Starting phenix.real_space_refine on Wed Feb 4 19:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxf_16317/02_2026/8bxf_16317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxf_16317/02_2026/8bxf_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_16317/02_2026/8bxf_16317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxf_16317/02_2026/8bxf_16317.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxf_16317/02_2026/8bxf_16317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxf_16317/02_2026/8bxf_16317.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8385 2.51 5 N 2041 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12692 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2517 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2524 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 87 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 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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 Time building chain proxies: 3.07, per 1000 atoms: 0.24 Number of scatterers: 12692 At special positions: 0 Unit cell: (90.944, 90.16, 121.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2186 8.00 N 2041 7.00 C 8385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 606.2 milliseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 36.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 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: 2.21 Time building geometry restraints manager: 1.28 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: 7102 1.57 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 13012 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 13007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16985 2.02 - 4.05: 683 4.05 - 6.07: 105 6.07 - 8.10: 45 8.10 - 10.12: 10 Bond angle restraints: 17828 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 17823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 6828 15.42 - 30.83: 614 30.83 - 46.25: 179 46.25 - 61.66: 20 61.66 - 77.08: 15 Dihedral angle restraints: 7656 sinusoidal: 2816 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 7653 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: 2151 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 2148 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4363 2.87 - 3.38: 11502 3.38 - 3.89: 21098 3.89 - 4.39: 22881 4.39 - 4.90: 40701 Nonbonded interactions: 100545 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 261 " model vdw 2.365 3.040 nonbonded pdb=" O VAL E 257 " pdb=" OG1 THR E 261 " model vdw 2.366 3.040 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.366 3.040 nonbonded pdb=" O VAL C 257 " pdb=" OG1 THR C 261 " model vdw 2.366 3.040 nonbonded pdb=" O VAL D 257 " pdb=" OG1 THR D 261 " model vdw 2.367 3.040 ... (remaining 100540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) selection = (chain 'C' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 501)) selection = (chain 'D' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) selection = (chain 'E' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- 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 : 0.005 0.049 13022 Z= 0.227 Angle : 0.956 10.124 17853 Z= 0.503 Chirality : 0.056 0.233 2185 Planarity : 0.007 0.043 2146 Dihedral : 13.512 77.077 4511 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.19), residues: 1610 helix: -0.93 (0.19), residues: 530 sheet: -1.31 (0.25), residues: 450 loop : -1.72 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.014 0.001 TYR B 178 PHE 0.054 0.004 PHE E 425 TRP 0.013 0.002 TRP D 70 HIS 0.021 0.003 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00452 (13012) covalent geometry : angle 0.95677 (17828) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.93447 ( 10) hydrogen bonds : bond 0.12179 ( 615) hydrogen bonds : angle 6.75507 ( 1935) link_NAG-ASN : bond 0.00233 ( 5) link_NAG-ASN : angle 0.44399 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 306 time to evaluate : 0.303 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: 0.7623 (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: 0.1065 time to fit residues: 46.9176 Evaluate side-chains 232 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117303 restraints weight = 20284.024| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.14 r_work: 0.3433 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13022 Z= 0.138 Angle : 0.576 8.098 17853 Z= 0.295 Chirality : 0.044 0.141 2185 Planarity : 0.004 0.032 2146 Dihedral : 4.371 17.011 1870 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.44 % Allowed : 9.99 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.20), residues: 1610 helix: 0.66 (0.21), residues: 535 sheet: -1.37 (0.26), residues: 440 loop : -1.45 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.006 0.001 TYR E 121 PHE 0.013 0.001 PHE E 425 TRP 0.012 0.001 TRP B 70 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00310 (13012) covalent geometry : angle 0.57615 (17828) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.65905 ( 10) hydrogen bonds : bond 0.03659 ( 615) hydrogen bonds : angle 4.57092 ( 1935) link_NAG-ASN : bond 0.00226 ( 5) link_NAG-ASN : angle 0.72856 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.436 Fit side-chains REVERT: A 127 MET cc_start: 0.7998 (mtt) cc_final: 0.7743 (mtp) REVERT: A 219 ILE cc_start: 0.8091 (tt) cc_final: 0.7740 (tt) REVERT: A 222 GLN cc_start: 0.8781 (mt0) cc_final: 0.8525 (mt0) REVERT: A 301 MET cc_start: 0.8384 (tmm) cc_final: 0.8082 (tmm) REVERT: B 127 MET cc_start: 0.8002 (mtt) cc_final: 0.7727 (mtp) REVERT: B 222 GLN cc_start: 0.8623 (mt0) cc_final: 0.8378 (mt0) REVERT: B 227 MET cc_start: 0.8576 (ppp) cc_final: 0.8212 (ppp) REVERT: B 301 MET cc_start: 0.8417 (tmm) cc_final: 0.8144 (tmm) REVERT: C 219 ILE cc_start: 0.8147 (tt) cc_final: 0.7886 (tt) REVERT: C 301 MET cc_start: 0.8458 (tmm) cc_final: 0.8157 (tmm) REVERT: D 127 MET cc_start: 0.8078 (mtt) cc_final: 0.7832 (mtp) REVERT: D 219 ILE cc_start: 0.8108 (tt) cc_final: 0.7859 (tt) REVERT: D 222 GLN cc_start: 0.8648 (mt0) cc_final: 0.8340 (mt0) REVERT: D 265 MET cc_start: 0.7373 (ttt) cc_final: 0.6997 (ttm) REVERT: D 301 MET cc_start: 0.8471 (tmm) cc_final: 0.8172 (tmm) REVERT: E 222 GLN cc_start: 0.8650 (mt0) cc_final: 0.8289 (mt0) REVERT: E 265 MET cc_start: 0.7135 (ttt) cc_final: 0.6674 (ttm) REVERT: E 301 MET cc_start: 0.8427 (tmm) cc_final: 0.8106 (tmm) outliers start: 19 outliers final: 8 residues processed: 259 average time/residue: 0.0931 time to fit residues: 36.8271 Evaluate side-chains 233 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 146 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117526 restraints weight = 20292.836| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.12 r_work: 0.3432 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13022 Z= 0.110 Angle : 0.548 7.760 17853 Z= 0.276 Chirality : 0.042 0.138 2185 Planarity : 0.004 0.029 2146 Dihedral : 3.981 17.061 1870 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.36 % Allowed : 14.16 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1610 helix: 1.43 (0.22), residues: 535 sheet: -1.40 (0.26), residues: 440 loop : -1.15 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 16 TYR 0.006 0.001 TYR D 121 PHE 0.006 0.001 PHE D 289 TRP 0.012 0.001 TRP C 70 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00243 (13012) covalent geometry : angle 0.54811 (17828) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.67436 ( 10) hydrogen bonds : bond 0.03313 ( 615) hydrogen bonds : angle 4.22318 ( 1935) link_NAG-ASN : bond 0.00148 ( 5) link_NAG-ASN : angle 0.60707 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.469 Fit side-chains REVERT: A 127 MET cc_start: 0.7921 (mtt) cc_final: 0.7711 (mtp) REVERT: A 222 GLN cc_start: 0.8747 (mt0) cc_final: 0.8522 (mt0) REVERT: A 265 MET cc_start: 0.7145 (ttt) cc_final: 0.6909 (ttt) REVERT: A 269 ASP cc_start: 0.8948 (t0) cc_final: 0.8649 (t0) REVERT: A 301 MET cc_start: 0.8323 (tmm) cc_final: 0.7969 (tmm) REVERT: B 222 GLN cc_start: 0.8630 (mt0) cc_final: 0.8373 (mt0) REVERT: B 301 MET cc_start: 0.8419 (tmm) cc_final: 0.8088 (tmm) REVERT: C 66 ILE cc_start: 0.9035 (pt) cc_final: 0.8676 (pt) REVERT: C 301 MET cc_start: 0.8468 (tmm) cc_final: 0.8185 (tmm) REVERT: D 127 MET cc_start: 0.7984 (mtt) cc_final: 0.7751 (mtp) REVERT: D 265 MET cc_start: 0.7318 (ttt) cc_final: 0.6990 (ttm) REVERT: D 301 MET cc_start: 0.8477 (tmm) cc_final: 0.8197 (tmm) REVERT: E 222 GLN cc_start: 0.8652 (mt0) cc_final: 0.8319 (mt0) REVERT: E 265 MET cc_start: 0.7223 (ttt) cc_final: 0.6831 (ttm) REVERT: E 301 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8250 (tmm) outliers start: 18 outliers final: 9 residues processed: 260 average time/residue: 0.0850 time to fit residues: 34.2714 Evaluate side-chains 232 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 140 LEU 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 148 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.141758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116209 restraints weight = 20178.466| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.08 r_work: 0.3413 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13022 Z= 0.113 Angle : 0.535 7.872 17853 Z= 0.268 Chirality : 0.042 0.137 2185 Planarity : 0.003 0.025 2146 Dihedral : 3.776 16.666 1870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.97 % Allowed : 17.03 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1610 helix: 1.85 (0.22), residues: 535 sheet: -1.37 (0.25), residues: 440 loop : -0.98 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 133 TYR 0.006 0.001 TYR C 67 PHE 0.007 0.001 PHE D 145 TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00257 (13012) covalent geometry : angle 0.53438 (17828) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.63264 ( 10) hydrogen bonds : bond 0.03108 ( 615) hydrogen bonds : angle 4.04493 ( 1935) link_NAG-ASN : bond 0.00126 ( 5) link_NAG-ASN : angle 0.64673 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.439 Fit side-chains REVERT: A 127 MET cc_start: 0.7891 (mtt) cc_final: 0.7657 (mtp) REVERT: A 222 GLN cc_start: 0.8688 (mt0) cc_final: 0.8482 (mt0) REVERT: A 223 TYR cc_start: 0.8385 (t80) cc_final: 0.8058 (t80) REVERT: A 269 ASP cc_start: 0.8985 (t0) cc_final: 0.8612 (t0) REVERT: A 301 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8159 (tmm) REVERT: B 222 GLN cc_start: 0.8578 (mt0) cc_final: 0.8351 (mt0) REVERT: B 265 MET cc_start: 0.8492 (ttm) cc_final: 0.7728 (mtp) REVERT: B 301 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: C 301 MET cc_start: 0.8391 (tmm) cc_final: 0.8106 (tmm) REVERT: D 127 MET cc_start: 0.7948 (mtt) cc_final: 0.7701 (mtp) REVERT: D 219 ILE cc_start: 0.8267 (tt) cc_final: 0.8027 (tt) REVERT: E 19 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8825 (ttpp) outliers start: 26 outliers final: 12 residues processed: 267 average time/residue: 0.0919 time to fit residues: 37.7594 Evaluate side-chains 248 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.159165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133868 restraints weight = 19909.953| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.08 r_work: 0.3691 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.118 Angle : 0.549 8.215 17853 Z= 0.273 Chirality : 0.042 0.137 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.734 16.425 1870 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.10 % Allowed : 17.87 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.22), residues: 1610 helix: 2.02 (0.22), residues: 535 sheet: -1.30 (0.25), residues: 440 loop : -0.88 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.007 0.001 TYR A 67 PHE 0.007 0.001 PHE D 145 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00273 (13012) covalent geometry : angle 0.54924 (17828) SS BOND : bond 0.00216 ( 5) SS BOND : angle 0.62138 ( 10) hydrogen bonds : bond 0.03055 ( 615) hydrogen bonds : angle 3.97995 ( 1935) link_NAG-ASN : bond 0.00121 ( 5) link_NAG-ASN : angle 0.66476 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.482 Fit side-chains REVERT: A 127 MET cc_start: 0.7899 (mtt) cc_final: 0.7669 (mtp) REVERT: A 223 TYR cc_start: 0.8367 (t80) cc_final: 0.8021 (t80) REVERT: A 252 TYR cc_start: 0.8983 (t80) cc_final: 0.8729 (t80) REVERT: A 265 MET cc_start: 0.7754 (ttp) cc_final: 0.7088 (mtp) REVERT: A 269 ASP cc_start: 0.9027 (t0) cc_final: 0.8646 (t0) REVERT: A 301 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8140 (tmm) REVERT: A 431 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7578 (tt) REVERT: B 222 GLN cc_start: 0.8641 (mt0) cc_final: 0.8424 (mt0) REVERT: B 301 MET cc_start: 0.8339 (tmm) cc_final: 0.8111 (tmm) REVERT: C 183 LYS cc_start: 0.8397 (ptpt) cc_final: 0.7912 (mtmt) REVERT: C 301 MET cc_start: 0.8334 (tmm) cc_final: 0.8020 (tmm) REVERT: D 127 MET cc_start: 0.8027 (mtt) cc_final: 0.7809 (mtp) REVERT: E 19 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8838 (ttpp) REVERT: E 219 ILE cc_start: 0.8221 (tt) cc_final: 0.7955 (tt) REVERT: E 265 MET cc_start: 0.7121 (ttt) cc_final: 0.6655 (ttm) outliers start: 41 outliers final: 19 residues processed: 270 average time/residue: 0.0884 time to fit residues: 37.2951 Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 301 MET 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 C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 8.9990 chunk 114 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.162716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138786 restraints weight = 19599.272| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.95 r_work: 0.3820 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13022 Z= 0.101 Angle : 0.550 8.512 17853 Z= 0.272 Chirality : 0.042 0.135 2185 Planarity : 0.003 0.031 2146 Dihedral : 3.712 18.578 1870 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.27 % Allowed : 18.47 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1610 helix: 2.11 (0.22), residues: 535 sheet: -1.20 (0.26), residues: 440 loop : -0.74 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 133 TYR 0.009 0.001 TYR D 223 PHE 0.006 0.001 PHE A 241 TRP 0.011 0.001 TRP E 70 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00224 (13012) covalent geometry : angle 0.54938 (17828) SS BOND : bond 0.00254 ( 5) SS BOND : angle 0.59057 ( 10) hydrogen bonds : bond 0.02954 ( 615) hydrogen bonds : angle 3.93650 ( 1935) link_NAG-ASN : bond 0.00134 ( 5) link_NAG-ASN : angle 0.65743 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.491 Fit side-chains REVERT: A 117 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 127 MET cc_start: 0.7804 (mtt) cc_final: 0.7596 (mtp) REVERT: A 184 GLU cc_start: 0.8141 (tp30) cc_final: 0.7928 (tp30) REVERT: A 223 TYR cc_start: 0.8293 (t80) cc_final: 0.7942 (t80) REVERT: A 265 MET cc_start: 0.7725 (ttp) cc_final: 0.6903 (mtp) REVERT: A 269 ASP cc_start: 0.8902 (t0) cc_final: 0.8557 (t0) REVERT: A 301 MET cc_start: 0.8360 (tmm) cc_final: 0.8155 (tmm) REVERT: A 431 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7771 (tt) REVERT: B 66 ILE cc_start: 0.8892 (pt) cc_final: 0.8629 (pt) REVERT: C 183 LYS cc_start: 0.8391 (ptpt) cc_final: 0.7899 (mtmt) REVERT: C 301 MET cc_start: 0.8382 (tmm) cc_final: 0.8126 (tmm) REVERT: D 127 MET cc_start: 0.7819 (mtt) cc_final: 0.7583 (mtp) REVERT: D 265 MET cc_start: 0.8428 (ttm) cc_final: 0.7946 (mtp) REVERT: E 19 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8878 (ttpp) REVERT: E 265 MET cc_start: 0.7002 (ttt) cc_final: 0.6772 (ttm) outliers start: 30 outliers final: 15 residues processed: 279 average time/residue: 0.0909 time to fit residues: 39.5009 Evaluate side-chains 264 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 19 LYS 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 D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.120926 restraints weight = 19905.232| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.02 r_work: 0.3491 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13022 Z= 0.143 Angle : 0.583 8.867 17853 Z= 0.287 Chirality : 0.043 0.147 2185 Planarity : 0.003 0.024 2146 Dihedral : 3.769 18.492 1870 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.35 % Allowed : 19.00 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1610 helix: 2.15 (0.22), residues: 535 sheet: -1.28 (0.25), residues: 445 loop : -0.72 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.009 0.001 TYR D 67 PHE 0.008 0.001 PHE E 145 TRP 0.013 0.001 TRP C 65 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00338 (13012) covalent geometry : angle 0.58300 (17828) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.54020 ( 10) hydrogen bonds : bond 0.03074 ( 615) hydrogen bonds : angle 4.03051 ( 1935) link_NAG-ASN : bond 0.00081 ( 5) link_NAG-ASN : angle 0.75049 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.629 Fit side-chains REVERT: A 117 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7923 (mm) REVERT: A 127 MET cc_start: 0.7914 (mtt) cc_final: 0.7670 (mtp) REVERT: A 184 GLU cc_start: 0.8351 (tp30) cc_final: 0.8119 (tp30) REVERT: A 265 MET cc_start: 0.7777 (ttp) cc_final: 0.7205 (mtp) REVERT: A 266 MET cc_start: 0.8446 (mmm) cc_final: 0.8163 (mtt) REVERT: A 269 ASP cc_start: 0.9013 (t0) cc_final: 0.8644 (t0) REVERT: A 301 MET cc_start: 0.8341 (tmm) cc_final: 0.8072 (tmm) REVERT: A 431 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7548 (tt) REVERT: B 127 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: B 184 GLU cc_start: 0.8413 (tp30) cc_final: 0.8111 (tp30) REVERT: C 183 LYS cc_start: 0.8456 (ptpt) cc_final: 0.8053 (mtmt) REVERT: C 265 MET cc_start: 0.7494 (ttt) cc_final: 0.7149 (mtp) REVERT: C 301 MET cc_start: 0.8348 (tmm) cc_final: 0.8035 (tmm) REVERT: D 127 MET cc_start: 0.8029 (mtt) cc_final: 0.7810 (mtp) REVERT: D 265 MET cc_start: 0.8557 (ttm) cc_final: 0.7913 (mtp) outliers start: 31 outliers final: 19 residues processed: 275 average time/residue: 0.0892 time to fit residues: 38.4271 Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122243 restraints weight = 19828.284| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.02 r_work: 0.3513 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.114 Angle : 0.571 8.826 17853 Z= 0.281 Chirality : 0.043 0.139 2185 Planarity : 0.003 0.027 2146 Dihedral : 3.720 18.468 1870 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.97 % Allowed : 20.44 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1610 helix: 2.22 (0.22), residues: 535 sheet: -1.24 (0.25), residues: 445 loop : -0.60 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.015 0.001 TYR D 223 PHE 0.007 0.001 PHE E 145 TRP 0.011 0.001 TRP E 65 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00264 (13012) covalent geometry : angle 0.57067 (17828) SS BOND : bond 0.00230 ( 5) SS BOND : angle 0.51753 ( 10) hydrogen bonds : bond 0.02942 ( 615) hydrogen bonds : angle 3.94793 ( 1935) link_NAG-ASN : bond 0.00093 ( 5) link_NAG-ASN : angle 0.70712 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.420 Fit side-chains REVERT: A 117 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 127 MET cc_start: 0.7854 (mtt) cc_final: 0.7605 (mtp) REVERT: A 183 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8163 (ptmt) REVERT: A 269 ASP cc_start: 0.9053 (t0) cc_final: 0.8682 (t0) REVERT: A 301 MET cc_start: 0.8356 (tmm) cc_final: 0.8087 (tmm) REVERT: A 431 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7583 (tt) REVERT: B 127 MET cc_start: 0.7919 (mtt) cc_final: 0.7651 (mtp) REVERT: C 183 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8113 (mtmt) REVERT: C 265 MET cc_start: 0.7362 (ttt) cc_final: 0.7076 (ttt) REVERT: C 301 MET cc_start: 0.8361 (tmm) cc_final: 0.8064 (tmm) REVERT: D 127 MET cc_start: 0.7951 (mtt) cc_final: 0.7688 (mtp) REVERT: D 265 MET cc_start: 0.8461 (ttm) cc_final: 0.7954 (mtp) REVERT: E 19 LYS cc_start: 0.9130 (ttpp) cc_final: 0.8729 (mtpp) outliers start: 26 outliers final: 17 residues processed: 264 average time/residue: 0.0914 time to fit residues: 37.6767 Evaluate side-chains 266 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 160 THR 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 231 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain 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 254 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 97 optimal weight: 0.0370 chunk 13 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124319 restraints weight = 19794.741| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.03 r_work: 0.3525 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13022 Z= 0.100 Angle : 0.566 9.108 17853 Z= 0.278 Chirality : 0.042 0.133 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.700 18.920 1870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 21.50 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1610 helix: 2.39 (0.22), residues: 530 sheet: -1.19 (0.25), residues: 445 loop : -0.60 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.019 0.001 TYR D 223 PHE 0.007 0.001 PHE A 241 TRP 0.012 0.001 TRP C 70 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00227 (13012) covalent geometry : angle 0.56602 (17828) SS BOND : bond 0.00229 ( 5) SS BOND : angle 0.48931 ( 10) hydrogen bonds : bond 0.02853 ( 615) hydrogen bonds : angle 3.90813 ( 1935) link_NAG-ASN : bond 0.00139 ( 5) link_NAG-ASN : angle 0.64494 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.480 Fit side-chains REVERT: A 19 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8544 (mtpp) REVERT: A 117 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 127 MET cc_start: 0.7793 (mtt) cc_final: 0.7573 (mtp) REVERT: A 183 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8261 (ptmt) REVERT: A 269 ASP cc_start: 0.9018 (t0) cc_final: 0.8637 (t0) REVERT: A 301 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (tmm) REVERT: A 431 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7566 (tt) REVERT: B 19 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: B 127 MET cc_start: 0.7821 (mtt) cc_final: 0.7553 (mtp) REVERT: C 66 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8773 (pt) REVERT: C 301 MET cc_start: 0.8346 (tmm) cc_final: 0.8048 (tmm) REVERT: D 19 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8636 (mtpp) REVERT: D 55 GLU cc_start: 0.8327 (mp0) cc_final: 0.8122 (mp0) REVERT: D 183 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8243 (ptmt) REVERT: D 265 MET cc_start: 0.8404 (ttm) cc_final: 0.7913 (mtp) REVERT: E 19 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8716 (mtpp) outliers start: 20 outliers final: 12 residues processed: 264 average time/residue: 0.0932 time to fit residues: 38.5034 Evaluate side-chains 261 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122837 restraints weight = 19836.090| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.02 r_work: 0.3512 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.119 Angle : 0.579 9.053 17853 Z= 0.284 Chirality : 0.043 0.135 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.700 19.256 1870 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 21.12 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1610 helix: 2.31 (0.22), residues: 535 sheet: -1.18 (0.25), residues: 445 loop : -0.55 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.018 0.001 TYR D 223 PHE 0.009 0.001 PHE D 241 TRP 0.011 0.001 TRP C 65 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00278 (13012) covalent geometry : angle 0.57905 (17828) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.46309 ( 10) hydrogen bonds : bond 0.02914 ( 615) hydrogen bonds : angle 3.93270 ( 1935) link_NAG-ASN : bond 0.00115 ( 5) link_NAG-ASN : angle 0.70556 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.544 Fit side-chains REVERT: A 19 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8561 (mtpp) REVERT: A 117 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7826 (mm) REVERT: A 127 MET cc_start: 0.7840 (mtt) cc_final: 0.7599 (mtp) REVERT: A 183 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8255 (ptmt) REVERT: A 265 MET cc_start: 0.7251 (ttp) cc_final: 0.6737 (ttt) REVERT: A 269 ASP cc_start: 0.9014 (t0) cc_final: 0.8575 (t0) REVERT: A 301 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: A 431 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7566 (tt) REVERT: B 19 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8765 (mtpp) REVERT: B 127 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: B 265 MET cc_start: 0.8530 (ttm) cc_final: 0.8200 (mtp) REVERT: B 266 MET cc_start: 0.8495 (mmm) cc_final: 0.8197 (mtt) REVERT: C 66 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8833 (pt) REVERT: C 301 MET cc_start: 0.8330 (tmm) cc_final: 0.8035 (tmm) REVERT: D 19 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8649 (mtpp) REVERT: D 265 MET cc_start: 0.8467 (ttm) cc_final: 0.7943 (mtp) REVERT: E 19 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8715 (mtpp) REVERT: E 66 ILE cc_start: 0.8873 (pt) cc_final: 0.8660 (pt) REVERT: E 265 MET cc_start: 0.8338 (ttm) cc_final: 0.7728 (mtp) REVERT: E 266 MET cc_start: 0.8411 (mmm) cc_final: 0.7991 (mtt) outliers start: 24 outliers final: 14 residues processed: 257 average time/residue: 0.0962 time to fit residues: 38.4625 Evaluate side-chains 258 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 132 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123129 restraints weight = 19787.321| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.02 r_work: 0.3521 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.118 Angle : 0.582 9.195 17853 Z= 0.286 Chirality : 0.043 0.136 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.750 19.349 1870 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.89 % Allowed : 21.04 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.22), residues: 1610 helix: 2.30 (0.22), residues: 535 sheet: -1.17 (0.26), residues: 445 loop : -0.52 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.017 0.001 TYR D 223 PHE 0.007 0.001 PHE D 145 TRP 0.012 0.001 TRP B 65 HIS 0.005 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00276 (13012) covalent geometry : angle 0.58228 (17828) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.49547 ( 10) hydrogen bonds : bond 0.02903 ( 615) hydrogen bonds : angle 3.94795 ( 1935) link_NAG-ASN : bond 0.00101 ( 5) link_NAG-ASN : angle 0.71638 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.29 seconds wall clock time: 42 minutes 10.61 seconds (2530.61 seconds total)