Starting phenix.real_space_refine on Tue Aug 4 12:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi0_16886/08_2026/8oi0_16886.cif" } resolution = 2.9 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 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-2.2rc3-6140/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: 0.88, per 1000 atoms: 0.32 Number of scatterers: 2784 At special positions: 0 Unit cell: (105.28, 111.86, 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: 0.27 Conformation dependent library (CDL) restraints added in 140.0 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: 6.628A pdb=" N ASP A 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR I 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP I 358 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR Q 361 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.487A 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: 6.199A pdb=" N LYS B 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.190A 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: 6.321A pdb=" N ASP B 358 " --> pdb=" O ASN J 359 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR J 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 360 " --> pdb=" O THR J 361 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP J 358 " --> pdb=" O ASN R 359 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR R 361 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.371A 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: 6.870A pdb=" N LYS C 353 " --> pdb=" O ILE K 354 " (cutoff:3.500A) removed outlier: 6.859A 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: 6.579A pdb=" N ASP E 358 " --> pdb=" O ASN M 359 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR M 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E 360 " --> pdb=" O THR M 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP M 358 " --> pdb=" O ASN U 359 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR U 361 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 6.683A 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: 6.320A pdb=" N LYS F 353 " --> pdb=" O ILE N 354 " (cutoff:3.500A) removed outlier: 6.299A 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: 6.290A pdb=" N ASP F 358 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR N 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 360 " --> pdb=" O THR N 361 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP N 358 " --> pdb=" O ASN V 359 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR V 361 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 6.394A 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: 6.988A pdb=" N LYS G 353 " --> pdb=" O ILE O 354 " (cutoff:3.500A) removed outlier: 6.942A 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 36 hydrogen bonds defined for protein. 108 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: 0.31 Time building geometry restraints manager: 0.38 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: 298 1.33 - 1.40: 483 1.40 - 1.47: 443 1.47 - 1.54: 1176 Bond restraints: 2832 Sorted by residual: bond pdb=" ND1 HIA F 362 " pdb=" CE1 HIA F 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 S 362 " pdb=" CE1 HIA S 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" ND1 HIA B 362 " pdb=" CE1 HIA B 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 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 2.08e+00 bond pdb=" ND1 HIA U 362 " pdb=" CE1 HIA U 362 " ideal model delta sigma weight residual 1.349 1.320 0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 2827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 3647 1.94 - 3.88: 139 3.88 - 5.82: 18 5.82 - 7.76: 2 7.76 - 9.70: 10 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 117.30 127.00 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C01 VP1 L 401 " pdb=" O03 VP1 L 401 " pdb=" C04 VP1 L 401 " ideal model delta sigma weight residual 117.30 126.96 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C01 VP1 D 401 " pdb=" O03 VP1 D 401 " pdb=" C04 VP1 D 401 " ideal model delta sigma weight residual 117.30 126.92 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C04 VP1 T 401 " pdb=" C05 VP1 T 401 " pdb=" C12 VP1 T 401 " ideal model delta sigma weight residual 109.50 118.40 -8.90 3.00e+00 1.11e-01 8.80e+00 angle pdb=" C04 VP1 D 401 " pdb=" C05 VP1 D 401 " pdb=" C12 VP1 D 401 " ideal model delta sigma weight residual 109.50 118.38 -8.88 3.00e+00 1.11e-01 8.76e+00 ... (remaining 3811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.12: 1386 11.12 - 22.24: 153 22.24 - 33.36: 33 33.36 - 44.49: 3 44.49 - 55.61: 9 Dihedral angle restraints: 1584 sinusoidal: 720 harmonic: 864 Sorted by residual: dihedral pdb=" CB LYS D 353 " pdb=" CG LYS D 353 " pdb=" CD LYS D 353 " pdb=" CE LYS D 353 " ideal model delta sinusoidal sigma weight residual -180.00 -125.25 -54.75 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB LYS L 353 " pdb=" CG LYS L 353 " pdb=" CD LYS L 353 " pdb=" CE LYS L 353 " ideal model delta sinusoidal sigma weight residual -180.00 -125.27 -54.73 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB LYS T 353 " pdb=" CG LYS T 353 " pdb=" CD LYS T 353 " pdb=" CE LYS T 353 " ideal model delta sinusoidal sigma weight residual -180.00 -125.33 -54.67 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 1581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 324 0.052 - 0.103: 92 0.103 - 0.155: 10 0.155 - 0.206: 0 0.206 - 0.258: 6 Chirality restraints: 432 Sorted by residual: 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 -2.48 -0.26 2.00e-01 2.50e+01 1.66e+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 -2.48 -0.26 2.00e-01 2.50e+01 1.65e+00 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 -2.49 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 429 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 D 401 " 0.032 2.00e-02 2.50e+03 1.83e-02 1.09e+01 pdb=" C06 VP1 D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C07 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 D 401 " -0.023 2.00e-02 2.50e+03 pdb=" C09 VP1 D 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 D 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 D 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C13 VP1 D 401 " -0.014 2.00e-02 2.50e+03 pdb=" C14 VP1 D 401 " -0.022 2.00e-02 2.50e+03 pdb=" C15 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 D 401 " 0.012 2.00e-02 2.50e+03 pdb=" C17 VP1 D 401 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 L 401 " 0.032 2.00e-02 2.50e+03 1.83e-02 1.09e+01 pdb=" C06 VP1 L 401 " 0.005 2.00e-02 2.50e+03 pdb=" C07 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 L 401 " -0.024 2.00e-02 2.50e+03 pdb=" C09 VP1 L 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 L 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 L 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 L 401 " -0.012 2.00e-02 2.50e+03 pdb=" C13 VP1 L 401 " -0.015 2.00e-02 2.50e+03 pdb=" C14 VP1 L 401 " -0.023 2.00e-02 2.50e+03 pdb=" C15 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 L 401 " 0.012 2.00e-02 2.50e+03 pdb=" C17 VP1 L 401 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 T 401 " 0.032 2.00e-02 2.50e+03 1.82e-02 1.08e+01 pdb=" C06 VP1 T 401 " 0.004 2.00e-02 2.50e+03 pdb=" C07 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 T 401 " -0.023 2.00e-02 2.50e+03 pdb=" C09 VP1 T 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 T 401 " 0.007 2.00e-02 2.50e+03 pdb=" C11 VP1 T 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 T 401 " -0.013 2.00e-02 2.50e+03 pdb=" C13 VP1 T 401 " -0.015 2.00e-02 2.50e+03 pdb=" C14 VP1 T 401 " -0.022 2.00e-02 2.50e+03 pdb=" C15 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 T 401 " 0.011 2.00e-02 2.50e+03 pdb=" C17 VP1 T 401 " 0.025 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 27 2.61 - 3.18: 2176 3.18 - 3.75: 3796 3.75 - 4.33: 6067 4.33 - 4.90: 10214 Nonbonded interactions: 22280 Sorted by model distance: nonbonded pdb=" O02 VP1 L 401 " pdb=" OG SER T 352 " model vdw 2.037 3.040 nonbonded pdb=" O02 VP1 D 401 " pdb=" OG SER L 352 " model vdw 2.134 3.040 nonbonded pdb=" O02 VP1 H 401 " pdb=" OG SER P 352 " model vdw 2.217 3.040 nonbonded pdb=" OG SER I 356 " pdb=" OD1 ASN I 359 " model vdw 2.226 3.040 nonbonded pdb=" OG SER Q 356 " pdb=" OD1 ASN Q 359 " model vdw 2.227 3.040 ... (remaining 22275 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: 2.700 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.570 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 2856 Z= 0.881 Angle : 1.006 9.702 3816 Z= 0.397 Chirality : 0.053 0.258 432 Planarity : 0.003 0.018 432 Dihedral : 10.482 55.608 1008 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -3.25 (0.37), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.28), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.36 ( 2832) covalent geometry : angle 1.00559 / 0.40 ( 3816) hydrogen bonds : bond 0.19300 / 11.08 ( 36) hydrogen bonds : angle 7.34614 / 4.10 ( 108) Misc. bond : bond 0.08783 / 4.44 ( 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 58 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.075 Fit side-chains REVERT: C 353 LYS cc_start: 0.8231 (mttt) cc_final: 0.7878 (mtpp) REVERT: E 353 LYS cc_start: 0.8671 (tttt) cc_final: 0.8282 (ttmt) REVERT: K 353 LYS cc_start: 0.8205 (mttt) cc_final: 0.7786 (mtpp) REVERT: M 353 LYS cc_start: 0.8650 (tttt) cc_final: 0.8242 (ttmt) REVERT: O 353 LYS cc_start: 0.8162 (tttt) cc_final: 0.7670 (ttmm) REVERT: S 353 LYS cc_start: 0.8401 (mttt) cc_final: 0.7982 (mtpp) REVERT: U 353 LYS cc_start: 0.8583 (tttt) cc_final: 0.8120 (ttmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2474 time to fit residues: 14.9407 Evaluate side-chains 37 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 351 GLN B 359 ASN F 351 GLN H 351 GLN J 351 GLN L 351 GLN N 351 GLN O 359 ASN P 351 GLN R 351 GLN V 351 GLN X 351 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089420 restraints weight = 4194.689| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.38 r_work: 0.3360 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2856 Z= 0.086 Angle : 0.409 3.994 3816 Z= 0.204 Chirality : 0.045 0.117 432 Planarity : 0.001 0.006 432 Dihedral : 9.671 59.915 504 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 12.88 % Favored : 86.74 % 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: -2.95 (0.41), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 ( 2832) covalent geometry : angle 0.40869 / 0.20 ( 3816) hydrogen bonds : bond 0.01557 / 0.85 ( 36) hydrogen bonds : angle 4.45198 / 2.40 ( 108) Misc. bond : bond 0.00050 / 0.02 ( 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 56 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.062 Fit side-chains REVERT: C 353 LYS cc_start: 0.8581 (mttt) cc_final: 0.8006 (mtpp) REVERT: E 353 LYS cc_start: 0.8981 (tttt) cc_final: 0.8562 (ttmt) REVERT: F 360 ILE cc_start: 0.8714 (mt) cc_final: 0.8502 (mp) REVERT: K 353 LYS cc_start: 0.8512 (mttt) cc_final: 0.7923 (mtpp) REVERT: M 353 LYS cc_start: 0.8882 (tttt) cc_final: 0.8395 (ttmt) REVERT: S 353 LYS cc_start: 0.8651 (mttt) cc_final: 0.8116 (mtpp) REVERT: U 353 LYS cc_start: 0.8801 (tttt) cc_final: 0.8287 (ttmt) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2243 time to fit residues: 13.1395 Evaluate side-chains 44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.110052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086745 restraints weight = 4191.678| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.38 r_work: 0.3322 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2856 Z= 0.129 Angle : 0.425 3.192 3816 Z= 0.213 Chirality : 0.045 0.117 432 Planarity : 0.001 0.006 432 Dihedral : 10.231 64.748 504 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 17.05 % Favored : 82.20 % 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: -2.78 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2832) covalent geometry : angle 0.42500 / 0.21 ( 3816) hydrogen bonds : bond 0.01719 / 0.98 ( 36) hydrogen bonds : angle 4.06136 / 2.27 ( 108) Misc. bond : bond 0.00077 / 0.04 ( 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 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: C 353 LYS cc_start: 0.8557 (mttt) cc_final: 0.7980 (mtpp) REVERT: E 353 LYS cc_start: 0.9006 (tttt) cc_final: 0.8566 (ttmt) REVERT: K 353 LYS cc_start: 0.8499 (mttt) cc_final: 0.7917 (mtpp) REVERT: M 353 LYS cc_start: 0.8899 (tttt) cc_final: 0.8407 (ttmt) REVERT: S 353 LYS cc_start: 0.8697 (mttt) cc_final: 0.8164 (mtpp) REVERT: U 353 LYS cc_start: 0.8826 (tttt) cc_final: 0.8288 (ttmt) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.2609 time to fit residues: 12.5263 Evaluate side-chains 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J 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: 10.0000 chunk 17 optimal weight: 0.0060 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 16 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.6537 > 50:) chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 0.0670 overall best weight: 2.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085057 restraints weight = 4157.646| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.38 r_work: 0.3291 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2856 Z= 0.175 Angle : 0.456 3.702 3816 Z= 0.226 Chirality : 0.046 0.147 432 Planarity : 0.001 0.006 432 Dihedral : 10.966 65.631 504 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 17.05 % Favored : 82.58 % 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: -2.89 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.33), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 2832) covalent geometry : angle 0.45636 / 0.23 ( 3816) hydrogen bonds : bond 0.01881 / 1.07 ( 36) hydrogen bonds : angle 4.10774 / 2.31 ( 108) Misc. bond : bond 0.00107 / 0.05 ( 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 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.110 Fit side-chains REVERT: C 353 LYS cc_start: 0.8598 (mttt) cc_final: 0.8018 (mtpp) REVERT: E 353 LYS cc_start: 0.9015 (tttt) cc_final: 0.8606 (ttmt) REVERT: K 353 LYS cc_start: 0.8528 (mttt) cc_final: 0.7944 (mtpp) REVERT: K 359 ASN cc_start: 0.8654 (m-40) cc_final: 0.8238 (m-40) REVERT: M 353 LYS cc_start: 0.8909 (tttt) cc_final: 0.8418 (ttmt) REVERT: O 359 ASN cc_start: 0.8506 (m-40) cc_final: 0.8180 (m-40) REVERT: S 353 LYS cc_start: 0.8715 (mttt) cc_final: 0.8208 (mtpp) REVERT: U 353 LYS cc_start: 0.8845 (tttt) cc_final: 0.8313 (ttmt) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.2959 time to fit residues: 13.3164 Evaluate side-chains 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087423 restraints weight = 4131.366| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.36 r_work: 0.3339 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2856 Z= 0.098 Angle : 0.379 3.262 3816 Z= 0.197 Chirality : 0.044 0.115 432 Planarity : 0.001 0.006 432 Dihedral : 10.130 64.752 504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 16.67 % Favored : 82.20 % 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 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.33), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 2832) covalent geometry : angle 0.37927 / 0.20 ( 3816) hydrogen bonds : bond 0.01373 / 0.77 ( 36) hydrogen bonds : angle 3.92704 / 2.18 ( 108) Misc. bond : bond 0.00054 / 0.03 ( 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 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.110 Fit side-chains REVERT: C 353 LYS cc_start: 0.8565 (mttt) cc_final: 0.8006 (mtpp) REVERT: E 353 LYS cc_start: 0.9014 (tttt) cc_final: 0.8589 (ttmt) REVERT: K 353 LYS cc_start: 0.8505 (mttt) cc_final: 0.7933 (mtpp) REVERT: K 359 ASN cc_start: 0.8649 (m-40) cc_final: 0.8231 (m-40) REVERT: M 353 LYS cc_start: 0.8896 (tttt) cc_final: 0.8402 (ttmt) REVERT: S 353 LYS cc_start: 0.8704 (mttt) cc_final: 0.8168 (mtpp) REVERT: U 353 LYS cc_start: 0.8815 (tttt) cc_final: 0.8278 (ttmt) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.2503 time to fit residues: 12.4850 Evaluate side-chains 41 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 353 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE 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: 10.0000 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082038 restraints weight = 4186.002| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3225 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 2856 Z= 0.432 Angle : 0.726 6.684 3816 Z= 0.334 Chirality : 0.056 0.238 432 Planarity : 0.002 0.008 432 Dihedral : 14.634 78.731 504 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.76 % Allowed : 17.42 % 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: -3.31 (0.40), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.43 ( 2832) covalent geometry : angle 0.72598 / 0.33 ( 3816) hydrogen bonds : bond 0.02773 / 1.55 ( 36) hydrogen bonds : angle 4.27297 / 2.49 ( 108) Misc. bond : bond 0.00212 / 0.11 ( 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 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.121 Fit side-chains REVERT: C 353 LYS cc_start: 0.8621 (mttt) cc_final: 0.8115 (mtpp) REVERT: E 353 LYS cc_start: 0.9076 (tttt) cc_final: 0.8668 (ttmt) REVERT: G 353 LYS cc_start: 0.8720 (tttp) cc_final: 0.8183 (ttmm) REVERT: K 353 LYS cc_start: 0.8564 (mttt) cc_final: 0.8038 (mtpp) REVERT: K 359 ASN cc_start: 0.8744 (m-40) cc_final: 0.8416 (m-40) REVERT: M 353 LYS cc_start: 0.8968 (tttt) cc_final: 0.8494 (ttmt) REVERT: S 353 LYS cc_start: 0.8778 (mttt) cc_final: 0.8280 (mtpp) REVERT: U 353 LYS cc_start: 0.8917 (tttt) cc_final: 0.8414 (ttmt) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.2090 time to fit residues: 10.5512 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089345 restraints weight = 4126.006| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.31 r_work: 0.3366 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 2856 Z= 0.069 Angle : 0.379 3.820 3816 Z= 0.200 Chirality : 0.045 0.119 432 Planarity : 0.001 0.007 432 Dihedral : 10.910 68.189 504 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 18.56 % Favored : 81.44 % 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: -2.97 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00141 / 0.07 ( 2832) covalent geometry : angle 0.37930 / 0.20 ( 3816) hydrogen bonds : bond 0.01271 / 0.69 ( 36) hydrogen bonds : angle 3.87930 / 2.15 ( 108) Misc. bond : bond 0.00025 / 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 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.129 Fit side-chains REVERT: C 353 LYS cc_start: 0.8607 (mttt) cc_final: 0.8024 (mtpp) REVERT: E 353 LYS cc_start: 0.8998 (tttt) cc_final: 0.8586 (ttmt) REVERT: K 353 LYS cc_start: 0.8489 (mttt) cc_final: 0.7941 (mtpp) REVERT: K 359 ASN cc_start: 0.8644 (m-40) cc_final: 0.8209 (m-40) REVERT: M 353 LYS cc_start: 0.8877 (tttt) cc_final: 0.8384 (ttmt) REVERT: S 353 LYS cc_start: 0.8676 (mttt) cc_final: 0.8137 (mtpp) REVERT: U 353 LYS cc_start: 0.8796 (tttt) cc_final: 0.8240 (ttmt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3036 time to fit residues: 15.4660 Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.106411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082831 restraints weight = 4254.794| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.38 r_work: 0.3247 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2856 Z= 0.320 Angle : 0.607 5.209 3816 Z= 0.288 Chirality : 0.051 0.210 432 Planarity : 0.002 0.007 432 Dihedral : 13.502 81.912 504 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.38 % Allowed : 17.42 % Favored : 82.20 % 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: -3.19 (0.41), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.32), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.32 ( 2832) covalent geometry : angle 0.60701 / 0.29 ( 3816) hydrogen bonds : bond 0.02447 / 1.39 ( 36) hydrogen bonds : angle 4.23899 / 2.43 ( 108) Misc. bond : bond 0.00165 / 0.08 ( 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 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.073 Fit side-chains REVERT: C 353 LYS cc_start: 0.8558 (mttt) cc_final: 0.8043 (mtpp) REVERT: E 353 LYS cc_start: 0.9085 (tttt) cc_final: 0.8651 (ttmt) REVERT: G 353 LYS cc_start: 0.8721 (tttp) cc_final: 0.8121 (ttmm) REVERT: K 353 LYS cc_start: 0.8522 (mttt) cc_final: 0.7972 (mtpp) REVERT: K 359 ASN cc_start: 0.8673 (m-40) cc_final: 0.8245 (m-40) REVERT: M 353 LYS cc_start: 0.8933 (tttt) cc_final: 0.8439 (ttmt) REVERT: S 353 LYS cc_start: 0.8763 (mttt) cc_final: 0.8244 (mtpp) REVERT: U 353 LYS cc_start: 0.8884 (tttt) cc_final: 0.8347 (ttmt) outliers start: 1 outliers final: 2 residues processed: 43 average time/residue: 0.3051 time to fit residues: 13.7004 Evaluate side-chains 44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.109883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086864 restraints weight = 4194.136| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.35 r_work: 0.3327 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2856 Z= 0.099 Angle : 0.404 4.191 3816 Z= 0.212 Chirality : 0.045 0.117 432 Planarity : 0.001 0.007 432 Dihedral : 11.440 72.232 504 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 17.05 % 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: -3.00 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 2832) covalent geometry : angle 0.40424 / 0.21 ( 3816) hydrogen bonds : bond 0.01402 / 0.79 ( 36) hydrogen bonds : angle 3.93694 / 2.20 ( 108) Misc. bond : bond 0.00043 / 0.02 ( 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 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.110 Fit side-chains REVERT: C 353 LYS cc_start: 0.8608 (mttt) cc_final: 0.8025 (mtpp) REVERT: E 353 LYS cc_start: 0.9027 (tttt) cc_final: 0.8608 (ttmt) REVERT: G 353 LYS cc_start: 0.8731 (tttp) cc_final: 0.8109 (ttmm) REVERT: K 353 LYS cc_start: 0.8502 (mttt) cc_final: 0.7945 (mtpp) REVERT: K 359 ASN cc_start: 0.8659 (m-40) cc_final: 0.8224 (m-40) REVERT: M 353 LYS cc_start: 0.8890 (tttt) cc_final: 0.8399 (ttmt) REVERT: S 353 LYS cc_start: 0.8710 (mttt) cc_final: 0.8167 (mtpp) REVERT: U 353 LYS cc_start: 0.8819 (tttt) cc_final: 0.8272 (ttmt) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.2886 time to fit residues: 14.1851 Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.107539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083946 restraints weight = 4234.230| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.37 r_work: 0.3272 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2856 Z= 0.205 Angle : 0.496 4.194 3816 Z= 0.247 Chirality : 0.047 0.163 432 Planarity : 0.002 0.007 432 Dihedral : 12.500 73.770 504 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 17.05 % Favored : 82.58 % 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: -3.05 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.32), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 ( 2832) covalent geometry : angle 0.49601 / 0.25 ( 3816) hydrogen bonds : bond 0.01998 / 1.16 ( 36) hydrogen bonds : angle 4.06352 / 2.32 ( 108) Misc. bond : bond 0.00113 / 0.06 ( 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 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.064 Fit side-chains REVERT: C 353 LYS cc_start: 0.8635 (mttt) cc_final: 0.8057 (mtpp) REVERT: E 353 LYS cc_start: 0.9055 (tttt) cc_final: 0.8632 (ttmt) REVERT: G 353 LYS cc_start: 0.8718 (tttp) cc_final: 0.8133 (ttmm) REVERT: K 353 LYS cc_start: 0.8521 (mttt) cc_final: 0.7973 (mtpp) REVERT: K 359 ASN cc_start: 0.8659 (m-40) cc_final: 0.8204 (m-40) REVERT: M 353 LYS cc_start: 0.8925 (tttt) cc_final: 0.8439 (ttmt) REVERT: S 353 LYS cc_start: 0.8727 (mttt) cc_final: 0.8217 (mtpp) REVERT: U 353 LYS cc_start: 0.8857 (tttt) cc_final: 0.8319 (ttmt) outliers start: 1 outliers final: 2 residues processed: 43 average time/residue: 0.2913 time to fit residues: 13.0739 Evaluate side-chains 44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.0030 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 overall best weight: 2.0054 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.109285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086009 restraints weight = 4143.541| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.34 r_work: 0.3282 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2856 Z= 0.132 Angle : 0.430 4.167 3816 Z= 0.222 Chirality : 0.045 0.115 432 Planarity : 0.001 0.007 432 Dihedral : 11.881 68.314 504 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 17.42 % 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: -2.97 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.33), residues: 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2832) covalent geometry : angle 0.42973 / 0.22 ( 3816) hydrogen bonds : bond 0.01606 / 0.91 ( 36) hydrogen bonds : angle 3.94730 / 2.24 ( 108) Misc. bond : bond 0.00067 / 0.03 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1061.54 seconds wall clock time: 18 minutes 49.30 seconds (1129.30 seconds total)