Starting phenix.real_space_refine on Wed Jul 1 21:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.map" model { file = "/net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohp_16883/07_2026/8ohp_16883.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1800 2.51 5 N 456 2.21 5 O 528 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2784 Number of models: 1 Model: "" Number of chains: 24 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 Chain: "S" 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 S 401 " pdbres="VAL S 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: "T" 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 T 401 " pdbres="VAL T 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: "U" 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 U 401 " pdbres="VAL U 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: "V" 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 V 401 " pdbres="VAL V 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: "W" 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 W 401 " pdbres="VAL W 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: "X" 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 X 401 " pdbres="VAL X 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: 0.70, per 1000 atoms: 0.25 Number of scatterers: 2784 At special positions: 0 Unit cell: (96.82, 109.98, 33.84, 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 528 8.00 N 456 7.00 C 1800 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 52.3 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.438A pdb=" N ASP A 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR I 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP I 358 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR Q 361 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE I 360 " --> pdb=" O THR Q 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.523A pdb=" N LYS B 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS J 353 " --> pdb=" O ILE R 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: 6.306A pdb=" N ASP B 358 " --> pdb=" O ASN J 359 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR J 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 360 " --> pdb=" O THR J 361 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP J 358 " --> pdb=" O ASN R 359 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR R 361 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE J 360 " --> pdb=" O THR R 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 removed outlier: 7.103A pdb=" N LYS C 353 " --> pdb=" O ILE K 354 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS K 353 " --> pdb=" O ILE S 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 358 through 361 Processing sheet with id=AA7, first strand: chain 'D' and resid 353 through 354 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 Processing sheet with id=AB1, first strand: chain 'E' and resid 358 through 361 removed outlier: 6.394A pdb=" N ASP E 358 " --> pdb=" O ASN M 359 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR M 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE E 360 " --> pdb=" O THR M 361 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP M 358 " --> pdb=" O ASN U 359 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR U 361 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE M 360 " --> pdb=" O THR U 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 353 through 354 removed outlier: 6.467A pdb=" N LYS F 353 " --> pdb=" O ILE N 354 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS N 353 " --> pdb=" O ILE V 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 357 through 361 removed outlier: 6.362A pdb=" N ASP F 358 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR N 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 360 " --> pdb=" O THR N 361 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP N 358 " --> pdb=" O ASN V 359 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR V 361 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE N 360 " --> pdb=" O THR V 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 353 through 354 removed outlier: 6.937A pdb=" N LYS G 353 " --> pdb=" O ILE O 354 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS O 353 " --> pdb=" O ILE W 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 358 through 361 Processing sheet with id=AB6, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'H' and resid 357 through 361 removed outlier: 3.547A pdb=" N THR P 361 " --> pdb=" O ILE X 360 " (cutoff:3.500A) 35 hydrogen bonds defined for protein. 105 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: 0.22 Time building geometry restraints manager: 0.23 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: 432 1.26 - 1.33: 338 1.33 - 1.40: 431 1.40 - 1.47: 455 1.47 - 1.54: 1176 Bond restraints: 2832 Sorted by residual: bond pdb=" ND1 HIA N 362 " pdb=" CE1 HIA N 362 " ideal model delta sigma weight residual 1.349 1.321 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" ND1 HIA X 362 " pdb=" CE1 HIA X 362 " ideal model delta sigma weight residual 1.349 1.321 0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" ND1 HIA E 362 " pdb=" CE1 HIA E 362 " ideal model delta sigma weight residual 1.349 1.321 0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" ND1 HIA B 362 " pdb=" CE1 HIA B 362 " ideal model delta sigma weight residual 1.349 1.321 0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" ND1 HIA U 362 " pdb=" CE1 HIA U 362 " ideal model delta sigma weight residual 1.349 1.321 0.028 2.00e-02 2.50e+03 2.00e+00 ... (remaining 2827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 3626 1.84 - 3.69: 143 3.69 - 5.53: 35 5.53 - 7.37: 6 7.37 - 9.21: 6 Bond angle restraints: 3816 Sorted by residual: angle pdb=" C01 VP1 T 401 " pdb=" O03 VP1 T 401 " pdb=" C04 VP1 T 401 " ideal model delta sigma weight residual 117.30 126.51 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" C01 VP1 L 401 " pdb=" O03 VP1 L 401 " pdb=" C04 VP1 L 401 " ideal model delta sigma weight residual 117.30 126.44 -9.14 3.00e+00 1.11e-01 9.27e+00 angle pdb=" C01 VP1 D 401 " pdb=" O03 VP1 D 401 " pdb=" C04 VP1 D 401 " ideal model delta sigma weight residual 117.30 126.43 -9.13 3.00e+00 1.11e-01 9.27e+00 angle pdb=" C04 VP1 D 401 " pdb=" C05 VP1 D 401 " pdb=" C12 VP1 D 401 " ideal model delta sigma weight residual 109.50 117.62 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" C04 VP1 T 401 " pdb=" C05 VP1 T 401 " pdb=" C12 VP1 T 401 " ideal model delta sigma weight residual 109.50 117.60 -8.10 3.00e+00 1.11e-01 7.28e+00 ... (remaining 3811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 1404 11.90 - 23.79: 120 23.79 - 35.68: 45 35.68 - 47.58: 9 47.58 - 59.47: 6 Dihedral angle restraints: 1584 sinusoidal: 720 harmonic: 864 Sorted by residual: dihedral pdb=" CA SER R 352 " pdb=" C SER R 352 " pdb=" N LYS R 353 " pdb=" CA LYS R 353 " ideal model delta harmonic sigma weight residual 180.00 165.26 14.74 0 5.00e+00 4.00e-02 8.69e+00 dihedral pdb=" CA SER B 352 " pdb=" C SER B 352 " pdb=" N LYS B 353 " pdb=" CA LYS B 353 " ideal model delta harmonic sigma weight residual 180.00 165.29 14.71 0 5.00e+00 4.00e-02 8.65e+00 dihedral pdb=" CA SER J 352 " pdb=" C SER J 352 " pdb=" N LYS J 353 " pdb=" CA LYS J 353 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 ... (remaining 1581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 302 0.043 - 0.086: 85 0.086 - 0.129: 39 0.129 - 0.172: 0 0.172 - 0.215: 6 Chirality restraints: 432 Sorted by residual: chirality pdb=" C05 VP1 D 401 " pdb=" C04 VP1 D 401 " pdb=" C06 VP1 D 401 " pdb=" C12 VP1 D 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C05 VP1 L 401 " pdb=" C04 VP1 L 401 " pdb=" C06 VP1 L 401 " pdb=" C12 VP1 L 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C05 VP1 T 401 " pdb=" C04 VP1 T 401 " pdb=" C06 VP1 T 401 " pdb=" C12 VP1 T 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 429 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 T 401 " 0.029 2.00e-02 2.50e+03 1.59e-02 8.21e+00 pdb=" C06 VP1 T 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 T 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 T 401 " -0.012 2.00e-02 2.50e+03 pdb=" C10 VP1 T 401 " 0.005 2.00e-02 2.50e+03 pdb=" C11 VP1 T 401 " 0.023 2.00e-02 2.50e+03 pdb=" C12 VP1 T 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 T 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 T 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 T 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 T 401 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 L 401 " 0.028 2.00e-02 2.50e+03 1.58e-02 8.09e+00 pdb=" C06 VP1 L 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 L 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 L 401 " -0.013 2.00e-02 2.50e+03 pdb=" C10 VP1 L 401 " 0.005 2.00e-02 2.50e+03 pdb=" C11 VP1 L 401 " 0.023 2.00e-02 2.50e+03 pdb=" C12 VP1 L 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 L 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 L 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 L 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 L 401 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 D 401 " 0.028 2.00e-02 2.50e+03 1.57e-02 7.99e+00 pdb=" C06 VP1 D 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 D 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C10 VP1 D 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 D 401 " 0.022 2.00e-02 2.50e+03 pdb=" C12 VP1 D 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 D 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 D 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 D 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 D 401 " 0.022 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 683 2.81 - 3.33: 1986 3.33 - 3.85: 4573 3.85 - 4.38: 5072 4.38 - 4.90: 9229 Nonbonded interactions: 21543 Sorted by model distance: nonbonded pdb=" OG SER A 356 " pdb=" OD1 ASN A 359 " model vdw 2.283 3.040 nonbonded pdb=" OG SER I 356 " pdb=" OD1 ASN I 359 " model vdw 2.283 3.040 nonbonded pdb=" OG SER Q 356 " pdb=" OD1 ASN Q 359 " model vdw 2.284 3.040 nonbonded pdb=" OG SER M 356 " pdb=" OD1 ASN M 359 " model vdw 2.311 3.040 nonbonded pdb=" OG SER E 356 " pdb=" OD1 ASN E 359 " model vdw 2.312 3.040 ... (remaining 21538 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.480 Find NCS groups from input model: 0.030 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 0.090 2856 Z= 0.895 Angle : 0.954 9.215 3816 Z= 0.391 Chirality : 0.050 0.215 432 Planarity : 0.003 0.016 432 Dihedral : 11.271 59.473 1008 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -3.72 (0.36), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.38 ( 2832) covalent geometry : angle 0.95384 / 0.39 ( 3816) hydrogen bonds : bond 0.32127 / 16.98 ( 35) hydrogen bonds : angle 6.61139 / 3.92 ( 105) Misc. bond : bond 0.08862 / 4.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2322 time to fit residues: 20.2609 Evaluate side-chains 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 351 GLN G 359 ASN H 351 GLN N 351 GLN O 359 ASN P 351 GLN V 351 GLN W 359 ASN X 351 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.115424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.095881 restraints weight = 4987.533| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.97 r_work: 0.3719 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2856 Z= 0.089 Angle : 0.464 6.892 3816 Z= 0.227 Chirality : 0.045 0.125 432 Planarity : 0.001 0.006 432 Dihedral : 9.791 56.115 504 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.65 % Allowed : 19.32 % Favored : 78.03 % 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: -3.31 (0.37), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.29), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 ( 2832) covalent geometry : angle 0.46439 / 0.23 ( 3816) hydrogen bonds : bond 0.01999 / 1.11 ( 35) hydrogen bonds : angle 4.39234 / 2.31 ( 105) Misc. bond : bond 0.00050 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: U 353 LYS cc_start: 0.8643 (tttm) cc_final: 0.8131 (ttmt) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.2273 time to fit residues: 20.4732 Evaluate side-chains 63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain X residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 359 ASN P 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.116282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.096829 restraints weight = 5076.438| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.95 r_work: 0.3744 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2856 Z= 0.099 Angle : 0.453 6.068 3816 Z= 0.225 Chirality : 0.044 0.123 432 Planarity : 0.001 0.003 432 Dihedral : 10.508 61.372 504 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 23.86 % Favored : 74.24 % 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: -2.84 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.32), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2832) covalent geometry : angle 0.45256 / 0.22 ( 3816) hydrogen bonds : bond 0.02199 / 1.23 ( 35) hydrogen bonds : angle 4.07320 / 2.08 ( 105) Misc. bond : bond 0.00045 / 0.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 353 LYS cc_start: 0.8592 (tttm) cc_final: 0.8068 (ttmt) outliers start: 5 outliers final: 1 residues processed: 70 average time/residue: 0.1958 time to fit residues: 14.5381 Evaluate side-chains 62 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.113368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.093844 restraints weight = 5062.012| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.93 r_work: 0.3684 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2856 Z= 0.136 Angle : 0.467 6.097 3816 Z= 0.235 Chirality : 0.045 0.116 432 Planarity : 0.001 0.003 432 Dihedral : 11.097 65.497 504 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 26.52 % Favored : 71.59 % 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: -2.69 (0.45), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2832) covalent geometry : angle 0.46742 / 0.24 ( 3816) hydrogen bonds : bond 0.01914 / 1.15 ( 35) hydrogen bonds : angle 3.91332 / 1.98 ( 105) Misc. bond : bond 0.00081 / 0.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: P 358 ASP cc_start: 0.8543 (m-30) cc_final: 0.8320 (m-30) REVERT: U 353 LYS cc_start: 0.8498 (tttm) cc_final: 0.8005 (ttpt) REVERT: X 358 ASP cc_start: 0.8683 (m-30) cc_final: 0.8233 (m-30) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.2106 time to fit residues: 12.7607 Evaluate side-chains 55 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain I residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.112331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.092807 restraints weight = 5028.922| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.90 r_work: 0.3672 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2856 Z= 0.158 Angle : 0.485 6.280 3816 Z= 0.242 Chirality : 0.046 0.123 432 Planarity : 0.001 0.004 432 Dihedral : 11.245 67.514 504 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.41 % Allowed : 24.62 % Favored : 71.97 % 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: -2.68 (0.45), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 2832) covalent geometry : angle 0.48475 / 0.24 ( 3816) hydrogen bonds : bond 0.02066 / 1.23 ( 35) hydrogen bonds : angle 3.87254 / 1.97 ( 105) Misc. bond : bond 0.00094 / 0.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.8384 (t70) cc_final: 0.7964 (t70) REVERT: P 358 ASP cc_start: 0.8606 (m-30) cc_final: 0.8396 (m-30) REVERT: U 353 LYS cc_start: 0.8501 (tttm) cc_final: 0.8015 (ttpt) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.1906 time to fit residues: 12.1249 Evaluate side-chains 58 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain Q residue 356 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.111131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091400 restraints weight = 5030.138| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.90 r_work: 0.3651 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2856 Z= 0.189 Angle : 0.521 6.632 3816 Z= 0.257 Chirality : 0.046 0.126 432 Planarity : 0.001 0.004 432 Dihedral : 11.579 71.480 504 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.41 % Allowed : 25.38 % Favored : 71.21 % 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: -2.68 (0.45), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 2832) covalent geometry : angle 0.52064 / 0.26 ( 3816) hydrogen bonds : bond 0.02191 / 1.29 ( 35) hydrogen bonds : angle 3.87170 / 1.98 ( 105) Misc. bond : bond 0.00115 / 0.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7981 (t70) REVERT: P 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8370 (m-30) REVERT: U 353 LYS cc_start: 0.8500 (tttm) cc_final: 0.8019 (ttpt) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1607 time to fit residues: 9.5214 Evaluate side-chains 56 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain Q residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.119051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.100263 restraints weight = 4999.575| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.91 r_work: 0.3807 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.026 2856 Z= 0.064 Angle : 0.413 6.977 3816 Z= 0.206 Chirality : 0.045 0.115 432 Planarity : 0.001 0.004 432 Dihedral : 10.892 62.812 504 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.27 % Allowed : 25.76 % Favored : 71.97 % 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: -2.64 (0.45), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00143 / 0.06 ( 2832) covalent geometry : angle 0.41267 / 0.21 ( 3816) hydrogen bonds : bond 0.01931 / 1.10 ( 35) hydrogen bonds : angle 3.68683 / 1.88 ( 105) Misc. bond : bond 0.00016 / 0.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7683 (t0) REVERT: P 358 ASP cc_start: 0.8398 (m-30) cc_final: 0.8161 (m-30) REVERT: U 353 LYS cc_start: 0.8393 (tttm) cc_final: 0.7921 (ttpt) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1829 time to fit residues: 13.2926 Evaluate side-chains 67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain Q residue 356 SER Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 overall best weight: 1.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.116892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.097426 restraints weight = 5067.187| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.96 r_work: 0.3757 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2856 Z= 0.090 Angle : 0.434 7.554 3816 Z= 0.215 Chirality : 0.044 0.113 432 Planarity : 0.001 0.003 432 Dihedral : 10.987 66.588 504 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 26.89 % Favored : 71.21 % 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: -2.47 (0.46), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.35), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 2832) covalent geometry : angle 0.43372 / 0.22 ( 3816) hydrogen bonds : bond 0.01747 / 0.99 ( 35) hydrogen bonds : angle 3.79710 / 1.94 ( 105) Misc. bond : bond 0.00040 / 0.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7704 (t0) REVERT: P 358 ASP cc_start: 0.8397 (m-30) cc_final: 0.8126 (m-30) REVERT: U 353 LYS cc_start: 0.8397 (tttm) cc_final: 0.7907 (ttpt) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.1629 time to fit residues: 10.9570 Evaluate side-chains 62 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain Q residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.121240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.102070 restraints weight = 5003.531| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.93 r_work: 0.3822 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2856 Z= 0.069 Angle : 0.439 8.715 3816 Z= 0.215 Chirality : 0.045 0.114 432 Planarity : 0.001 0.003 432 Dihedral : 10.862 63.720 504 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 27.27 % Favored : 71.21 % 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: -2.38 (0.46), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.07 ( 2832) covalent geometry : angle 0.43869 / 0.22 ( 3816) hydrogen bonds : bond 0.01955 / 1.09 ( 35) hydrogen bonds : angle 3.87592 / 1.97 ( 105) Misc. bond : bond 0.00020 / 0.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7678 (t0) REVERT: G 353 LYS cc_start: 0.8540 (tttm) cc_final: 0.7159 (tptt) REVERT: P 358 ASP cc_start: 0.8384 (m-30) cc_final: 0.8119 (m-30) REVERT: U 353 LYS cc_start: 0.8358 (tttm) cc_final: 0.7875 (ttpt) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1597 time to fit residues: 11.2445 Evaluate side-chains 67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain Q residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.115918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.096231 restraints weight = 5102.163| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.95 r_work: 0.3737 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2856 Z= 0.113 Angle : 0.476 8.601 3816 Z= 0.236 Chirality : 0.045 0.112 432 Planarity : 0.001 0.016 432 Dihedral : 11.085 68.330 504 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 27.27 % Favored : 70.83 % 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: -2.26 (0.48), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.11 ( 2832) covalent geometry : angle 0.47640 / 0.24 ( 3816) hydrogen bonds : bond 0.01885 / 1.06 ( 35) hydrogen bonds : angle 3.90628 / 1.98 ( 105) Misc. bond : bond 0.00060 / 0.03 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 358 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7675 (t0) REVERT: G 353 LYS cc_start: 0.8605 (tttm) cc_final: 0.7154 (tptt) REVERT: I 353 LYS cc_start: 0.8669 (tttm) cc_final: 0.8016 (ttmt) REVERT: P 358 ASP cc_start: 0.8413 (m-30) cc_final: 0.8142 (m-30) REVERT: U 353 LYS cc_start: 0.8398 (tttm) cc_final: 0.7927 (ttpt) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1673 time to fit residues: 10.6186 Evaluate side-chains 61 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain Q residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.112588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092786 restraints weight = 5022.728| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.93 r_work: 0.3694 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2856 Z= 0.157 Angle : 0.521 8.477 3816 Z= 0.258 Chirality : 0.047 0.121 432 Planarity : 0.001 0.013 432 Dihedral : 11.613 71.875 504 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.27 % Allowed : 26.89 % Favored : 70.83 % 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 (0.48), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 2832) covalent geometry : angle 0.52112 / 0.26 ( 3816) hydrogen bonds : bond 0.02075 / 1.17 ( 35) hydrogen bonds : angle 3.75208 / 1.92 ( 105) Misc. bond : bond 0.00090 / 0.05 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.59 seconds wall clock time: 20 minutes 11.86 seconds (1211.86 seconds total)