263 TRP cc_start: 0.8130 (m-10) cc_final: 0.7882 (m-10) REVERT: C 287 MET cc_start: 0.9041 (tpt) cc_final: 0.8659 (tpp) REVERT: E 206 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7772 (pp) REVERT: E 251 MET cc_start: 0.8526 (mpp) cc_final: 0.8230 (mpp) REVERT: E 263 TRP cc_start: 0.8167 (m-10) cc_final: 0.7796 (m-10) REVERT: E 308 ASP cc_start: 0.8561 (m-30) cc_final: 0.8262 (m-30) REVERT: E 400 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7129 (ptp90) REVERT: E 437 ARG cc_start: 0.4889 (mtm180) cc_final: 0.4662 (ptp-170) REVERT: D 251 MET cc_start: 0.8687 (mpp) cc_final: 0.8459 (mpp) REVERT: D 263 TRP cc_start: 0.8174 (m-10) cc_final: 0.7701 (m-10) REVERT: B 256 LEU cc_start: 0.9054 (tp) cc_final: 0.8749 (tt) REVERT: B 263 TRP cc_start: 0.8161 (m-10) cc_final: 0.7840 (m-10) outliers start: 54 outliers final: 37 residues processed: 189 average time/residue: 0.1109 time to fit residues: 32.5109 Evaluate side-chains 181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 319 PHE 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 258 ILE 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 206 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 298 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 117 ILE Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 264 VAL 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 206 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 92 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.083882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070323 restraints weight = 47612.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072882 restraints weight = 24129.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074604 restraints weight = 14999.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075731 restraints weight = 10661.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076472 restraints weight = 8312.592| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14700 Z= 0.133 Angle : 0.669 9.710 19946 Z= 0.325 Chirality : 0.043 0.160 2257 Planarity : 0.003 0.043 2483 Dihedral : 4.915 41.083 1915 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.11 % Allowed : 21.21 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1740 helix: 2.60 (0.19), residues: 660 sheet: 0.14 (0.28), residues: 400 loop : -1.94 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.018 0.001 TYR B 246 PHE 0.012 0.001 PHE D 169 TRP 0.006 0.001 TRP A 92 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14700) covalent geometry : angle 0.66869 / 0.32 (19946) hydrogen bonds : bond 0.03241 / 2.13 ( 635) hydrogen bonds : angle 3.54452 / 2.47 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 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 195 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8797 (pt) REVERT: A 263 TRP cc_start: 0.8043 (m-10) cc_final: 0.7808 (m-10) REVERT: A 311 MET cc_start: 0.8057 (mtp) cc_final: 0.7696 (ttm) REVERT: C 32 MET cc_start: 0.7940 (pmm) cc_final: 0.7726 (pmm) REVERT: C 257 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8834 (tp) REVERT: C 263 TRP cc_start: 0.8124 (m-10) cc_final: 0.7871 (m-10) REVERT: C 287 MET cc_start: 0.9045 (tpt) cc_final: 0.8746 (tpp) REVERT: C 308 ASP cc_start: 0.8715 (m-30) cc_final: 0.8470 (m-30) REVERT: E 206 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7786 (pp) REVERT: E 251 MET cc_start: 0.8536 (mpp) cc_final: 0.8275 (mpp) REVERT: E 263 TRP cc_start: 0.8198 (m-10) cc_final: 0.7816 (m-10) REVERT: E 308 ASP cc_start: 0.8524 (m-30) cc_final: 0.8222 (m-30) REVERT: D 263 TRP cc_start: 0.8182 (m-10) cc_final: 0.7700 (m-10) REVERT: B 256 LEU cc_start: 0.9063 (tp) cc_final: 0.8749 (tt) REVERT: B 263 TRP cc_start: 0.8175 (m-10) cc_final: 0.7835 (m-10) REVERT: B 311 MET cc_start: 0.7894 (mtp) cc_final: 0.7681 (ttm) outliers start: 49 outliers final: 39 residues processed: 186 average time/residue: 0.1018 time to fit residues: 29.6305 Evaluate side-chains 178 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 261 LEU 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 258 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 420 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 206 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 264 VAL 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 316 LEU Chi-restraints excluded: chain B residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 101 optimal weight: 0.0270 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069890 restraints weight = 46706.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072513 restraints weight = 24035.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074300 restraints weight = 15259.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075489 restraints weight = 11050.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076253 restraints weight = 8749.868| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14700 Z= 0.120 Angle : 0.681 12.691 19946 Z= 0.325 Chirality : 0.043 0.173 2257 Planarity : 0.003 0.045 2483 Dihedral : 4.762 38.016 1915 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.60 % Allowed : 21.65 % Favored : 75.75 % 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: 0.56 (0.21), residues: 1740 helix: 2.59 (0.19), residues: 660 sheet: 0.25 (0.28), residues: 400 loop : -1.93 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 295 TYR 0.019 0.001 TYR B 246 PHE 0.009 0.001 PHE C 266 TRP 0.006 0.001 TRP E 263 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14700) covalent geometry : angle 0.68086 / 0.32 (19946) hydrogen bonds : bond 0.03096 / 2.04 ( 635) hydrogen bonds : angle 3.50319 / 2.45 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 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 191 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7682 (t0) cc_final: 0.7335 (t0) REVERT: A 212 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8855 (pt) REVERT: A 263 TRP cc_start: 0.8102 (m-10) cc_final: 0.7871 (m-10) REVERT: A 311 MET cc_start: 0.7927 (mtp) cc_final: 0.7582 (ttm) REVERT: C 257 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8841 (tp) REVERT: C 263 TRP cc_start: 0.8150 (m-10) cc_final: 0.7909 (m-10) REVERT: C 287 MET cc_start: 0.9079 (tpt) cc_final: 0.8744 (tpp) REVERT: E 206 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7789 (pp) REVERT: E 263 TRP cc_start: 0.8192 (m-10) cc_final: 0.7800 (m-10) REVERT: E 308 ASP cc_start: 0.8479 (m-30) cc_final: 0.8211 (m-30) REVERT: D 263 TRP cc_start: 0.8261 (m-10) cc_final: 0.7953 (m-10) REVERT: B 256 LEU cc_start: 0.9045 (tp) cc_final: 0.8724 (tt) REVERT: B 263 TRP cc_start: 0.8224 (m-10) cc_final: 0.7874 (m-10) outliers start: 41 outliers final: 30 residues processed: 183 average time/residue: 0.1051 time to fit residues: 30.1930 Evaluate side-chains 176 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 288 THR 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 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 206 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 258 ILE 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 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068997 restraints weight = 47255.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071536 restraints weight = 24562.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073325 restraints weight = 15794.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074576 restraints weight = 11426.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075393 restraints weight = 9005.342| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14700 Z= 0.134 Angle : 0.710 12.683 19946 Z= 0.336 Chirality : 0.043 0.172 2257 Planarity : 0.003 0.043 2483 Dihedral : 4.796 37.760 1915 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.41 % Allowed : 22.10 % Favored : 75.49 % 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: 0.55 (0.21), residues: 1740 helix: 2.56 (0.19), residues: 660 sheet: 0.30 (0.28), residues: 400 loop : -1.95 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 295 TYR 0.013 0.001 TYR B 246 PHE 0.010 0.001 PHE C 266 TRP 0.006 0.001 TRP A 92 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14700) covalent geometry : angle 0.71013 / 0.34 (19946) hydrogen bonds : bond 0.03196 / 2.09 ( 635) hydrogen bonds : angle 3.52405 / 2.46 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.79 seconds wall clock time: 38 minutes 25.56 seconds (2305.56 seconds total)