Starting phenix.real_space_refine on Wed Jun 3 09:34:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohi_16881/06_2026/8ohi_16881.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 342 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2088 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 A 401 " pdbres="VAL A 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 B 401 " pdbres="VAL B 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 C 401 " pdbres="VAL C 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 D 401 " pdbres="VAL D 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 E 401 " pdbres="VAL E 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 F 401 " pdbres="VAL F 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 G 401 " pdbres="VAL G 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 H 401 " pdbres="VAL H 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 I 401 " pdbres="VAL I 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 J 401 " pdbres="VAL J 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 K 401 " pdbres="VAL K 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 L 401 " pdbres="VAL L 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 M 401 " pdbres="VAL M 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 N 401 " pdbres="VAL N 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 O 401 " pdbres="VAL O 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 P 401 " pdbres="VAL P 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 Q 401 " pdbres="VAL Q 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 R 401 " pdbres="VAL R 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.71, per 1000 atoms: 0.34 Number of scatterers: 2088 At special positions: 0 Unit cell: (66.74, 89.3, 32.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 396 8.00 N 342 7.00 C 1350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 53.3 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.214A pdb=" N GLN A 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE G 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS A 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN G 351 " --> pdb=" O SER M 352 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE M 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS G 353 " --> pdb=" O ILE M 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AA3, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.138A pdb=" N LYS B 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LYS H 353 " --> pdb=" O ILE N 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 357 through 361 removed outlier: 6.634A pdb=" N ASP B 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR H 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP H 358 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR N 361 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE H 360 " --> pdb=" O THR N 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA6, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.288A pdb=" N LEU C 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE I 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN C 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU I 357 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE O 360 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN I 359 " --> pdb=" O ILE O 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.611A pdb=" N GLN D 351 " --> pdb=" O SER J 352 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE J 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS D 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN J 351 " --> pdb=" O SER P 352 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE P 354 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS J 353 " --> pdb=" O ILE P 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.488A pdb=" N LYS E 353 " --> pdb=" O ILE K 354 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS K 353 " --> pdb=" O ILE Q 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.499A pdb=" N ASP E 358 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR K 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE E 360 " --> pdb=" O THR K 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'F' and resid 358 through 361 removed outlier: 6.557A pdb=" N ASP F 358 " --> pdb=" O ASN L 359 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR L 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE F 360 " --> pdb=" O THR L 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 24 hydrogen bonds defined for protein. 72 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: 0.20 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 324 1.26 - 1.33: 240 1.33 - 1.40: 354 1.40 - 1.47: 324 1.47 - 1.54: 882 Bond restraints: 2124 Sorted by residual: bond pdb=" ND1 HIA M 362 " pdb=" CE1 HIA M 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" ND1 HIA P 362 " pdb=" CE1 HIA P 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" ND1 HIA D 362 " pdb=" CE1 HIA D 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" ND1 HIA E 362 " pdb=" CE1 HIA E 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" ND1 HIA A 362 " pdb=" CE1 HIA A 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 2119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2380 0.83 - 1.66: 323 1.66 - 2.49: 58 2.49 - 3.32: 41 3.32 - 4.15: 60 Bond angle restraints: 2862 Sorted by residual: angle pdb=" O02 VP1 C 401 " pdb=" C01 VP1 C 401 " pdb=" O03 VP1 C 401 " ideal model delta sigma weight residual 128.83 124.68 4.15 3.00e+00 1.11e-01 1.91e+00 angle pdb=" O02 VP1 I 401 " pdb=" C01 VP1 I 401 " pdb=" O03 VP1 I 401 " ideal model delta sigma weight residual 128.83 124.72 4.11 3.00e+00 1.11e-01 1.88e+00 angle pdb=" O02 VP1 L 401 " pdb=" C01 VP1 L 401 " pdb=" O03 VP1 L 401 " ideal model delta sigma weight residual 128.83 124.73 4.10 3.00e+00 1.11e-01 1.87e+00 angle pdb=" O02 VP1 R 401 " pdb=" C01 VP1 R 401 " pdb=" O03 VP1 R 401 " ideal model delta sigma weight residual 128.83 124.74 4.09 3.00e+00 1.11e-01 1.86e+00 angle pdb=" O02 VP1 O 401 " pdb=" C01 VP1 O 401 " pdb=" O03 VP1 O 401 " ideal model delta sigma weight residual 128.83 124.75 4.08 3.00e+00 1.11e-01 1.85e+00 ... (remaining 2857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 1122 17.33 - 34.67: 52 34.67 - 52.00: 8 52.00 - 69.33: 0 69.33 - 86.66: 6 Dihedral angle restraints: 1188 sinusoidal: 540 harmonic: 648 Sorted by residual: dihedral pdb=" CA LYS O 353 " pdb=" C LYS O 353 " pdb=" N ILE O 354 " pdb=" CA ILE O 354 " ideal model delta harmonic sigma weight residual 180.00 165.25 14.75 0 5.00e+00 4.00e-02 8.71e+00 dihedral pdb=" CA LYS C 353 " pdb=" C LYS C 353 " pdb=" N ILE C 354 " pdb=" CA ILE C 354 " ideal model delta harmonic sigma weight residual 180.00 165.26 14.74 0 5.00e+00 4.00e-02 8.68e+00 dihedral pdb=" CA LYS I 353 " pdb=" C LYS I 353 " pdb=" N ILE I 354 " pdb=" CA ILE I 354 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 ... (remaining 1185 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 181 0.027 - 0.054: 86 0.054 - 0.080: 18 0.080 - 0.107: 18 0.107 - 0.133: 21 Chirality restraints: 324 Sorted by residual: chirality pdb=" CA ILE C 360 " pdb=" N ILE C 360 " pdb=" C ILE C 360 " pdb=" CB ILE C 360 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE O 360 " pdb=" N ILE O 360 " pdb=" C ILE O 360 " pdb=" CB ILE O 360 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE I 360 " pdb=" N ILE I 360 " pdb=" C ILE I 360 " pdb=" CB ILE I 360 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 321 not shown) Planarity restraints: 324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 M 401 " -0.010 2.00e-02 2.50e+03 5.78e-03 1.08e+00 pdb=" C06 VP1 M 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 M 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 M 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 M 401 " -0.002 2.00e-02 2.50e+03 pdb=" C11 VP1 M 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C13 VP1 M 401 " 0.005 2.00e-02 2.50e+03 pdb=" C14 VP1 M 401 " 0.007 2.00e-02 2.50e+03 pdb=" C15 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 M 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 M 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 G 401 " -0.010 2.00e-02 2.50e+03 5.77e-03 1.08e+00 pdb=" C06 VP1 G 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 G 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 G 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 G 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 G 401 " -0.001 2.00e-02 2.50e+03 pdb=" C11 VP1 G 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 G 401 " 0.002 2.00e-02 2.50e+03 pdb=" C13 VP1 G 401 " 0.005 2.00e-02 2.50e+03 pdb=" C14 VP1 G 401 " 0.008 2.00e-02 2.50e+03 pdb=" C15 VP1 G 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 G 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 G 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 A 401 " -0.009 2.00e-02 2.50e+03 5.71e-03 1.06e+00 pdb=" C06 VP1 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 A 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 A 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 A 401 " -0.001 2.00e-02 2.50e+03 pdb=" C11 VP1 A 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C13 VP1 A 401 " 0.004 2.00e-02 2.50e+03 pdb=" C14 VP1 A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C15 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 A 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 A 401 " -0.008 2.00e-02 2.50e+03 ... (remaining 321 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 588 2.83 - 3.35: 1479 3.35 - 3.86: 3527 3.86 - 4.38: 3797 4.38 - 4.90: 6951 Nonbonded interactions: 16342 Sorted by model distance: nonbonded pdb=" OG SER B 352 " pdb=" O02 VP1 H 401 " model vdw 2.311 3.040 nonbonded pdb=" OG SER H 352 " pdb=" O02 VP1 N 401 " model vdw 2.316 3.040 nonbonded pdb=" NZ LYS Q 353 " pdb=" OD2 ASP Q 358 " model vdw 2.368 3.120 nonbonded pdb=" NZ LYS E 353 " pdb=" OD2 ASP E 358 " model vdw 2.368 3.120 nonbonded pdb=" NZ LYS K 353 " pdb=" OD2 ASP K 358 " model vdw 2.369 3.120 ... (remaining 16337 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.580 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 3.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.011 0.089 2142 Z= 0.862 Angle : 0.850 4.149 2862 Z= 0.336 Chirality : 0.046 0.133 324 Planarity : 0.002 0.006 324 Dihedral : 12.411 86.662 756 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.32 ( 2124) covalent geometry : angle 0.85007 / 0.34 ( 2862) hydrogen bonds : bond 0.16066 / 8.17 ( 24) hydrogen bonds : angle 7.25511 / 4.22 ( 72) Misc. bond : bond 0.08751 / 4.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.089 Fit side-chains REVERT: A 358 ASP cc_start: 0.7787 (m-30) cc_final: 0.7428 (m-30) REVERT: B 359 ASN cc_start: 0.8323 (t0) cc_final: 0.8115 (t0) REVERT: C 353 LYS cc_start: 0.8168 (mttt) cc_final: 0.7953 (mtpt) REVERT: C 359 ASN cc_start: 0.7986 (p0) cc_final: 0.7399 (p0) REVERT: D 356 SER cc_start: 0.9157 (p) cc_final: 0.8903 (t) REVERT: E 358 ASP cc_start: 0.7930 (m-30) cc_final: 0.7712 (m-30) REVERT: I 353 LYS cc_start: 0.8361 (mttt) cc_final: 0.8029 (mtpt) REVERT: L 359 ASN cc_start: 0.8141 (m-40) cc_final: 0.7929 (m-40) REVERT: P 356 SER cc_start: 0.9207 (p) cc_final: 0.8807 (t) REVERT: R 359 ASN cc_start: 0.8382 (m-40) cc_final: 0.7979 (m-40) outliers start: 3 outliers final: 4 residues processed: 43 average time/residue: 0.4638 time to fit residues: 20.4506 Evaluate side-chains 43 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN I 359 ASN M 351 GLN N 359 ASN Q 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086377 restraints weight = 2766.940| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.98 r_work: 0.3097 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2142 Z= 0.071 Angle : 0.364 3.100 2862 Z= 0.186 Chirality : 0.046 0.134 324 Planarity : 0.001 0.007 324 Dihedral : 12.720 89.227 383 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.38), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00147 / 0.07 ( 2124) covalent geometry : angle 0.36410 / 0.19 ( 2862) hydrogen bonds : bond 0.02285 / 1.20 ( 24) hydrogen bonds : angle 4.36969 / 2.46 ( 72) Misc. bond : bond 0.00050 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.083 Fit side-chains REVERT: A 358 ASP cc_start: 0.7764 (m-30) cc_final: 0.7208 (m-30) REVERT: C 353 LYS cc_start: 0.8772 (mttt) cc_final: 0.8465 (mtpt) REVERT: C 359 ASN cc_start: 0.7998 (p0) cc_final: 0.7506 (p0) REVERT: E 358 ASP cc_start: 0.8399 (m-30) cc_final: 0.8183 (m-30) REVERT: F 353 LYS cc_start: 0.8670 (mttt) cc_final: 0.8344 (mtmt) REVERT: I 353 LYS cc_start: 0.8454 (mttt) cc_final: 0.8147 (mtpt) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.4628 time to fit residues: 20.8505 Evaluate side-chains 39 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 359 ASN M 351 GLN N 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086113 restraints weight = 2829.866| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.97 r_work: 0.3022 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2142 Z= 0.081 Angle : 0.343 2.825 2862 Z= 0.178 Chirality : 0.045 0.129 324 Planarity : 0.001 0.005 324 Dihedral : 12.641 89.737 380 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 13.64 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 ( 2124) covalent geometry : angle 0.34347 / 0.18 ( 2862) hydrogen bonds : bond 0.01983 / 1.07 ( 24) hydrogen bonds : angle 3.78679 / 2.06 ( 72) Misc. bond : bond 0.00063 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.088 Fit side-chains REVERT: A 358 ASP cc_start: 0.7813 (m-30) cc_final: 0.7192 (m-30) REVERT: C 353 LYS cc_start: 0.8779 (mttt) cc_final: 0.8490 (mtpt) REVERT: C 359 ASN cc_start: 0.8037 (p0) cc_final: 0.7594 (p0) REVERT: E 358 ASP cc_start: 0.8358 (m-30) cc_final: 0.8135 (m-30) REVERT: F 353 LYS cc_start: 0.8712 (mttt) cc_final: 0.8422 (mtmt) REVERT: I 353 LYS cc_start: 0.8450 (mttt) cc_final: 0.8153 (mtpt) REVERT: M 358 ASP cc_start: 0.8015 (m-30) cc_final: 0.7812 (m-30) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.4730 time to fit residues: 18.4217 Evaluate side-chains 37 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082055 restraints weight = 2833.116| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.90 r_work: 0.2965 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2142 Z= 0.319 Angle : 0.575 4.305 2862 Z= 0.276 Chirality : 0.047 0.135 324 Planarity : 0.002 0.005 324 Dihedral : 16.861 89.135 380 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 13.64 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.32 ( 2124) covalent geometry : angle 0.57534 / 0.28 ( 2862) hydrogen bonds : bond 0.02734 / 1.50 ( 24) hydrogen bonds : angle 4.23448 / 2.35 ( 72) Misc. bond : bond 0.00154 / 0.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.091 Fit side-chains REVERT: A 358 ASP cc_start: 0.7888 (m-30) cc_final: 0.7354 (m-30) REVERT: C 353 LYS cc_start: 0.8814 (mttt) cc_final: 0.8547 (mtpt) REVERT: C 359 ASN cc_start: 0.8263 (p0) cc_final: 0.7695 (p0) REVERT: E 358 ASP cc_start: 0.8353 (m-30) cc_final: 0.8093 (m-30) REVERT: F 353 LYS cc_start: 0.8660 (mttt) cc_final: 0.8376 (mtmt) REVERT: I 353 LYS cc_start: 0.8603 (mttt) cc_final: 0.8320 (mtpt) REVERT: I 359 ASN cc_start: 0.7904 (p0) cc_final: 0.7603 (p0) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.5246 time to fit residues: 20.3699 Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085404 restraints weight = 2793.283| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.90 r_work: 0.3002 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2142 Z= 0.107 Angle : 0.369 2.957 2862 Z= 0.189 Chirality : 0.045 0.127 324 Planarity : 0.001 0.004 324 Dihedral : 13.946 89.523 378 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 14.65 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 2124) covalent geometry : angle 0.36874 / 0.19 ( 2862) hydrogen bonds : bond 0.01733 / 0.95 ( 24) hydrogen bonds : angle 3.81862 / 2.02 ( 72) Misc. bond : bond 0.00080 / 0.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.083 Fit side-chains REVERT: A 358 ASP cc_start: 0.7808 (m-30) cc_final: 0.7234 (m-30) REVERT: C 353 LYS cc_start: 0.8768 (mttt) cc_final: 0.8503 (mtpt) REVERT: C 359 ASN cc_start: 0.8102 (p0) cc_final: 0.7725 (p0) REVERT: E 358 ASP cc_start: 0.8353 (m-30) cc_final: 0.8139 (m-30) REVERT: F 353 LYS cc_start: 0.8683 (mttt) cc_final: 0.8406 (mtmt) REVERT: I 353 LYS cc_start: 0.8455 (mttt) cc_final: 0.8188 (mtpt) outliers start: 3 outliers final: 4 residues processed: 36 average time/residue: 0.5397 time to fit residues: 19.8522 Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN H 359 ASN I 359 ASN N 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083780 restraints weight = 2798.563| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.89 r_work: 0.2991 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2142 Z= 0.179 Angle : 0.428 3.313 2862 Z= 0.214 Chirality : 0.045 0.125 324 Planarity : 0.001 0.005 324 Dihedral : 15.332 88.340 378 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.54 % Allowed : 14.65 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 2124) covalent geometry : angle 0.42792 / 0.21 ( 2862) hydrogen bonds : bond 0.02045 / 1.11 ( 24) hydrogen bonds : angle 3.93654 / 2.09 ( 72) Misc. bond : bond 0.00111 / 0.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.099 Fit side-chains REVERT: A 358 ASP cc_start: 0.7842 (m-30) cc_final: 0.7252 (m-30) REVERT: C 353 LYS cc_start: 0.8756 (mttt) cc_final: 0.8474 (mtpt) REVERT: C 359 ASN cc_start: 0.8081 (p0) cc_final: 0.7583 (p0) REVERT: E 358 ASP cc_start: 0.8350 (m-30) cc_final: 0.8114 (m-30) REVERT: F 353 LYS cc_start: 0.8699 (mttt) cc_final: 0.8424 (mtmt) REVERT: I 353 LYS cc_start: 0.8531 (mttt) cc_final: 0.8267 (mtpt) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.5409 time to fit residues: 20.4576 Evaluate side-chains 37 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain L residue 353 LYS Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN H 359 ASN I 359 ASN N 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084543 restraints weight = 2815.341| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.93 r_work: 0.2996 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2142 Z= 0.126 Angle : 0.377 2.878 2862 Z= 0.193 Chirality : 0.045 0.125 324 Planarity : 0.001 0.004 324 Dihedral : 14.314 89.054 378 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 15.66 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 2124) covalent geometry : angle 0.37693 / 0.19 ( 2862) hydrogen bonds : bond 0.01753 / 0.95 ( 24) hydrogen bonds : angle 3.85277 / 2.02 ( 72) Misc. bond : bond 0.00090 / 0.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.088 Fit side-chains REVERT: A 358 ASP cc_start: 0.7780 (m-30) cc_final: 0.7169 (m-30) REVERT: C 353 LYS cc_start: 0.8739 (mttt) cc_final: 0.8439 (mtpt) REVERT: C 359 ASN cc_start: 0.8043 (p0) cc_final: 0.7547 (p0) REVERT: E 358 ASP cc_start: 0.8344 (m-30) cc_final: 0.8100 (m-30) REVERT: F 353 LYS cc_start: 0.8683 (mttt) cc_final: 0.8374 (mtmt) REVERT: I 353 LYS cc_start: 0.8423 (mttt) cc_final: 0.8125 (mtpt) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.5194 time to fit residues: 19.1255 Evaluate side-chains 37 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain L residue 353 LYS Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN H 359 ASN I 359 ASN N 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082666 restraints weight = 2763.559| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.90 r_work: 0.2976 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2142 Z= 0.244 Angle : 0.492 3.750 2862 Z= 0.242 Chirality : 0.045 0.131 324 Planarity : 0.002 0.005 324 Dihedral : 16.383 89.288 378 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.54 % Allowed : 15.15 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 ( 2124) covalent geometry : angle 0.49231 / 0.24 ( 2862) hydrogen bonds : bond 0.02278 / 1.24 ( 24) hydrogen bonds : angle 4.07841 / 2.20 ( 72) Misc. bond : bond 0.00131 / 0.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.084 Fit side-chains REVERT: A 358 ASP cc_start: 0.7805 (m-30) cc_final: 0.7200 (m-30) REVERT: C 353 LYS cc_start: 0.8742 (mttt) cc_final: 0.8426 (mtpt) REVERT: C 359 ASN cc_start: 0.8119 (p0) cc_final: 0.7579 (p0) REVERT: E 358 ASP cc_start: 0.8329 (m-30) cc_final: 0.8077 (m-30) REVERT: F 353 LYS cc_start: 0.8717 (mttt) cc_final: 0.8397 (mtmt) REVERT: I 353 LYS cc_start: 0.8530 (mttt) cc_final: 0.8224 (mtpt) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.4739 time to fit residues: 18.4201 Evaluate side-chains 38 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN G 351 GLN H 359 ASN I 359 ASN N 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086478 restraints weight = 2797.429| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.92 r_work: 0.3045 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2142 Z= 0.073 Angle : 0.336 2.431 2862 Z= 0.176 Chirality : 0.045 0.128 324 Planarity : 0.001 0.004 324 Dihedral : 13.133 89.888 378 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00153 / 0.07 ( 2124) covalent geometry : angle 0.33614 / 0.18 ( 2862) hydrogen bonds : bond 0.01426 / 0.77 ( 24) hydrogen bonds : angle 3.71094 / 1.92 ( 72) Misc. bond : bond 0.00053 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.082 Fit side-chains REVERT: C 353 LYS cc_start: 0.8740 (mttt) cc_final: 0.8438 (mtpt) REVERT: E 358 ASP cc_start: 0.8348 (m-30) cc_final: 0.8119 (m-30) REVERT: F 353 LYS cc_start: 0.8672 (mttt) cc_final: 0.8369 (mtmt) REVERT: I 353 LYS cc_start: 0.8429 (mttt) cc_final: 0.8123 (mtpt) outliers start: 5 outliers final: 5 residues processed: 34 average time/residue: 0.4877 time to fit residues: 16.9727 Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN G 351 GLN H 359 ASN I 359 ASN N 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085303 restraints weight = 2833.107| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2142 Z= 0.122 Angle : 0.372 2.877 2862 Z= 0.191 Chirality : 0.045 0.126 324 Planarity : 0.001 0.004 324 Dihedral : 13.617 89.149 378 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 2124) covalent geometry : angle 0.37198 / 0.19 ( 2862) hydrogen bonds : bond 0.01667 / 0.90 ( 24) hydrogen bonds : angle 3.76244 / 1.98 ( 72) Misc. bond : bond 0.00092 / 0.05 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.063 Fit side-chains REVERT: A 358 ASP cc_start: 0.7802 (m-30) cc_final: 0.7171 (m-30) REVERT: C 353 LYS cc_start: 0.8759 (mttt) cc_final: 0.8479 (mtpt) REVERT: C 359 ASN cc_start: 0.8023 (p0) cc_final: 0.7610 (p0) REVERT: F 353 LYS cc_start: 0.8700 (mttt) cc_final: 0.8427 (mtmt) REVERT: I 353 LYS cc_start: 0.8475 (mttt) cc_final: 0.8197 (mtpt) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.4785 time to fit residues: 18.0939 Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN H 359 ASN N 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083649 restraints weight = 2825.853| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.91 r_work: 0.2994 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2142 Z= 0.149 Angle : 0.401 3.109 2862 Z= 0.205 Chirality : 0.045 0.123 324 Planarity : 0.001 0.005 324 Dihedral : 14.407 88.649 378 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 2124) covalent geometry : angle 0.40113 / 0.20 ( 2862) hydrogen bonds : bond 0.01835 / 1.00 ( 24) hydrogen bonds : angle 3.88585 / 2.05 ( 72) Misc. bond : bond 0.00101 / 0.05 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1014.47 seconds wall clock time: 18 minutes 45.19 seconds (1125.19 seconds total)