Starting phenix.real_space_refine on Wed Jun 11 11:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxf_16317/06_2025/8bxf_16317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxf_16317/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bxf_16317/06_2025/8bxf_16317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxf_16317/06_2025/8bxf_16317.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxf_16317/06_2025/8bxf_16317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxf_16317/06_2025/8bxf_16317.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} 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: 6.35, per 1000 atoms: 0.50 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: 2.78 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.72 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: 4.08 Time building geometry restraints manager: 3.28 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 443 or resid 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 443 or resid 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 443 or resid 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 443 or resid 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: 6.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.350 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- 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 : 5.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (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 TRP 0.013 0.002 TRP D 70 HIS 0.021 0.003 HIS C 58 PHE 0.054 0.004 PHE E 425 TYR 0.014 0.001 TYR B 178 ARG 0.002 0.000 ARG D 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 5) link_NAG-ASN : angle 0.44399 ( 15) hydrogen bonds : bond 0.12179 ( 615) hydrogen bonds : angle 6.75507 ( 1935) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.93447 ( 10) covalent geometry : bond 0.00448 (13001) covalent geometry : angle 0.95425 (17799) *********************** 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 : 2.095 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: 0.3312 time to fit residues: 145.5865 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 : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.145915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120256 restraints weight = 20102.547| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.10 r_work: 0.3479 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1793 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= 0.152 Angle : 0.589 8.411 17824 Z= 0.300 Chirality : 0.044 0.148 2185 Planarity : 0.004 0.033 2139 Dihedral : 4.370 17.184 1870 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.51 % Allowed : 10.67 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1610 helix: 0.67 (0.21), residues: 535 sheet: -1.40 (0.26), residues: 440 loop : -1.44 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 70 HIS 0.003 0.001 HIS A 58 PHE 0.013 0.001 PHE A 241 TYR 0.010 0.001 TYR B 199 ARG 0.004 0.000 ARG C 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 5) link_NAG-ASN : angle 0.66566 ( 15) hydrogen bonds : bond 0.03704 ( 615) hydrogen bonds : angle 4.57919 ( 1935) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.75008 ( 10) covalent geometry : bond 0.00343 (13001) covalent geometry : angle 0.58875 (17799) *********************** 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 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.428 Fit side-chains REVERT: A 127 MET cc_start: 0.8001 (mtt) cc_final: 0.7755 (mtp) REVERT: A 222 GLN cc_start: 0.8778 (mt0) cc_final: 0.8530 (mt0) REVERT: A 301 MET cc_start: 0.8340 (tmm) cc_final: 0.8020 (tmm) REVERT: B 127 MET cc_start: 0.8074 (mtt) cc_final: 0.7797 (mtp) REVERT: B 222 GLN cc_start: 0.8662 (mt0) cc_final: 0.8419 (mt0) REVERT: B 301 MET cc_start: 0.8395 (tmm) cc_final: 0.8134 (tmm) REVERT: C 219 ILE cc_start: 0.8157 (tt) cc_final: 0.7889 (tt) REVERT: C 301 MET cc_start: 0.8437 (tmm) cc_final: 0.8136 (tmm) REVERT: D 127 MET cc_start: 0.8127 (mtt) cc_final: 0.7888 (mtp) REVERT: D 219 ILE cc_start: 0.8127 (tt) cc_final: 0.7877 (tt) REVERT: D 222 GLN cc_start: 0.8663 (mt0) cc_final: 0.8359 (mt0) REVERT: D 265 MET cc_start: 0.7467 (ttt) cc_final: 0.7054 (ttm) REVERT: D 301 MET cc_start: 0.8459 (tmm) cc_final: 0.8149 (tmm) REVERT: E 222 GLN cc_start: 0.8636 (mt0) cc_final: 0.8273 (mt0) REVERT: E 265 MET cc_start: 0.7314 (ttt) cc_final: 0.6854 (ttm) REVERT: E 301 MET cc_start: 0.8425 (tmm) cc_final: 0.8103 (tmm) outliers start: 20 outliers final: 9 residues processed: 259 average time/residue: 0.2455 time to fit residues: 96.0965 Evaluate side-chains 231 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 140 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 D residue 170 LEU Chi-restraints excluded: chain E residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.145649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120334 restraints weight = 20300.948| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.11 r_work: 0.3470 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13011 Z= 0.114 Angle : 0.552 7.773 17824 Z= 0.276 Chirality : 0.042 0.139 2185 Planarity : 0.004 0.029 2139 Dihedral : 3.964 17.500 1870 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.36 % Allowed : 15.67 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1610 helix: 1.48 (0.22), residues: 535 sheet: -1.49 (0.25), residues: 440 loop : -1.13 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 70 HIS 0.003 0.001 HIS B 58 PHE 0.007 0.001 PHE E 145 TYR 0.007 0.001 TYR D 121 ARG 0.003 0.000 ARG C 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 0.61829 ( 15) hydrogen bonds : bond 0.03321 ( 615) hydrogen bonds : angle 4.18165 ( 1935) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.70297 ( 10) covalent geometry : bond 0.00255 (13001) covalent geometry : angle 0.55182 (17799) *********************** 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 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 1.314 Fit side-chains REVERT: A 127 MET cc_start: 0.7947 (mtt) cc_final: 0.7738 (mtp) REVERT: A 222 GLN cc_start: 0.8733 (mt0) cc_final: 0.8526 (mt0) REVERT: A 269 ASP cc_start: 0.8962 (t0) cc_final: 0.8623 (t0) REVERT: A 301 MET cc_start: 0.8306 (tmm) cc_final: 0.7916 (tmm) REVERT: B 222 GLN cc_start: 0.8626 (mt0) cc_final: 0.8382 (mt0) REVERT: B 301 MET cc_start: 0.8364 (tmm) cc_final: 0.8076 (tmm) REVERT: C 301 MET cc_start: 0.8429 (tmm) cc_final: 0.8126 (tmm) REVERT: D 127 MET cc_start: 0.7997 (mtt) cc_final: 0.7770 (mtp) REVERT: D 222 GLN cc_start: 0.8677 (mt0) cc_final: 0.8464 (mt0) REVERT: D 248 GLU cc_start: 0.7418 (pm20) cc_final: 0.7207 (pm20) REVERT: D 265 MET cc_start: 0.7317 (ttt) cc_final: 0.7036 (ttm) REVERT: E 66 ILE cc_start: 0.8985 (pt) cc_final: 0.8723 (pt) REVERT: E 301 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8117 (tmm) outliers start: 18 outliers final: 9 residues processed: 259 average time/residue: 0.2142 time to fit residues: 84.1777 Evaluate side-chains 234 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU 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 C residue 55 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 32 VAL 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 149 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 62 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 = 0.3925 r_free = 0.3925 target = 0.142523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117244 restraints weight = 20060.712| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.06 r_work: 0.3451 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2356 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= 0.129 Angle : 0.552 7.981 17824 Z= 0.275 Chirality : 0.042 0.138 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.789 14.323 1870 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 18.62 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1610 helix: 1.85 (0.22), residues: 535 sheet: -1.48 (0.25), residues: 455 loop : -0.96 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 65 HIS 0.003 0.001 HIS A 58 PHE 0.008 0.001 PHE D 145 TYR 0.007 0.001 TYR C 67 ARG 0.002 0.000 ARG C 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 5) link_NAG-ASN : angle 0.67901 ( 15) hydrogen bonds : bond 0.03162 ( 615) hydrogen bonds : angle 4.05570 ( 1935) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.63508 ( 10) covalent geometry : bond 0.00299 (13001) covalent geometry : angle 0.55200 (17799) *********************** 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 292 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 2.243 Fit side-chains REVERT: A 127 MET cc_start: 0.7962 (mtt) cc_final: 0.7711 (mtp) REVERT: A 223 TYR cc_start: 0.8411 (t80) cc_final: 0.8064 (t80) REVERT: A 265 MET cc_start: 0.7778 (ttp) cc_final: 0.7218 (mtp) REVERT: A 269 ASP cc_start: 0.8937 (t0) cc_final: 0.8556 (t0) REVERT: B 222 GLN cc_start: 0.8648 (mt0) cc_final: 0.8439 (mt0) REVERT: B 265 MET cc_start: 0.8489 (ttm) cc_final: 0.7799 (mtp) REVERT: B 301 MET cc_start: 0.8391 (tmm) cc_final: 0.8177 (tmm) REVERT: C 301 MET cc_start: 0.8410 (tmm) cc_final: 0.8147 (tmm) REVERT: D 127 MET cc_start: 0.8068 (mtt) cc_final: 0.7828 (mtp) REVERT: D 219 ILE cc_start: 0.8112 (tt) cc_final: 0.7877 (tt) REVERT: E 19 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8832 (ttpp) REVERT: E 301 MET cc_start: 0.8356 (tmm) cc_final: 0.8120 (tmm) outliers start: 32 outliers final: 18 residues processed: 278 average time/residue: 0.2387 time to fit residues: 102.2484 Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 432 THR 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 160 THR Chi-restraints excluded: chain E residue 183 LYS 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 86 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.143488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118262 restraints weight = 20187.273| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.06 r_work: 0.3446 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13011 Z= 0.131 Angle : 0.563 8.379 17824 Z= 0.280 Chirality : 0.043 0.138 2185 Planarity : 0.003 0.031 2139 Dihedral : 3.799 15.055 1870 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.35 % Allowed : 19.30 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1610 helix: 1.98 (0.22), residues: 535 sheet: -1.35 (0.25), residues: 440 loop : -0.83 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.004 0.001 HIS A 68 PHE 0.008 0.001 PHE E 145 TYR 0.009 0.001 TYR C 67 ARG 0.002 0.000 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.69436 ( 15) hydrogen bonds : bond 0.03130 ( 615) hydrogen bonds : angle 4.04231 ( 1935) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.62724 ( 10) covalent geometry : bond 0.00305 (13001) covalent geometry : angle 0.56254 (17799) *********************** 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 278 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 1.856 Fit side-chains REVERT: A 127 MET cc_start: 0.7942 (mtt) cc_final: 0.7702 (mtp) REVERT: A 223 TYR cc_start: 0.8420 (t80) cc_final: 0.8001 (t80) REVERT: A 252 TYR cc_start: 0.9021 (t80) cc_final: 0.8784 (t80) REVERT: A 265 MET cc_start: 0.7697 (ttp) cc_final: 0.7252 (mtp) REVERT: A 269 ASP cc_start: 0.8958 (t0) cc_final: 0.8559 (t0) REVERT: A 431 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7585 (tt) REVERT: B 173 GLN cc_start: 0.8106 (mp10) cc_final: 0.6938 (pm20) REVERT: B 222 GLN cc_start: 0.8636 (mt0) cc_final: 0.8426 (mt0) REVERT: B 265 MET cc_start: 0.8480 (ttm) cc_final: 0.7813 (mtp) REVERT: B 301 MET cc_start: 0.8426 (tmm) cc_final: 0.8166 (tmm) REVERT: B 431 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7464 (tt) REVERT: C 66 ILE cc_start: 0.9099 (pt) cc_final: 0.8797 (pt) REVERT: C 173 GLN cc_start: 0.8129 (mp10) cc_final: 0.6906 (pt0) REVERT: C 183 LYS cc_start: 0.8432 (ptpt) cc_final: 0.7900 (mtmt) REVERT: C 301 MET cc_start: 0.8453 (tmm) cc_final: 0.8190 (tmm) REVERT: C 431 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7408 (tt) REVERT: D 127 MET cc_start: 0.7916 (mtt) cc_final: 0.7662 (mtp) REVERT: D 173 GLN cc_start: 0.8244 (mp10) cc_final: 0.7183 (pt0) REVERT: D 219 ILE cc_start: 0.8272 (tt) cc_final: 0.8031 (tt) REVERT: E 19 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8829 (ttpp) REVERT: E 183 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8094 (mtmm) REVERT: E 301 MET cc_start: 0.8396 (tmm) cc_final: 0.8141 (tmm) REVERT: E 431 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7361 (tt) outliers start: 31 outliers final: 21 residues processed: 267 average time/residue: 0.2922 time to fit residues: 121.0163 Evaluate side-chains 260 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 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 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 431 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 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 0.0050 chunk 128 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.144828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119507 restraints weight = 20332.554| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.08 r_work: 0.3471 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13011 Z= 0.107 Angle : 0.549 8.446 17824 Z= 0.271 Chirality : 0.042 0.136 2185 Planarity : 0.003 0.024 2139 Dihedral : 3.699 14.313 1870 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.73 % Allowed : 19.76 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1610 helix: 2.11 (0.22), residues: 535 sheet: -1.28 (0.25), residues: 440 loop : -0.66 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 70 HIS 0.004 0.001 HIS A 68 PHE 0.006 0.001 PHE D 145 TYR 0.008 0.001 TYR E 67 ARG 0.001 0.000 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 5) link_NAG-ASN : angle 0.67370 ( 15) hydrogen bonds : bond 0.02981 ( 615) hydrogen bonds : angle 3.95465 ( 1935) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.60335 ( 10) covalent geometry : bond 0.00244 (13001) covalent geometry : angle 0.54894 (17799) *********************** 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 284 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.656 Fit side-chains REVERT: A 117 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 127 MET cc_start: 0.7917 (mtt) cc_final: 0.7693 (mtp) REVERT: A 184 GLU cc_start: 0.8323 (tp30) cc_final: 0.8094 (tp30) REVERT: A 223 TYR cc_start: 0.8402 (t80) cc_final: 0.7973 (t80) REVERT: A 265 MET cc_start: 0.7658 (ttp) cc_final: 0.7140 (mtp) REVERT: A 269 ASP cc_start: 0.8966 (t0) cc_final: 0.8571 (t0) REVERT: A 431 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 127 MET cc_start: 0.8027 (mtt) cc_final: 0.7750 (mtp) REVERT: B 173 GLN cc_start: 0.8163 (mp10) cc_final: 0.7005 (pm20) REVERT: B 184 GLU cc_start: 0.8395 (tp30) cc_final: 0.8123 (tp30) REVERT: B 265 MET cc_start: 0.8402 (ttm) cc_final: 0.7672 (mtp) REVERT: B 301 MET cc_start: 0.8423 (tmm) cc_final: 0.8039 (tmm) REVERT: B 431 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7466 (tt) REVERT: C 66 ILE cc_start: 0.9082 (pt) cc_final: 0.8792 (pt) REVERT: C 173 GLN cc_start: 0.8156 (mp10) cc_final: 0.6956 (pt0) REVERT: C 301 MET cc_start: 0.8424 (tmm) cc_final: 0.8069 (tmm) REVERT: C 431 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7423 (tt) REVERT: D 127 MET cc_start: 0.7989 (mtt) cc_final: 0.7747 (mtp) REVERT: D 173 GLN cc_start: 0.8319 (mp10) cc_final: 0.7288 (pt0) REVERT: D 265 MET cc_start: 0.7441 (ttp) cc_final: 0.7080 (ttm) REVERT: E 183 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8157 (mtmt) REVERT: E 265 MET cc_start: 0.7173 (ttt) cc_final: 0.6577 (ttm) REVERT: E 301 MET cc_start: 0.8377 (tmm) cc_final: 0.8131 (tmm) REVERT: E 431 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7396 (tt) outliers start: 36 outliers final: 15 residues processed: 270 average time/residue: 0.3563 time to fit residues: 148.4274 Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 B residue 19 LYS Chi-restraints excluded: chain B residue 87 LYS 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 B residue 256 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 431 LEU 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 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN D 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.139499 restraints weight = 20705.995| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.91 r_work: 0.3807 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13011 Z= 0.179 Angle : 0.608 8.814 17824 Z= 0.298 Chirality : 0.044 0.141 2185 Planarity : 0.003 0.027 2139 Dihedral : 3.849 15.745 1870 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.03 % Allowed : 20.89 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1610 helix: 2.06 (0.22), residues: 535 sheet: -1.37 (0.25), residues: 445 loop : -0.70 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 65 HIS 0.005 0.001 HIS A 68 PHE 0.010 0.001 PHE E 145 TYR 0.012 0.001 TYR D 67 ARG 0.001 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 5) link_NAG-ASN : angle 0.83756 ( 15) hydrogen bonds : bond 0.03223 ( 615) hydrogen bonds : angle 4.14342 ( 1935) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.55139 ( 10) covalent geometry : bond 0.00425 (13001) covalent geometry : angle 0.60731 (17799) *********************** 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 283 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.581 Fit side-chains REVERT: A 117 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (mm) REVERT: A 127 MET cc_start: 0.7933 (mtt) cc_final: 0.7684 (mtp) REVERT: A 183 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8170 (ptmt) REVERT: A 227 MET cc_start: 0.8660 (ppp) cc_final: 0.8416 (tmm) REVERT: A 265 MET cc_start: 0.7865 (ttp) cc_final: 0.7378 (mtp) REVERT: A 269 ASP cc_start: 0.8923 (t0) cc_final: 0.8541 (t0) REVERT: A 431 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 127 MET cc_start: 0.7997 (mtt) cc_final: 0.7724 (mtp) REVERT: B 173 GLN cc_start: 0.8168 (mp10) cc_final: 0.7031 (pm20) REVERT: B 265 MET cc_start: 0.8482 (ttm) cc_final: 0.7860 (mtp) REVERT: B 301 MET cc_start: 0.8385 (tmm) cc_final: 0.8118 (tmm) REVERT: B 431 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7753 (tt) REVERT: C 66 ILE cc_start: 0.9117 (pt) cc_final: 0.8873 (pt) REVERT: C 173 GLN cc_start: 0.8127 (mp10) cc_final: 0.7021 (pt0) REVERT: C 231 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8658 (tt) REVERT: C 301 MET cc_start: 0.8393 (tmm) cc_final: 0.8076 (tmm) REVERT: C 431 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7683 (tt) REVERT: D 127 MET cc_start: 0.7964 (mtt) cc_final: 0.7729 (mtp) REVERT: D 150 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6864 (mm-40) REVERT: D 173 GLN cc_start: 0.8241 (mp10) cc_final: 0.7281 (pt0) REVERT: E 173 GLN cc_start: 0.8132 (mp10) cc_final: 0.7097 (pm20) REVERT: E 183 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8227 (mtmt) REVERT: E 301 MET cc_start: 0.8369 (tmm) cc_final: 0.8126 (tmm) REVERT: E 431 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7689 (tt) outliers start: 40 outliers final: 21 residues processed: 269 average time/residue: 0.2150 time to fit residues: 88.9430 Evaluate side-chains 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 248 GLU 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 19 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS 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 C residue 431 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 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.170872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.142224 restraints weight = 20793.647| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.95 r_work: 0.3845 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13011 Z= 0.124 Angle : 0.581 9.131 17824 Z= 0.284 Chirality : 0.043 0.143 2185 Planarity : 0.003 0.025 2139 Dihedral : 3.784 16.429 1870 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.42 % Allowed : 22.56 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1610 helix: 2.25 (0.22), residues: 530 sheet: -1.37 (0.25), residues: 445 loop : -0.64 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.005 0.001 HIS A 68 PHE 0.010 0.001 PHE E 289 TYR 0.017 0.001 TYR D 223 ARG 0.001 0.000 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 5) link_NAG-ASN : angle 0.72349 ( 15) hydrogen bonds : bond 0.02997 ( 615) hydrogen bonds : angle 4.02874 ( 1935) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.52304 ( 10) covalent geometry : bond 0.00290 (13001) covalent geometry : angle 0.58109 (17799) *********************** 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 275 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.447 Fit side-chains REVERT: A 117 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7837 (mm) REVERT: A 127 MET cc_start: 0.7861 (mtt) cc_final: 0.7636 (mtp) REVERT: A 183 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8242 (ptmt) REVERT: A 245 LEU cc_start: 0.8672 (mm) cc_final: 0.7959 (pt) REVERT: A 265 MET cc_start: 0.7784 (ttp) cc_final: 0.7306 (mtp) REVERT: A 269 ASP cc_start: 0.8942 (t0) cc_final: 0.8549 (t0) REVERT: A 431 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 127 MET cc_start: 0.7889 (mtt) cc_final: 0.7608 (mtp) REVERT: B 173 GLN cc_start: 0.8224 (mp10) cc_final: 0.7058 (pm20) REVERT: B 265 MET cc_start: 0.8438 (ttm) cc_final: 0.8117 (mtp) REVERT: B 301 MET cc_start: 0.8334 (tmm) cc_final: 0.8086 (tmm) REVERT: B 431 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 66 ILE cc_start: 0.9099 (pt) cc_final: 0.8881 (pt) REVERT: C 173 GLN cc_start: 0.8120 (mp10) cc_final: 0.6999 (pt0) REVERT: C 301 MET cc_start: 0.8357 (tmm) cc_final: 0.8087 (tmm) REVERT: C 431 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7689 (tt) REVERT: D 19 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8665 (mtpp) REVERT: D 127 MET cc_start: 0.7917 (mtt) cc_final: 0.7659 (mtp) REVERT: D 150 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6709 (mm-40) REVERT: D 173 GLN cc_start: 0.8257 (mp10) cc_final: 0.7285 (pt0) REVERT: E 173 GLN cc_start: 0.8128 (mp10) cc_final: 0.7129 (pm20) REVERT: E 183 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8213 (mtmt) REVERT: E 289 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8467 (t80) REVERT: E 301 MET cc_start: 0.8336 (tmm) cc_final: 0.8099 (tmm) REVERT: E 431 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7690 (tt) outliers start: 32 outliers final: 20 residues processed: 260 average time/residue: 0.2033 time to fit residues: 81.3979 Evaluate side-chains 259 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 248 GLU 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 19 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 45 VAL 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 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.169846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141433 restraints weight = 20706.993| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.94 r_work: 0.3836 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2868 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= 0.140 Angle : 0.592 9.485 17824 Z= 0.288 Chirality : 0.043 0.137 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.784 18.117 1870 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.57 % Allowed : 22.71 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1610 helix: 2.18 (0.22), residues: 535 sheet: -1.39 (0.25), residues: 445 loop : -0.60 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 65 HIS 0.005 0.001 HIS A 68 PHE 0.010 0.001 PHE E 289 TYR 0.016 0.001 TYR D 223 ARG 0.001 0.000 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 5) link_NAG-ASN : angle 0.76086 ( 15) hydrogen bonds : bond 0.03039 ( 615) hydrogen bonds : angle 4.03455 ( 1935) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.47091 ( 10) covalent geometry : bond 0.00331 (13001) covalent geometry : angle 0.59235 (17799) *********************** 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 276 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 1.362 Fit side-chains REVERT: A 117 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 127 MET cc_start: 0.7894 (mtt) cc_final: 0.7665 (mtp) REVERT: A 183 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8253 (ptmt) REVERT: A 265 MET cc_start: 0.7797 (ttp) cc_final: 0.7300 (mtp) REVERT: A 269 ASP cc_start: 0.8945 (t0) cc_final: 0.8555 (t0) REVERT: A 431 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 66 ILE cc_start: 0.8908 (pt) cc_final: 0.8706 (pt) REVERT: B 127 MET cc_start: 0.7895 (mtt) cc_final: 0.7620 (mtp) REVERT: B 173 GLN cc_start: 0.8253 (mp10) cc_final: 0.7082 (pm20) REVERT: B 265 MET cc_start: 0.8420 (ttm) cc_final: 0.8138 (mtp) REVERT: B 266 MET cc_start: 0.8510 (mmm) cc_final: 0.8302 (mtt) REVERT: B 301 MET cc_start: 0.8372 (tmm) cc_final: 0.8112 (tmm) REVERT: B 431 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7757 (tt) REVERT: C 173 GLN cc_start: 0.8171 (mp10) cc_final: 0.6958 (pt0) REVERT: C 301 MET cc_start: 0.8393 (tmm) cc_final: 0.8118 (tmm) REVERT: C 431 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7709 (tt) REVERT: D 19 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8672 (mtpp) REVERT: D 127 MET cc_start: 0.7918 (mtt) cc_final: 0.7661 (mtp) REVERT: D 150 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6726 (mm-40) REVERT: D 173 GLN cc_start: 0.8298 (mp10) cc_final: 0.7324 (pt0) REVERT: D 183 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8325 (ptmt) REVERT: E 19 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8740 (mtpp) REVERT: E 173 GLN cc_start: 0.8169 (mp10) cc_final: 0.7146 (pm20) REVERT: E 183 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8327 (mtmm) REVERT: E 289 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (t80) REVERT: E 301 MET cc_start: 0.8353 (tmm) cc_final: 0.8096 (tmm) REVERT: E 431 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7699 (tt) outliers start: 34 outliers final: 20 residues processed: 262 average time/residue: 0.2083 time to fit residues: 83.8768 Evaluate side-chains 264 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 248 GLU 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 19 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 45 VAL 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 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN C 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.165035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141356 restraints weight = 19456.947| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.87 r_work: 0.3871 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13011 Z= 0.111 Angle : 0.579 9.990 17824 Z= 0.282 Chirality : 0.043 0.135 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.741 19.064 1870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.27 % Allowed : 23.01 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1610 helix: 2.25 (0.22), residues: 535 sheet: -1.34 (0.25), residues: 445 loop : -0.52 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 70 HIS 0.005 0.001 HIS A 68 PHE 0.010 0.001 PHE E 289 TYR 0.020 0.001 TYR D 223 ARG 0.001 0.000 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 5) link_NAG-ASN : angle 0.68829 ( 15) hydrogen bonds : bond 0.02916 ( 615) hydrogen bonds : angle 3.93780 ( 1935) SS BOND : bond 0.00259 ( 5) SS BOND : angle 0.50658 ( 10) covalent geometry : bond 0.00256 (13001) covalent geometry : angle 0.57856 (17799) ********************** 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 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8618 (mtpp) REVERT: A 117 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 183 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8256 (ptmt) REVERT: A 245 LEU cc_start: 0.8646 (mm) cc_final: 0.7949 (pt) REVERT: A 265 MET cc_start: 0.7773 (ttp) cc_final: 0.7298 (mtp) REVERT: A 269 ASP cc_start: 0.8905 (t0) cc_final: 0.8514 (t0) REVERT: A 431 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7967 (tt) REVERT: B 19 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8802 (mtpp) REVERT: B 127 MET cc_start: 0.7808 (mtt) cc_final: 0.7536 (mtp) REVERT: B 266 MET cc_start: 0.8541 (mmm) cc_final: 0.8233 (mtt) REVERT: B 301 MET cc_start: 0.8355 (tmm) cc_final: 0.8132 (tmm) REVERT: B 431 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7798 (tt) REVERT: C 173 GLN cc_start: 0.8126 (mp10) cc_final: 0.6979 (pt0) REVERT: C 301 MET cc_start: 0.8374 (tmm) cc_final: 0.8120 (tmm) REVERT: C 431 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7789 (tt) REVERT: D 19 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8654 (mtpp) REVERT: D 127 MET cc_start: 0.7823 (mtt) cc_final: 0.7604 (mtp) REVERT: D 173 GLN cc_start: 0.8288 (mp10) cc_final: 0.7308 (pt0) REVERT: D 305 MET cc_start: 0.7303 (ptp) cc_final: 0.6887 (ptp) REVERT: E 19 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8742 (mtpp) REVERT: E 183 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8320 (mtmm) REVERT: E 289 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8441 (t80) REVERT: E 301 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8057 (tmm) REVERT: E 431 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7760 (tt) outliers start: 30 outliers final: 17 residues processed: 256 average time/residue: 0.2105 time to fit residues: 84.4028 Evaluate side-chains 257 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 45 VAL 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 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.0010 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 0.1980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145480 restraints weight = 20661.178| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.94 r_work: 0.3888 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13011 Z= 0.102 Angle : 0.570 9.732 17824 Z= 0.277 Chirality : 0.042 0.134 2185 Planarity : 0.003 0.028 2139 Dihedral : 3.668 19.225 1870 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 22.63 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1610 helix: 2.29 (0.22), residues: 535 sheet: -1.29 (0.25), residues: 445 loop : -0.47 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 70 HIS 0.005 0.001 HIS A 68 PHE 0.010 0.001 PHE E 289 TYR 0.020 0.001 TYR D 223 ARG 0.001 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 5) link_NAG-ASN : angle 0.67635 ( 15) hydrogen bonds : bond 0.02835 ( 615) hydrogen bonds : angle 3.88178 ( 1935) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.42476 ( 10) covalent geometry : bond 0.00235 (13001) covalent geometry : angle 0.57017 (17799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5939.94 seconds wall clock time: 107 minutes 55.37 seconds (6475.37 seconds total)