Starting phenix.real_space_refine on Sat Aug 23 14:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxf_16317/08_2025/8bxf_16317.map" } resolution = 3.4 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= -0.001 sd= 0.076 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 80 5.16 5 C 8385 2.51 5 N 2041 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2517 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 7 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.66, per 1000 atoms: 0.13 Number of scatterers: 12692 At special positions: 0 Unit cell: (90.944, 90.16, 121.52, 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 80 16.00 O 2186 8.00 N 2041 7.00 C 8385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.04 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 406.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 36.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.776A pdb=" N ARG A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 417 through 443 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 305 Processing helix chain 'B' and resid 417 through 443 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.737A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 239 removed outlier: 4.782A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 417 through 443 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.738A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP D 81 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 417 through 443 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP E 81 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 305 Processing helix chain 'E' and resid 417 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 71 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN A 40 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 39 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 169 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 41 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 71 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN B 40 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 71 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN C 40 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN D 71 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN D 40 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 39 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR D 169 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 41 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC1, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC2, first strand: chain 'D' and resid 197 through 199 Processing sheet with id=AC3, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AC4, first strand: chain 'E' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 71 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN E 40 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 39 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 169 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 41 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'E' and resid 197 through 199 695 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3172 1.33 - 1.45: 2598 1.45 - 1.57: 7091 1.57 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 13001 Sorted by residual: bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.24e-02 6.50e+03 4.78e+00 bond pdb=" N LEU C 140 " pdb=" CA LEU C 140 " ideal model delta sigma weight residual 1.457 1.483 -0.027 1.24e-02 6.50e+03 4.59e+00 bond pdb=" CB PHE D 425 " pdb=" CG PHE D 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.59e+00 bond pdb=" N MET D 301 " pdb=" CA MET D 301 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.54e+00 bond pdb=" CB PHE C 425 " pdb=" CG PHE C 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.52e+00 ... (remaining 12996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16963 2.02 - 4.05: 678 4.05 - 6.07: 103 6.07 - 8.10: 45 8.10 - 10.12: 10 Bond angle restraints: 17799 Sorted by residual: angle pdb=" C TYR A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta sigma weight residual 122.08 127.82 -5.74 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C TYR E 199 " pdb=" N ASN E 200 " pdb=" CA ASN E 200 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C TYR C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta sigma weight residual 122.08 127.74 -5.66 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C TYR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta sigma weight residual 122.08 127.72 -5.64 1.47e+00 4.63e-01 1.47e+01 angle pdb=" C TYR B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta sigma weight residual 122.08 127.71 -5.63 1.47e+00 4.63e-01 1.47e+01 ... (remaining 17794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 6813 15.42 - 30.83: 607 30.83 - 46.25: 175 46.25 - 61.66: 20 61.66 - 77.08: 15 Dihedral angle restraints: 7630 sinusoidal: 2790 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.24 45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.24 45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.26 45.74 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 7627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1462 0.047 - 0.093: 498 0.093 - 0.140: 171 0.140 - 0.186: 34 0.186 - 0.233: 20 Chirality restraints: 2185 Sorted by residual: chirality pdb=" CA MET E 227 " pdb=" N MET E 227 " pdb=" C MET E 227 " pdb=" CB MET E 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET A 227 " pdb=" N MET A 227 " pdb=" C MET A 227 " pdb=" CB MET A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET D 227 " pdb=" N MET D 227 " pdb=" C MET D 227 " pdb=" CB MET D 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2182 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 425 " 0.016 2.00e-02 2.50e+03 2.39e-02 9.96e+00 pdb=" CG PHE E 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE E 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 425 " 0.016 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 425 " -0.016 2.00e-02 2.50e+03 2.37e-02 9.84e+00 pdb=" CG PHE D 425 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 425 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 425 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 425 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 425 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 425 " 0.001 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 11 2.19 - 2.86: 4284 2.86 - 3.54: 17177 3.54 - 4.22: 29094 4.22 - 4.90: 50019 Nonbonded interactions: 100585 Sorted by model distance: nonbonded pdb=" CB ASN E 200 " pdb=" CG ASN E 200 " model vdw 1.507 3.670 nonbonded pdb=" CB ASN C 172 " pdb=" CG ASN C 172 " model vdw 1.514 3.670 nonbonded pdb=" CB ASN B 172 " pdb=" CG ASN B 172 " model vdw 1.514 3.670 nonbonded pdb=" CB ASN E 172 " pdb=" CG ASN E 172 " model vdw 1.515 3.670 nonbonded pdb=" CB ASN D 172 " pdb=" CG ASN D 172 " model vdw 1.515 3.670 ... (remaining 100580 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' selection = (chain 'B' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) selection = (chain 'C' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 501)) selection = (chain 'D' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) selection = (chain 'E' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.049 13011 Z= 0.226 Angle : 0.954 10.124 17824 Z= 0.500 Chirality : 0.056 0.233 2185 Planarity : 0.007 0.043 2139 Dihedral : 13.468 77.077 4485 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.19), residues: 1610 helix: -0.93 (0.19), residues: 530 sheet: -1.31 (0.25), residues: 450 loop : -1.72 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.014 0.001 TYR B 178 PHE 0.054 0.004 PHE E 425 TRP 0.013 0.002 TRP D 70 HIS 0.021 0.003 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00448 (13001) covalent geometry : angle 0.95425 (17799) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.93447 ( 10) hydrogen bonds : bond 0.12179 ( 615) hydrogen bonds : angle 6.75507 ( 1935) link_NAG-ASN : bond 0.00233 ( 5) link_NAG-ASN : angle 0.44399 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 306 time to evaluate : 0.412 Fit side-chains REVERT: A 219 ILE cc_start: 0.8458 (tt) cc_final: 0.8191 (tt) REVERT: A 222 GLN cc_start: 0.8353 (mt0) cc_final: 0.8075 (mt0) REVERT: A 301 MET cc_start: 0.7955 (tmm) cc_final: 0.7699 (tmm) REVERT: B 219 ILE cc_start: 0.8474 (tt) cc_final: 0.8209 (tt) REVERT: B 222 GLN cc_start: 0.8269 (mt0) cc_final: 0.7959 (mt0) REVERT: B 301 MET cc_start: 0.7904 (tmm) cc_final: 0.7624 (tmm) REVERT: C 219 ILE cc_start: 0.8332 (tt) cc_final: 0.7954 (tp) REVERT: C 301 MET cc_start: 0.7964 (tmm) cc_final: 0.7710 (tmm) REVERT: D 16 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: D 66 ILE cc_start: 0.8897 (pt) cc_final: 0.8654 (pt) REVERT: D 219 ILE cc_start: 0.8457 (tt) cc_final: 0.8161 (tt) REVERT: D 222 GLN cc_start: 0.8311 (mt0) cc_final: 0.7869 (mp10) REVERT: D 301 MET cc_start: 0.7960 (tmm) cc_final: 0.7637 (tmm) REVERT: E 219 ILE cc_start: 0.8358 (tt) cc_final: 0.8092 (tt) REVERT: E 222 GLN cc_start: 0.8354 (mt0) cc_final: 0.8079 (mt0) REVERT: E 301 MET cc_start: 0.7926 (tmm) cc_final: 0.7583 (tmm) outliers start: 5 outliers final: 0 residues processed: 311 average time/residue: 0.0969 time to fit residues: 42.5202 Evaluate side-chains 232 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121525 restraints weight = 20227.595| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.14 r_work: 0.3493 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13011 Z= 0.136 Angle : 0.576 8.273 17824 Z= 0.294 Chirality : 0.044 0.146 2185 Planarity : 0.004 0.033 2139 Dihedral : 4.383 17.217 1870 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.14 % Allowed : 10.67 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.20), residues: 1610 helix: 0.66 (0.21), residues: 535 sheet: -1.38 (0.26), residues: 440 loop : -1.44 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.008 0.001 TYR B 199 PHE 0.013 0.001 PHE A 241 TRP 0.013 0.001 TRP B 70 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00304 (13001) covalent geometry : angle 0.57624 (17799) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.72277 ( 10) hydrogen bonds : bond 0.03710 ( 615) hydrogen bonds : angle 4.57437 ( 1935) link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 0.64912 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.313 Fit side-chains REVERT: A 127 MET cc_start: 0.8001 (mtt) cc_final: 0.7744 (mtp) REVERT: A 219 ILE cc_start: 0.8058 (tt) cc_final: 0.7711 (tt) REVERT: A 222 GLN cc_start: 0.8772 (mt0) cc_final: 0.8527 (mt0) REVERT: A 301 MET cc_start: 0.8351 (tmm) cc_final: 0.8053 (tmm) REVERT: B 127 MET cc_start: 0.8000 (mtt) cc_final: 0.7734 (mtp) REVERT: B 222 GLN cc_start: 0.8637 (mt0) cc_final: 0.8382 (mt0) REVERT: B 227 MET cc_start: 0.8601 (ppp) cc_final: 0.8249 (ppp) REVERT: B 301 MET cc_start: 0.8387 (tmm) cc_final: 0.8108 (tmm) REVERT: C 219 ILE cc_start: 0.8146 (tt) cc_final: 0.7878 (tt) REVERT: C 301 MET cc_start: 0.8450 (tmm) cc_final: 0.8149 (tmm) REVERT: D 127 MET cc_start: 0.8088 (mtt) cc_final: 0.7843 (mtp) REVERT: D 219 ILE cc_start: 0.8120 (tt) cc_final: 0.7869 (tt) REVERT: D 222 GLN cc_start: 0.8654 (mt0) cc_final: 0.8338 (mt0) REVERT: D 265 MET cc_start: 0.7403 (ttt) cc_final: 0.7097 (ttm) REVERT: D 301 MET cc_start: 0.8437 (tmm) cc_final: 0.8123 (tmm) REVERT: E 222 GLN cc_start: 0.8631 (mt0) cc_final: 0.8264 (mt0) REVERT: E 265 MET cc_start: 0.7218 (ttt) cc_final: 0.6749 (ttm) REVERT: E 301 MET cc_start: 0.8428 (tmm) cc_final: 0.8103 (tmm) outliers start: 15 outliers final: 4 residues processed: 253 average time/residue: 0.0789 time to fit residues: 30.2018 Evaluate side-chains 231 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 0.0370 chunk 156 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.147707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122266 restraints weight = 20217.616| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.12 r_work: 0.3496 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13011 Z= 0.104 Angle : 0.540 7.670 17824 Z= 0.272 Chirality : 0.042 0.137 2185 Planarity : 0.004 0.029 2139 Dihedral : 3.963 16.958 1870 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 15.06 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1610 helix: 1.50 (0.22), residues: 535 sheet: -1.43 (0.25), residues: 440 loop : -1.14 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 16 TYR 0.006 0.001 TYR C 252 PHE 0.006 0.001 PHE A 298 TRP 0.013 0.001 TRP C 70 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00228 (13001) covalent geometry : angle 0.53957 (17799) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.65755 ( 10) hydrogen bonds : bond 0.03307 ( 615) hydrogen bonds : angle 4.19935 ( 1935) link_NAG-ASN : bond 0.00154 ( 5) link_NAG-ASN : angle 0.59938 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.661 Fit side-chains REVERT: A 127 MET cc_start: 0.7913 (mtt) cc_final: 0.7710 (mtp) REVERT: A 222 GLN cc_start: 0.8744 (mt0) cc_final: 0.8524 (mt0) REVERT: A 265 MET cc_start: 0.7287 (ttt) cc_final: 0.7055 (ttt) REVERT: A 269 ASP cc_start: 0.8965 (t0) cc_final: 0.8671 (t0) REVERT: A 301 MET cc_start: 0.8269 (tmm) cc_final: 0.7808 (tmm) REVERT: B 222 GLN cc_start: 0.8605 (mt0) cc_final: 0.8351 (mt0) REVERT: B 301 MET cc_start: 0.8370 (tmm) cc_final: 0.7980 (tmm) REVERT: C 66 ILE cc_start: 0.9001 (pt) cc_final: 0.8634 (pt) REVERT: C 301 MET cc_start: 0.8450 (tmm) cc_final: 0.8158 (tmm) REVERT: D 127 MET cc_start: 0.7948 (mtt) cc_final: 0.7719 (mtp) REVERT: D 222 GLN cc_start: 0.8661 (mt0) cc_final: 0.8442 (mt0) REVERT: D 265 MET cc_start: 0.7254 (ttt) cc_final: 0.6947 (ttm) REVERT: D 301 MET cc_start: 0.8429 (tmm) cc_final: 0.8135 (tmm) REVERT: E 66 ILE cc_start: 0.8964 (pt) cc_final: 0.8698 (pt) REVERT: E 222 GLN cc_start: 0.8635 (mt0) cc_final: 0.8318 (mt0) REVERT: E 265 MET cc_start: 0.7203 (ttt) cc_final: 0.6791 (ttm) REVERT: E 301 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8220 (tmm) outliers start: 16 outliers final: 10 residues processed: 268 average time/residue: 0.0730 time to fit residues: 30.5963 Evaluate side-chains 238 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 301 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.143660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118151 restraints weight = 20209.176| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.10 r_work: 0.3458 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13011 Z= 0.123 Angle : 0.543 7.318 17824 Z= 0.272 Chirality : 0.042 0.137 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.772 15.488 1870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.42 % Allowed : 16.73 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.22), residues: 1610 helix: 1.86 (0.22), residues: 535 sheet: -1.40 (0.25), residues: 455 loop : -0.98 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 16 TYR 0.006 0.001 TYR C 67 PHE 0.007 0.001 PHE C 298 TRP 0.011 0.001 TRP C 65 HIS 0.003 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00283 (13001) covalent geometry : angle 0.54285 (17799) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.64826 ( 10) hydrogen bonds : bond 0.03167 ( 615) hydrogen bonds : angle 4.08703 ( 1935) link_NAG-ASN : bond 0.00114 ( 5) link_NAG-ASN : angle 0.66495 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.301 Fit side-chains REVERT: A 127 MET cc_start: 0.7935 (mtt) cc_final: 0.7696 (mtp) REVERT: A 223 TYR cc_start: 0.8379 (t80) cc_final: 0.8037 (t80) REVERT: A 269 ASP cc_start: 0.8988 (t0) cc_final: 0.8611 (t0) REVERT: A 301 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7252 (mmt) REVERT: B 222 GLN cc_start: 0.8642 (mt0) cc_final: 0.8416 (mt0) REVERT: B 265 MET cc_start: 0.8517 (ttm) cc_final: 0.7741 (mtp) REVERT: C 183 LYS cc_start: 0.8386 (ptpt) cc_final: 0.7828 (mtmt) REVERT: C 301 MET cc_start: 0.8381 (tmm) cc_final: 0.8097 (tmm) REVERT: D 127 MET cc_start: 0.8030 (mtt) cc_final: 0.7805 (mtp) REVERT: D 222 GLN cc_start: 0.8648 (mt0) cc_final: 0.8434 (mt0) REVERT: E 19 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8809 (ttpp) outliers start: 32 outliers final: 15 residues processed: 271 average time/residue: 0.0801 time to fit residues: 33.5004 Evaluate side-chains 248 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118777 restraints weight = 20312.124| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.11 r_work: 0.3478 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13011 Z= 0.112 Angle : 0.545 8.308 17824 Z= 0.270 Chirality : 0.042 0.136 2185 Planarity : 0.003 0.029 2139 Dihedral : 3.748 16.217 1870 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 18.40 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1610 helix: 2.03 (0.22), residues: 535 sheet: -1.32 (0.25), residues: 440 loop : -0.79 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 133 TYR 0.006 0.001 TYR A 67 PHE 0.007 0.001 PHE E 145 TRP 0.011 0.001 TRP C 65 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00257 (13001) covalent geometry : angle 0.54475 (17799) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.59880 ( 10) hydrogen bonds : bond 0.03048 ( 615) hydrogen bonds : angle 3.97630 ( 1935) link_NAG-ASN : bond 0.00122 ( 5) link_NAG-ASN : angle 0.66648 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.308 Fit side-chains REVERT: A 127 MET cc_start: 0.7907 (mtt) cc_final: 0.7671 (mtp) REVERT: A 223 TYR cc_start: 0.8371 (t80) cc_final: 0.8017 (t80) REVERT: A 252 TYR cc_start: 0.8975 (t80) cc_final: 0.8717 (t80) REVERT: A 265 MET cc_start: 0.7758 (ttp) cc_final: 0.7070 (mtp) REVERT: A 269 ASP cc_start: 0.8959 (t0) cc_final: 0.8583 (t0) REVERT: A 431 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7520 (tt) REVERT: B 222 GLN cc_start: 0.8629 (mt0) cc_final: 0.8408 (mt0) REVERT: C 173 GLN cc_start: 0.7944 (mp10) cc_final: 0.6796 (pt0) REVERT: C 183 LYS cc_start: 0.8414 (ptpt) cc_final: 0.7865 (mtmt) REVERT: C 301 MET cc_start: 0.8399 (tmm) cc_final: 0.8089 (tmm) REVERT: D 127 MET cc_start: 0.7880 (mtt) cc_final: 0.7663 (mtp) REVERT: D 219 ILE cc_start: 0.8117 (tt) cc_final: 0.7889 (tt) REVERT: D 265 MET cc_start: 0.7289 (ttp) cc_final: 0.7059 (ttm) REVERT: E 19 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8819 (ttpp) REVERT: E 219 ILE cc_start: 0.8241 (tt) cc_final: 0.7995 (tt) REVERT: E 265 MET cc_start: 0.7231 (ttt) cc_final: 0.6787 (ttm) outliers start: 32 outliers final: 14 residues processed: 266 average time/residue: 0.0714 time to fit residues: 29.6760 Evaluate side-chains 243 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 157 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120540 restraints weight = 20026.468| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.07 r_work: 0.3474 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13011 Z= 0.110 Angle : 0.549 8.404 17824 Z= 0.271 Chirality : 0.042 0.136 2185 Planarity : 0.003 0.033 2139 Dihedral : 3.720 15.399 1870 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.35 % Allowed : 17.56 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1610 helix: 2.11 (0.22), residues: 535 sheet: -1.24 (0.25), residues: 440 loop : -0.65 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 133 TYR 0.008 0.001 TYR C 67 PHE 0.006 0.001 PHE D 145 TRP 0.011 0.001 TRP C 70 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00253 (13001) covalent geometry : angle 0.54912 (17799) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.58931 ( 10) hydrogen bonds : bond 0.02995 ( 615) hydrogen bonds : angle 3.95381 ( 1935) link_NAG-ASN : bond 0.00112 ( 5) link_NAG-ASN : angle 0.67888 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.472 Fit side-chains REVERT: A 117 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 127 MET cc_start: 0.7880 (mtt) cc_final: 0.7653 (mtp) REVERT: A 184 GLU cc_start: 0.8368 (tp30) cc_final: 0.8099 (tp30) REVERT: A 223 TYR cc_start: 0.8372 (t80) cc_final: 0.7946 (t80) REVERT: A 265 MET cc_start: 0.7610 (ttp) cc_final: 0.7082 (mtp) REVERT: A 269 ASP cc_start: 0.8965 (t0) cc_final: 0.8576 (t0) REVERT: A 431 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7531 (tt) REVERT: B 222 GLN cc_start: 0.8601 (mt0) cc_final: 0.8385 (mt0) REVERT: C 173 GLN cc_start: 0.8097 (mp10) cc_final: 0.6881 (pt0) REVERT: C 183 LYS cc_start: 0.8443 (ptpt) cc_final: 0.7962 (mtmt) REVERT: C 301 MET cc_start: 0.8397 (tmm) cc_final: 0.8096 (tmm) REVERT: D 127 MET cc_start: 0.7959 (mtt) cc_final: 0.7716 (mtp) REVERT: D 219 ILE cc_start: 0.8211 (tt) cc_final: 0.7981 (tt) outliers start: 31 outliers final: 19 residues processed: 273 average time/residue: 0.0711 time to fit residues: 30.6291 Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117928 restraints weight = 20026.821| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.02 r_work: 0.3447 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13011 Z= 0.145 Angle : 0.587 8.737 17824 Z= 0.287 Chirality : 0.043 0.138 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.812 18.055 1870 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.65 % Allowed : 19.30 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1610 helix: 2.13 (0.22), residues: 535 sheet: -1.31 (0.25), residues: 445 loop : -0.64 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.010 0.001 TYR B 67 PHE 0.009 0.001 PHE A 241 TRP 0.014 0.001 TRP C 65 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00342 (13001) covalent geometry : angle 0.58642 (17799) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.51634 ( 10) hydrogen bonds : bond 0.03103 ( 615) hydrogen bonds : angle 4.04803 ( 1935) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 0.77545 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.489 Fit side-chains REVERT: A 117 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 127 MET cc_start: 0.7959 (mtt) cc_final: 0.7715 (mtp) REVERT: A 265 MET cc_start: 0.7688 (ttp) cc_final: 0.7178 (mtp) REVERT: A 431 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7614 (tt) REVERT: B 127 MET cc_start: 0.8066 (mtt) cc_final: 0.7817 (mtp) REVERT: B 173 GLN cc_start: 0.8151 (mp10) cc_final: 0.6932 (pm20) REVERT: B 184 GLU cc_start: 0.8401 (tp30) cc_final: 0.8125 (tp30) REVERT: B 222 GLN cc_start: 0.8643 (mt0) cc_final: 0.8412 (mt0) REVERT: B 266 MET cc_start: 0.8472 (mmm) cc_final: 0.8238 (mtt) REVERT: C 173 GLN cc_start: 0.8186 (mp10) cc_final: 0.6998 (pt0) REVERT: C 183 LYS cc_start: 0.8447 (ptpt) cc_final: 0.8030 (mtmt) REVERT: C 301 MET cc_start: 0.8388 (tmm) cc_final: 0.8080 (tmm) REVERT: D 127 MET cc_start: 0.8027 (mtt) cc_final: 0.7798 (mtp) REVERT: D 173 GLN cc_start: 0.8326 (mp10) cc_final: 0.7167 (pt0) REVERT: D 265 MET cc_start: 0.7548 (ttp) cc_final: 0.7189 (ttm) REVERT: E 173 GLN cc_start: 0.8130 (mp10) cc_final: 0.7051 (pm20) outliers start: 35 outliers final: 22 residues processed: 276 average time/residue: 0.0740 time to fit residues: 32.0768 Evaluate side-chains 274 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.165004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.140869 restraints weight = 19438.798| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.87 r_work: 0.3853 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13011 Z= 0.130 Angle : 0.592 8.958 17824 Z= 0.288 Chirality : 0.043 0.143 2185 Planarity : 0.003 0.028 2139 Dihedral : 3.794 19.399 1870 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.89 % Allowed : 21.65 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1610 helix: 2.19 (0.22), residues: 535 sheet: -1.29 (0.25), residues: 445 loop : -0.55 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 16 TYR 0.012 0.001 TYR D 223 PHE 0.008 0.001 PHE E 145 TRP 0.012 0.001 TRP E 65 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00305 (13001) covalent geometry : angle 0.59173 (17799) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.50650 ( 10) hydrogen bonds : bond 0.03027 ( 615) hydrogen bonds : angle 4.00424 ( 1935) link_NAG-ASN : bond 0.00064 ( 5) link_NAG-ASN : angle 0.74674 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.344 Fit side-chains REVERT: A 117 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7805 (mm) REVERT: A 127 MET cc_start: 0.7838 (mtt) cc_final: 0.7603 (mtp) REVERT: A 183 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8200 (ptmt) REVERT: A 265 MET cc_start: 0.7741 (ttp) cc_final: 0.7313 (mtp) REVERT: A 269 ASP cc_start: 0.8879 (t0) cc_final: 0.8577 (t0) REVERT: A 431 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7930 (tt) REVERT: B 66 ILE cc_start: 0.8902 (pt) cc_final: 0.8632 (pt) REVERT: B 127 MET cc_start: 0.7872 (mtt) cc_final: 0.7601 (mtp) REVERT: B 173 GLN cc_start: 0.7989 (mp10) cc_final: 0.6904 (pm20) REVERT: B 265 MET cc_start: 0.8430 (ttm) cc_final: 0.7974 (mtp) REVERT: B 266 MET cc_start: 0.8464 (mmm) cc_final: 0.7947 (mtt) REVERT: C 173 GLN cc_start: 0.8032 (mp10) cc_final: 0.6952 (pt0) REVERT: C 301 MET cc_start: 0.8327 (tmm) cc_final: 0.8085 (tmm) REVERT: D 127 MET cc_start: 0.7884 (mtt) cc_final: 0.7631 (mtp) REVERT: D 173 GLN cc_start: 0.8137 (mp10) cc_final: 0.7071 (pt0) REVERT: D 265 MET cc_start: 0.7524 (ttp) cc_final: 0.7176 (ttm) outliers start: 25 outliers final: 19 residues processed: 261 average time/residue: 0.0711 time to fit residues: 29.1143 Evaluate side-chains 257 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 13 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.165169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141004 restraints weight = 19446.091| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.87 r_work: 0.3857 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13011 Z= 0.126 Angle : 0.591 9.044 17824 Z= 0.287 Chirality : 0.043 0.139 2185 Planarity : 0.003 0.029 2139 Dihedral : 3.794 19.230 1870 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.04 % Allowed : 22.10 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.22), residues: 1610 helix: 2.31 (0.22), residues: 530 sheet: -1.28 (0.25), residues: 445 loop : -0.57 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.010 0.001 TYR D 223 PHE 0.011 0.001 PHE A 241 TRP 0.011 0.001 TRP C 65 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00295 (13001) covalent geometry : angle 0.59054 (17799) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.45922 ( 10) hydrogen bonds : bond 0.02993 ( 615) hydrogen bonds : angle 4.00110 ( 1935) link_NAG-ASN : bond 0.00074 ( 5) link_NAG-ASN : angle 0.74185 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.413 Fit side-chains REVERT: A 117 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7847 (mm) REVERT: A 127 MET cc_start: 0.7830 (mtt) cc_final: 0.7612 (mtp) REVERT: A 183 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8270 (ptmt) REVERT: A 265 MET cc_start: 0.7770 (ttp) cc_final: 0.7007 (mtp) REVERT: A 269 ASP cc_start: 0.8908 (t0) cc_final: 0.8616 (t0) REVERT: A 431 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (tt) REVERT: B 66 ILE cc_start: 0.8879 (pt) cc_final: 0.8604 (pt) REVERT: B 127 MET cc_start: 0.7878 (mtt) cc_final: 0.7614 (mtp) REVERT: B 173 GLN cc_start: 0.8043 (mp10) cc_final: 0.6985 (pm20) REVERT: B 266 MET cc_start: 0.8457 (mmm) cc_final: 0.8050 (mtt) REVERT: C 173 GLN cc_start: 0.8075 (mp10) cc_final: 0.7029 (pt0) REVERT: C 301 MET cc_start: 0.8324 (tmm) cc_final: 0.8086 (tmm) REVERT: D 19 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8640 (mtpp) REVERT: D 127 MET cc_start: 0.7879 (mtt) cc_final: 0.7635 (mtp) REVERT: D 150 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6674 (mm-40) REVERT: D 173 GLN cc_start: 0.8188 (mp10) cc_final: 0.7131 (pt0) REVERT: D 183 LYS cc_start: 0.8579 (ptpt) cc_final: 0.8371 (ptmt) REVERT: E 19 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8761 (mtpp) REVERT: E 265 MET cc_start: 0.7243 (ttt) cc_final: 0.6708 (ttm) outliers start: 27 outliers final: 20 residues processed: 255 average time/residue: 0.0781 time to fit residues: 31.0237 Evaluate side-chains 256 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 146 optimal weight: 0.0010 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 159 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145421 restraints weight = 20619.614| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.95 r_work: 0.3883 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13011 Z= 0.106 Angle : 0.580 9.148 17824 Z= 0.283 Chirality : 0.042 0.145 2185 Planarity : 0.003 0.032 2139 Dihedral : 3.752 19.120 1870 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.97 % Allowed : 22.10 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1610 helix: 2.27 (0.22), residues: 535 sheet: -1.31 (0.25), residues: 450 loop : -0.41 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.018 0.001 TYR D 223 PHE 0.011 0.001 PHE A 241 TRP 0.012 0.001 TRP A 70 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00244 (13001) covalent geometry : angle 0.58032 (17799) SS BOND : bond 0.00230 ( 5) SS BOND : angle 0.50654 ( 10) hydrogen bonds : bond 0.02902 ( 615) hydrogen bonds : angle 3.95338 ( 1935) link_NAG-ASN : bond 0.00122 ( 5) link_NAG-ASN : angle 0.68350 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.390 Fit side-chains REVERT: A 19 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8609 (mtpp) REVERT: A 117 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 127 MET cc_start: 0.7761 (mtt) cc_final: 0.7558 (mtp) REVERT: A 183 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8257 (ptmt) REVERT: A 265 MET cc_start: 0.7713 (ttp) cc_final: 0.7048 (mtp) REVERT: A 269 ASP cc_start: 0.8912 (t0) cc_final: 0.8607 (t0) REVERT: A 431 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7849 (tt) REVERT: B 19 LYS cc_start: 0.9158 (ttpt) cc_final: 0.8766 (mtpp) REVERT: B 66 ILE cc_start: 0.8871 (pt) cc_final: 0.8608 (pt) REVERT: B 127 MET cc_start: 0.7816 (mtt) cc_final: 0.7544 (mtp) REVERT: B 266 MET cc_start: 0.8444 (mmm) cc_final: 0.7965 (mtt) REVERT: C 173 GLN cc_start: 0.8169 (mp10) cc_final: 0.7079 (pt0) REVERT: C 301 MET cc_start: 0.8325 (tmm) cc_final: 0.8076 (tmm) REVERT: D 19 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8623 (mtpp) REVERT: D 173 GLN cc_start: 0.8228 (mp10) cc_final: 0.7146 (pt0) REVERT: D 265 MET cc_start: 0.7415 (ttp) cc_final: 0.7089 (ttm) REVERT: E 19 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8721 (mtpp) REVERT: E 66 ILE cc_start: 0.8883 (pt) cc_final: 0.8640 (pt) REVERT: E 265 MET cc_start: 0.7025 (ttt) cc_final: 0.6589 (ttm) outliers start: 26 outliers final: 17 residues processed: 261 average time/residue: 0.0790 time to fit residues: 32.2855 Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 132 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.166205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141960 restraints weight = 19424.455| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.88 r_work: 0.3873 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13011 Z= 0.122 Angle : 0.595 9.113 17824 Z= 0.289 Chirality : 0.043 0.138 2185 Planarity : 0.003 0.030 2139 Dihedral : 3.773 19.258 1870 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.82 % Allowed : 22.56 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1610 helix: 2.28 (0.22), residues: 535 sheet: -1.25 (0.25), residues: 445 loop : -0.48 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.020 0.001 TYR D 223 PHE 0.008 0.001 PHE E 289 TRP 0.011 0.001 TRP C 65 HIS 0.005 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00285 (13001) covalent geometry : angle 0.59489 (17799) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.45089 ( 10) hydrogen bonds : bond 0.02954 ( 615) hydrogen bonds : angle 3.99069 ( 1935) link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 0.72340 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.33 seconds wall clock time: 36 minutes 23.37 seconds (2183.37 seconds total)