Starting phenix.real_space_refine on Sun Aug 9 00:42:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.cif Found real_map, /net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25ho_80106/08_2026/25ho_80106.map" } resolution = 2.2 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= 0.003 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 20256 2.51 5 N 5280 2.21 5 O 6120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s 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: 31776 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "B" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "C" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "D" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "E" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "F" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "H" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "I" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "J" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "K" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "L" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "M" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "N" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "O" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "P" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "Q" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "R" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "S" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "T" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "U" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "V" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "W" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "X" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Time building chain proxies: 5.82, per 1000 atoms: 0.18 Number of scatterers: 31776 At special positions: 0 Unit cell: (135.05, 135.05, 135.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6120 8.00 N 5280 7.00 C 20256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS B 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS G 73 " - pdb=" SG CYS H 73 " distance=2.03 Simple disulfide: pdb=" SG CYS I 73 " - pdb=" SG CYS J 73 " distance=2.03 Simple disulfide: pdb=" SG CYS K 73 " - pdb=" SG CYS L 73 " distance=2.03 Simple disulfide: pdb=" SG CYS M 73 " - pdb=" SG CYS N 73 " distance=2.03 Simple disulfide: pdb=" SG CYS O 73 " - pdb=" SG CYS P 73 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 73 " - pdb=" SG CYS R 73 " distance=2.03 Simple disulfide: pdb=" SG CYS S 73 " - pdb=" SG CYS T 73 " distance=2.03 Simple disulfide: pdb=" SG CYS U 73 " - pdb=" SG CYS X 73 " distance=2.03 Simple disulfide: pdb=" SG CYS V 73 " - pdb=" SG CYS W 73 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7488 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 36 through 64 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 36 through 64 Processing helix chain 'B' and resid 82 through 111 Processing helix chain 'B' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'C' and resid 6 through 33 Processing helix chain 'C' and resid 36 through 64 Processing helix chain 'C' and resid 82 through 111 Processing helix chain 'C' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'D' and resid 6 through 33 Processing helix chain 'D' and resid 36 through 64 Processing helix chain 'D' and resid 82 through 111 Processing helix chain 'D' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'E' and resid 6 through 33 Processing helix chain 'E' and resid 36 through 64 Processing helix chain 'E' and resid 82 through 111 Processing helix chain 'E' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 166 Processing helix chain 'F' and resid 6 through 33 Processing helix chain 'F' and resid 36 through 64 Processing helix chain 'F' and resid 82 through 111 Processing helix chain 'F' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 166 Processing helix chain 'G' and resid 6 through 33 Processing helix chain 'G' and resid 36 through 64 Processing helix chain 'G' and resid 82 through 111 Processing helix chain 'G' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP G 122 " --> pdb=" O ASN G 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 166 Processing helix chain 'H' and resid 6 through 33 Processing helix chain 'H' and resid 36 through 64 Processing helix chain 'H' and resid 82 through 111 Processing helix chain 'H' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP H 122 " --> pdb=" O ASN H 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 Processing helix chain 'I' and resid 6 through 33 Processing helix chain 'I' and resid 36 through 64 Processing helix chain 'I' and resid 82 through 111 Processing helix chain 'I' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP I 122 " --> pdb=" O ASN I 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 166 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 36 through 64 Processing helix chain 'J' and resid 82 through 111 Processing helix chain 'J' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP J 122 " --> pdb=" O ASN J 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 166 Processing helix chain 'K' and resid 6 through 33 Processing helix chain 'K' and resid 36 through 64 Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'K' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 166 Processing helix chain 'L' and resid 6 through 33 Processing helix chain 'L' and resid 36 through 64 Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP L 122 " --> pdb=" O ASN L 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'M' and resid 6 through 33 Processing helix chain 'M' and resid 36 through 64 Processing helix chain 'M' and resid 82 through 111 Processing helix chain 'M' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP M 122 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 166 Processing helix chain 'N' and resid 6 through 33 Processing helix chain 'N' and resid 36 through 64 Processing helix chain 'N' and resid 82 through 111 Processing helix chain 'N' and resid 113 through 145 removed outlier: 4.390A pdb=" N TRP N 122 " --> pdb=" O ASN N 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR N 123 " --> pdb=" O PHE N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'O' and resid 6 through 33 Processing helix chain 'O' and resid 36 through 64 Processing helix chain 'O' and resid 82 through 111 Processing helix chain 'O' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP O 122 " --> pdb=" O ASN O 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 166 Processing helix chain 'P' and resid 6 through 33 Processing helix chain 'P' and resid 36 through 64 Processing helix chain 'P' and resid 82 through 111 Processing helix chain 'P' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP P 122 " --> pdb=" O ASN P 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR P 123 " --> pdb=" O PHE P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 166 Processing helix chain 'Q' and resid 6 through 33 Processing helix chain 'Q' and resid 36 through 64 Processing helix chain 'Q' and resid 82 through 111 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP Q 122 " --> pdb=" O ASN Q 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR Q 123 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 166 Processing helix chain 'R' and resid 6 through 33 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 82 through 111 Processing helix chain 'R' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP R 122 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 166 Processing helix chain 'S' and resid 6 through 33 Processing helix chain 'S' and resid 36 through 64 Processing helix chain 'S' and resid 82 through 111 Processing helix chain 'S' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP S 122 " --> pdb=" O ASN S 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 123 " --> pdb=" O PHE S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 166 Processing helix chain 'T' and resid 6 through 33 Processing helix chain 'T' and resid 36 through 64 Processing helix chain 'T' and resid 82 through 111 Processing helix chain 'T' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP T 122 " --> pdb=" O ASN T 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR T 123 " --> pdb=" O PHE T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 166 Processing helix chain 'U' and resid 6 through 33 Processing helix chain 'U' and resid 36 through 64 Processing helix chain 'U' and resid 82 through 111 Processing helix chain 'U' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP U 122 " --> pdb=" O ASN U 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 166 Processing helix chain 'V' and resid 6 through 33 Processing helix chain 'V' and resid 36 through 64 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP V 122 " --> pdb=" O ASN V 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR V 123 " --> pdb=" O PHE V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 166 Processing helix chain 'W' and resid 6 through 33 Processing helix chain 'W' and resid 36 through 64 Processing helix chain 'W' and resid 82 through 111 Processing helix chain 'W' and resid 113 through 145 removed outlier: 4.389A pdb=" N TRP W 122 " --> pdb=" O ASN W 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR W 123 " --> pdb=" O PHE W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 166 Processing helix chain 'X' and resid 6 through 33 Processing helix chain 'X' and resid 36 through 64 Processing helix chain 'X' and resid 82 through 111 Processing helix chain 'X' and resid 113 through 145 removed outlier: 4.388A pdb=" N TRP X 122 " --> pdb=" O ASN X 118 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR X 123 " --> pdb=" O PHE X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 166 2785 hydrogen bonds defined for protein. 8355 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: 6.05 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10464 1.34 - 1.46: 7454 1.46 - 1.58: 14386 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 32496 Sorted by residual: bond pdb=" C PHE V 44 " pdb=" O PHE V 44 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.77e-01 bond pdb=" C PHE E 44 " pdb=" O PHE E 44 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.44e-01 bond pdb=" C PHE W 44 " pdb=" O PHE W 44 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.06e-01 bond pdb=" C PHE M 44 " pdb=" O PHE M 44 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.06e-01 bond pdb=" C PHE H 44 " pdb=" O PHE H 44 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 7.75e-01 ... (remaining 32491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 42113 1.01 - 2.02: 1430 2.02 - 3.03: 237 3.03 - 4.03: 44 4.03 - 5.04: 24 Bond angle restraints: 43848 Sorted by residual: angle pdb=" C HIS I 34 " pdb=" N SER I 35 " pdb=" CA SER I 35 " ideal model delta sigma weight residual 122.61 125.47 -2.86 1.56e+00 4.11e-01 3.37e+00 angle pdb=" C HIS W 34 " pdb=" N SER W 35 " pdb=" CA SER W 35 " ideal model delta sigma weight residual 122.61 125.46 -2.85 1.56e+00 4.11e-01 3.33e+00 angle pdb=" C HIS A 34 " pdb=" N SER A 35 " pdb=" CA SER A 35 " ideal model delta sigma weight residual 122.61 125.45 -2.84 1.56e+00 4.11e-01 3.31e+00 angle pdb=" C HIS H 34 " pdb=" N SER H 35 " pdb=" CA SER H 35 " ideal model delta sigma weight residual 122.61 125.45 -2.84 1.56e+00 4.11e-01 3.31e+00 angle pdb=" C HIS T 34 " pdb=" N SER T 35 " pdb=" CA SER T 35 " ideal model delta sigma weight residual 122.61 125.45 -2.84 1.56e+00 4.11e-01 3.31e+00 ... (remaining 43843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 17018 17.61 - 35.23: 1606 35.23 - 52.84: 480 52.84 - 70.46: 156 70.46 - 88.07: 96 Dihedral angle restraints: 19356 sinusoidal: 7836 harmonic: 11520 Sorted by residual: dihedral pdb=" CB CYS O 73 " pdb=" SG CYS O 73 " pdb=" SG CYS P 73 " pdb=" CB CYS P 73 " ideal model delta sinusoidal sigma weight residual 93.00 158.92 -65.92 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS C 73 " pdb=" SG CYS C 73 " pdb=" SG CYS D 73 " pdb=" CB CYS D 73 " ideal model delta sinusoidal sigma weight residual 93.00 158.92 -65.92 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS I 73 " pdb=" SG CYS I 73 " pdb=" SG CYS J 73 " pdb=" CB CYS J 73 " ideal model delta sinusoidal sigma weight residual 93.00 158.92 -65.92 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 19353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2619 0.026 - 0.051: 1365 0.051 - 0.077: 587 0.077 - 0.103: 103 0.103 - 0.128: 30 Chirality restraints: 4704 Sorted by residual: chirality pdb=" CA PHE U 87 " pdb=" N PHE U 87 " pdb=" C PHE U 87 " pdb=" CB PHE U 87 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA PHE L 87 " pdb=" N PHE L 87 " pdb=" C PHE L 87 " pdb=" CB PHE L 87 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA PHE S 87 " pdb=" N PHE S 87 " pdb=" C PHE S 87 " pdb=" CB PHE S 87 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 4701 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 46 " 0.010 2.00e-02 2.50e+03 9.28e-03 1.29e+00 pdb=" CG HIS C 46 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS C 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS C 46 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS C 46 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 46 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 46 " 0.010 2.00e-02 2.50e+03 9.27e-03 1.29e+00 pdb=" CG HIS K 46 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS K 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 46 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS K 46 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS K 46 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 46 " -0.010 2.00e-02 2.50e+03 9.26e-03 1.29e+00 pdb=" CG HIS D 46 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS D 46 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 46 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS D 46 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS D 46 " -0.003 2.00e-02 2.50e+03 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 23666 3.12 - 3.56: 40865 3.56 - 4.01: 52658 4.01 - 4.45: 70594 4.45 - 4.90: 89897 Nonbonded interactions: 277680 Sorted by model distance: nonbonded pdb=" O HIS B 34 " pdb=" OG SER B 35 " model vdw 2.671 3.040 nonbonded pdb=" O HIS I 34 " pdb=" OG SER I 35 " model vdw 2.671 3.040 nonbonded pdb=" O HIS E 34 " pdb=" OG SER E 35 " model vdw 2.671 3.040 nonbonded pdb=" O HIS C 34 " pdb=" OG SER C 35 " model vdw 2.671 3.040 nonbonded pdb=" O HIS Q 34 " pdb=" OG SER Q 35 " model vdw 2.671 3.040 ... (remaining 277675 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: 0.14 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.840 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.003 0.022 32508 Z= 0.161 Angle : 0.469 5.042 43872 Z= 0.271 Chirality : 0.036 0.128 4704 Planarity : 0.003 0.020 5664 Dihedral : 17.523 88.071 11832 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: 4.95 (0.12), residues: 3840 helix: 3.69 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.68 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 165 TYR 0.010 0.002 TYR C 157 PHE 0.019 0.003 PHE U 44 TRP 0.006 0.002 TRP R 122 HIS 0.008 0.002 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (32496) covalent geometry : angle 0.46821 / 0.27 (43848) SS BOND : bond 0.00133 / 0.09 ( 12) SS BOND : angle 0.91281 / 0.62 ( 24) hydrogen bonds : bond 0.08744 / 5.82 ( 2785) hydrogen bonds : angle 3.59859 / 2.68 ( 8355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 1.264 Fit side-chains REVERT: A 8 LYS cc_start: 0.8330 (tttt) cc_final: 0.7615 (tmmt) REVERT: A 110 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7849 (ttpt) REVERT: A 147 GLU cc_start: 0.7300 (pt0) cc_final: 0.6658 (pm20) REVERT: B 8 LYS cc_start: 0.8324 (tttt) cc_final: 0.7625 (tmmt) REVERT: B 110 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7853 (ttpt) REVERT: B 147 GLU cc_start: 0.7299 (pt0) cc_final: 0.6749 (pm20) REVERT: C 8 LYS cc_start: 0.8315 (tttt) cc_final: 0.7601 (tmmt) REVERT: C 110 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7844 (ttpt) REVERT: C 147 GLU cc_start: 0.7303 (pt0) cc_final: 0.6757 (pm20) REVERT: D 8 LYS cc_start: 0.8322 (tttt) cc_final: 0.7617 (tmmt) REVERT: D 110 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7846 (ttpt) REVERT: D 147 GLU cc_start: 0.7301 (pt0) cc_final: 0.6657 (pm20) REVERT: E 8 LYS cc_start: 0.8325 (tttt) cc_final: 0.7618 (tmmt) REVERT: E 110 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7852 (ttpt) REVERT: E 147 GLU cc_start: 0.7302 (pt0) cc_final: 0.6753 (pm20) REVERT: F 8 LYS cc_start: 0.8324 (tttt) cc_final: 0.7620 (tmmt) REVERT: F 147 GLU cc_start: 0.7297 (pt0) cc_final: 0.6744 (pm20) REVERT: G 8 LYS cc_start: 0.8326 (tttt) cc_final: 0.7618 (tmmt) REVERT: G 110 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7858 (ttpt) REVERT: G 147 GLU cc_start: 0.7301 (pt0) cc_final: 0.6665 (pm20) REVERT: H 8 LYS cc_start: 0.8322 (tttt) cc_final: 0.7620 (tmmt) REVERT: H 110 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7855 (ttpt) REVERT: H 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6737 (pm20) REVERT: I 8 LYS cc_start: 0.8322 (tttt) cc_final: 0.7615 (tmmt) REVERT: I 110 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7853 (ttpt) REVERT: I 147 GLU cc_start: 0.7299 (pt0) cc_final: 0.6751 (pm20) REVERT: J 8 LYS cc_start: 0.8323 (tttt) cc_final: 0.7619 (tmmt) REVERT: J 147 GLU cc_start: 0.7300 (pt0) cc_final: 0.6746 (pm20) REVERT: K 8 LYS cc_start: 0.8325 (tttt) cc_final: 0.7623 (tmmt) REVERT: K 110 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7857 (ttpt) REVERT: K 147 GLU cc_start: 0.7294 (pt0) cc_final: 0.6742 (pm20) REVERT: L 8 LYS cc_start: 0.8323 (tttt) cc_final: 0.7613 (tmmt) REVERT: L 110 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7855 (ttpt) REVERT: L 147 GLU cc_start: 0.7296 (pt0) cc_final: 0.6656 (pm20) REVERT: M 8 LYS cc_start: 0.8319 (tttt) cc_final: 0.7609 (tmmt) REVERT: M 110 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7847 (ttpt) REVERT: M 147 GLU cc_start: 0.7302 (pt0) cc_final: 0.6754 (pm20) REVERT: N 8 LYS cc_start: 0.8320 (tttt) cc_final: 0.7614 (tmmt) REVERT: N 110 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7853 (ttpt) REVERT: N 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6651 (pm20) REVERT: O 8 LYS cc_start: 0.8325 (tttt) cc_final: 0.7613 (tmmt) REVERT: O 110 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7851 (ttpt) REVERT: O 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6752 (pm20) REVERT: P 8 LYS cc_start: 0.8319 (tttt) cc_final: 0.7598 (tmmt) REVERT: P 110 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7854 (ttpt) REVERT: P 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6752 (pm20) REVERT: Q 8 LYS cc_start: 0.8317 (tttt) cc_final: 0.7609 (tmmt) REVERT: Q 110 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7852 (ttpt) REVERT: Q 147 GLU cc_start: 0.7307 (pt0) cc_final: 0.6754 (pm20) REVERT: R 8 LYS cc_start: 0.8320 (tttt) cc_final: 0.7601 (tmmt) REVERT: R 110 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7851 (ttpt) REVERT: R 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6753 (pm20) REVERT: S 8 LYS cc_start: 0.8325 (tttt) cc_final: 0.7613 (tmmt) REVERT: S 110 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7857 (ttpt) REVERT: S 147 GLU cc_start: 0.7309 (pt0) cc_final: 0.6665 (pm20) REVERT: T 8 LYS cc_start: 0.8311 (tttt) cc_final: 0.7597 (tmmt) REVERT: T 110 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7853 (ttpt) REVERT: T 147 GLU cc_start: 0.7302 (pt0) cc_final: 0.6658 (pm20) REVERT: U 8 LYS cc_start: 0.8322 (tttt) cc_final: 0.7609 (tmmt) REVERT: U 110 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7850 (ttpt) REVERT: U 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6650 (pm20) REVERT: V 8 LYS cc_start: 0.8312 (tttt) cc_final: 0.7602 (tmmt) REVERT: V 110 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7848 (ttpt) REVERT: V 147 GLU cc_start: 0.7300 (pt0) cc_final: 0.6754 (pm20) REVERT: W 8 LYS cc_start: 0.8326 (tttt) cc_final: 0.7616 (tmmt) REVERT: W 110 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7848 (ttpt) REVERT: W 147 GLU cc_start: 0.7295 (pt0) cc_final: 0.6737 (pm20) REVERT: X 8 LYS cc_start: 0.8320 (tttt) cc_final: 0.7619 (tmmt) REVERT: X 110 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7856 (ttpt) REVERT: X 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6662 (pm20) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.7774 time to fit residues: 646.1205 Evaluate side-chains 720 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 65 ASN A 78 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS B 46 HIS B 65 ASN B 78 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS C 46 HIS C 65 ASN C 78 HIS C 107 HIS D 46 HIS D 65 ASN D 78 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS E 46 HIS E 65 ASN E 78 HIS E 107 HIS F 46 HIS F 65 ASN F 78 HIS F 107 HIS G 46 HIS G 65 ASN G 78 HIS G 107 HIS H 46 HIS H 65 ASN H 78 HIS ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS I 46 HIS I 65 ASN I 78 HIS I 107 HIS J 46 HIS J 65 ASN J 78 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 HIS K 46 HIS K 65 ASN K 78 HIS K 107 HIS L 46 HIS L 65 ASN L 78 HIS L 107 HIS M 46 HIS M 65 ASN M 78 HIS M 107 HIS N 46 HIS N 65 ASN N 78 HIS ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 HIS O 46 HIS O 65 ASN O 78 HIS ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 HIS P 46 HIS P 65 ASN P 78 HIS P 107 HIS Q 46 HIS Q 65 ASN Q 78 HIS ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 107 HIS R 46 HIS R 65 ASN R 78 HIS R 107 HIS S 46 HIS S 65 ASN S 78 HIS S 107 HIS T 46 HIS T 65 ASN T 78 HIS ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 107 HIS U 46 HIS U 65 ASN U 78 HIS U 107 HIS V 46 HIS V 65 ASN V 78 HIS ** V 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 107 HIS W 46 HIS W 65 ASN W 78 HIS W 107 HIS X 46 HIS X 65 ASN X 78 HIS X 107 HIS Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117925 restraints weight = 25061.966| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.97 r_work: 0.3156 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 32508 Z= 0.194 Angle : 0.510 5.497 43872 Z= 0.292 Chirality : 0.039 0.137 4704 Planarity : 0.003 0.025 5664 Dihedral : 3.875 13.986 4056 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.69 % Allowed : 7.59 % Favored : 91.72 % 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: 4.95 (0.12), residues: 3840 helix: 3.69 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.66 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG J 165 TYR 0.012 0.002 TYR C 157 PHE 0.022 0.003 PHE O 87 TRP 0.007 0.002 TRP C 122 HIS 0.009 0.002 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (32496) covalent geometry : angle 0.50986 / 0.29 (43848) SS BOND : bond 0.00283 / 0.18 ( 12) SS BOND : angle 0.90749 / 0.62 ( 24) hydrogen bonds : bond 0.07069 / 4.72 ( 2785) hydrogen bonds : angle 3.55156 / 2.64 ( 8355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 696 time to evaluate : 1.168 Fit side-chains REVERT: A 8 LYS cc_start: 0.8366 (tttt) cc_final: 0.7703 (tmmt) REVERT: A 147 GLU cc_start: 0.7238 (pt0) cc_final: 0.6557 (pm20) REVERT: B 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7735 (tmmt) REVERT: B 147 GLU cc_start: 0.7250 (pt0) cc_final: 0.6577 (pm20) REVERT: C 8 LYS cc_start: 0.8379 (tttt) cc_final: 0.7727 (tmmt) REVERT: C 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6569 (pm20) REVERT: D 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7728 (tmmt) REVERT: D 147 GLU cc_start: 0.7242 (pt0) cc_final: 0.6556 (pm20) REVERT: E 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7726 (tmmt) REVERT: E 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6567 (pm20) REVERT: F 8 LYS cc_start: 0.8381 (tttt) cc_final: 0.7732 (tmmt) REVERT: F 147 GLU cc_start: 0.7246 (pt0) cc_final: 0.6567 (pm20) REVERT: G 8 LYS cc_start: 0.8377 (tttt) cc_final: 0.7726 (tmmt) REVERT: G 147 GLU cc_start: 0.7246 (pt0) cc_final: 0.6569 (pm20) REVERT: H 8 LYS cc_start: 0.8381 (tttt) cc_final: 0.7726 (tmmt) REVERT: H 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6566 (pm20) REVERT: I 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7726 (tmmt) REVERT: I 147 GLU cc_start: 0.7249 (pt0) cc_final: 0.6574 (pm20) REVERT: J 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7727 (tmmt) REVERT: J 147 GLU cc_start: 0.7242 (pt0) cc_final: 0.6565 (pm20) REVERT: K 8 LYS cc_start: 0.8384 (tttt) cc_final: 0.7739 (tmmt) REVERT: K 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6571 (pm20) REVERT: L 8 LYS cc_start: 0.8385 (tttt) cc_final: 0.7728 (tmmt) REVERT: L 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6559 (pm20) REVERT: M 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7729 (tmmt) REVERT: M 147 GLU cc_start: 0.7245 (pt0) cc_final: 0.6568 (pm20) REVERT: N 8 LYS cc_start: 0.8383 (tttt) cc_final: 0.7731 (tmmt) REVERT: N 147 GLU cc_start: 0.7240 (pt0) cc_final: 0.6555 (pm20) REVERT: O 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7727 (tmmt) REVERT: O 147 GLU cc_start: 0.7253 (pt0) cc_final: 0.6572 (pm20) REVERT: P 8 LYS cc_start: 0.8377 (tttt) cc_final: 0.7720 (tmmt) REVERT: P 147 GLU cc_start: 0.7247 (pt0) cc_final: 0.6569 (pm20) REVERT: Q 8 LYS cc_start: 0.8377 (tttt) cc_final: 0.7728 (tmmt) REVERT: Q 147 GLU cc_start: 0.7251 (pt0) cc_final: 0.6572 (pm20) REVERT: R 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7721 (tmmt) REVERT: R 147 GLU cc_start: 0.7253 (pt0) cc_final: 0.6578 (pm20) REVERT: S 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7724 (tmmt) REVERT: S 147 GLU cc_start: 0.7248 (pt0) cc_final: 0.6566 (pm20) REVERT: T 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7718 (tmmt) REVERT: T 147 GLU cc_start: 0.7246 (pt0) cc_final: 0.6567 (pm20) REVERT: U 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7716 (tmmt) REVERT: U 147 GLU cc_start: 0.7245 (pt0) cc_final: 0.6565 (pm20) REVERT: V 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7724 (tmmt) REVERT: V 147 GLU cc_start: 0.7250 (pt0) cc_final: 0.6575 (pm20) REVERT: W 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7728 (tmmt) REVERT: W 147 GLU cc_start: 0.7238 (pt0) cc_final: 0.6557 (pm20) REVERT: X 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7732 (tmmt) REVERT: X 147 GLU cc_start: 0.7255 (pt0) cc_final: 0.6577 (pm20) outliers start: 24 outliers final: 0 residues processed: 696 average time/residue: 0.8283 time to fit residues: 663.8217 Evaluate side-chains 672 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 276 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 231 optimal weight: 0.0980 chunk 258 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS A 88 GLN A 103 ASN B 78 HIS B 88 GLN B 103 ASN C 78 HIS C 88 GLN C 103 ASN D 78 HIS D 88 GLN D 103 ASN E 78 HIS E 88 GLN E 103 ASN F 78 HIS F 88 GLN F 103 ASN G 78 HIS G 88 GLN G 103 ASN H 78 HIS H 88 GLN H 103 ASN I 78 HIS I 88 GLN I 103 ASN J 78 HIS J 88 GLN J 103 ASN K 78 HIS K 88 GLN K 103 ASN L 78 HIS L 88 GLN L 103 ASN M 78 HIS M 88 GLN M 103 ASN N 78 HIS N 88 GLN N 103 ASN O 78 HIS O 88 GLN O 103 ASN P 78 HIS P 88 GLN P 103 ASN Q 78 HIS Q 88 GLN Q 103 ASN R 78 HIS R 88 GLN R 103 ASN S 78 HIS S 88 GLN S 103 ASN T 78 HIS T 88 GLN T 103 ASN U 78 HIS U 88 GLN U 103 ASN V 78 HIS V 88 GLN V 103 ASN W 78 HIS W 88 GLN W 103 ASN X 78 HIS X 88 GLN X 103 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121275 restraints weight = 24874.457| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.98 r_work: 0.3203 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 32508 Z= 0.133 Angle : 0.402 4.303 43872 Z= 0.235 Chirality : 0.035 0.119 4704 Planarity : 0.002 0.013 5664 Dihedral : 3.573 11.337 4056 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.69 % Allowed : 8.33 % Favored : 90.98 % 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: 5.37 (0.12), residues: 3840 helix: 3.99 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.77 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 165 TYR 0.008 0.002 TYR C 123 PHE 0.017 0.002 PHE N 44 TRP 0.004 0.001 TRP L 122 HIS 0.005 0.001 HIS W 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (32496) covalent geometry : angle 0.40143 / 0.23 (43848) SS BOND : bond 0.00119 / 0.08 ( 12) SS BOND : angle 0.73581 / 0.50 ( 24) hydrogen bonds : bond 0.05731 / 3.82 ( 2785) hydrogen bonds : angle 3.31066 / 2.46 ( 8355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 720 time to evaluate : 1.214 Fit side-chains REVERT: A 8 LYS cc_start: 0.8264 (tttt) cc_final: 0.7581 (tmmt) REVERT: A 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6590 (pm20) REVERT: B 8 LYS cc_start: 0.8262 (tttt) cc_final: 0.7585 (tmmt) REVERT: B 147 GLU cc_start: 0.7216 (pt0) cc_final: 0.6669 (pm20) REVERT: C 8 LYS cc_start: 0.8260 (tttt) cc_final: 0.7576 (tmmt) REVERT: C 147 GLU cc_start: 0.7240 (pt0) cc_final: 0.6590 (pm20) REVERT: D 8 LYS cc_start: 0.8252 (tttt) cc_final: 0.7570 (tmmt) REVERT: D 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6586 (pm20) REVERT: E 8 LYS cc_start: 0.8261 (tttt) cc_final: 0.7580 (tmmt) REVERT: E 147 GLU cc_start: 0.7245 (pt0) cc_final: 0.6590 (pm20) REVERT: F 8 LYS cc_start: 0.8265 (tttt) cc_final: 0.7583 (tmmt) REVERT: F 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6591 (pm20) REVERT: G 8 LYS cc_start: 0.8263 (tttt) cc_final: 0.7582 (tmmt) REVERT: G 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6590 (pm20) REVERT: H 8 LYS cc_start: 0.8265 (tttt) cc_final: 0.7580 (tmmt) REVERT: H 147 GLU cc_start: 0.7240 (pt0) cc_final: 0.6664 (pm20) REVERT: I 8 LYS cc_start: 0.8258 (tttt) cc_final: 0.7574 (tmmt) REVERT: I 147 GLU cc_start: 0.7236 (pt0) cc_final: 0.6583 (pm20) REVERT: J 8 LYS cc_start: 0.8264 (tttt) cc_final: 0.7581 (tmmt) REVERT: J 147 GLU cc_start: 0.7219 (pt0) cc_final: 0.6669 (pm20) REVERT: K 8 LYS cc_start: 0.8260 (tttt) cc_final: 0.7582 (tmmt) REVERT: K 147 GLU cc_start: 0.7238 (pt0) cc_final: 0.6669 (pm20) REVERT: L 8 LYS cc_start: 0.8262 (tttt) cc_final: 0.7574 (tmmt) REVERT: L 147 GLU cc_start: 0.7247 (pt0) cc_final: 0.6589 (pm20) REVERT: M 8 LYS cc_start: 0.8257 (tttt) cc_final: 0.7576 (tmmt) REVERT: M 147 GLU cc_start: 0.7233 (pt0) cc_final: 0.6585 (pm20) REVERT: N 8 LYS cc_start: 0.8257 (tttt) cc_final: 0.7573 (tmmt) REVERT: N 147 GLU cc_start: 0.7240 (pt0) cc_final: 0.6585 (pm20) REVERT: O 8 LYS cc_start: 0.8255 (tttt) cc_final: 0.7569 (tmmt) REVERT: O 147 GLU cc_start: 0.7250 (pt0) cc_final: 0.6600 (pm20) REVERT: P 8 LYS cc_start: 0.8256 (tttt) cc_final: 0.7570 (tmmt) REVERT: P 147 GLU cc_start: 0.7246 (pt0) cc_final: 0.6596 (pm20) REVERT: Q 8 LYS cc_start: 0.8255 (tttt) cc_final: 0.7572 (tmmt) REVERT: Q 147 GLU cc_start: 0.7226 (pt0) cc_final: 0.6674 (pm20) REVERT: R 8 LYS cc_start: 0.8255 (tttt) cc_final: 0.7569 (tmmt) REVERT: R 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6595 (pm20) REVERT: S 8 LYS cc_start: 0.8254 (tttt) cc_final: 0.7570 (tmmt) REVERT: S 147 GLU cc_start: 0.7252 (pt0) cc_final: 0.6601 (pm20) REVERT: T 8 LYS cc_start: 0.8256 (tttt) cc_final: 0.7571 (tmmt) REVERT: T 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6593 (pm20) REVERT: U 8 LYS cc_start: 0.8257 (tttt) cc_final: 0.7567 (tmmt) REVERT: U 147 GLU cc_start: 0.7239 (pt0) cc_final: 0.6585 (pm20) REVERT: V 8 LYS cc_start: 0.8260 (tttt) cc_final: 0.7575 (tmmt) REVERT: V 147 GLU cc_start: 0.7234 (pt0) cc_final: 0.6585 (pm20) REVERT: W 8 LYS cc_start: 0.8255 (tttt) cc_final: 0.7571 (tmmt) REVERT: W 147 GLU cc_start: 0.7235 (pt0) cc_final: 0.6655 (pm20) REVERT: X 8 LYS cc_start: 0.8257 (tttt) cc_final: 0.7579 (tmmt) REVERT: X 147 GLU cc_start: 0.7243 (pt0) cc_final: 0.6596 (pm20) outliers start: 24 outliers final: 0 residues processed: 744 average time/residue: 0.7893 time to fit residues: 681.1569 Evaluate side-chains 696 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 382 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117676 restraints weight = 24767.190| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 0.98 r_work: 0.3152 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 32508 Z= 0.201 Angle : 0.515 5.736 43872 Z= 0.294 Chirality : 0.039 0.137 4704 Planarity : 0.003 0.028 5664 Dihedral : 3.844 13.890 4056 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % 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: 5.06 (0.12), residues: 3840 helix: 3.76 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG G 165 TYR 0.012 0.003 TYR C 157 PHE 0.023 0.004 PHE U 87 TRP 0.007 0.002 TRP A 122 HIS 0.008 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (32496) covalent geometry : angle 0.51447 / 0.29 (43848) SS BOND : bond 0.00345 / 0.22 ( 12) SS BOND : angle 0.81404 / 0.56 ( 24) hydrogen bonds : bond 0.07124 / 4.75 ( 2785) hydrogen bonds : angle 3.53415 / 2.63 ( 8355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.316 Fit side-chains REVERT: A 8 LYS cc_start: 0.8358 (tttt) cc_final: 0.7688 (tmmt) REVERT: A 147 GLU cc_start: 0.7255 (pt0) cc_final: 0.6544 (pm20) REVERT: B 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7682 (tmmt) REVERT: B 147 GLU cc_start: 0.7257 (pt0) cc_final: 0.6553 (pm20) REVERT: C 8 LYS cc_start: 0.8339 (tttt) cc_final: 0.7675 (tmmt) REVERT: C 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6554 (pm20) REVERT: D 8 LYS cc_start: 0.8338 (tttt) cc_final: 0.7671 (tmmt) REVERT: D 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6551 (pm20) REVERT: E 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7678 (tmmt) REVERT: E 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6555 (pm20) REVERT: F 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7677 (tmmt) REVERT: F 147 GLU cc_start: 0.7261 (pt0) cc_final: 0.6557 (pm20) REVERT: G 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7679 (tmmt) REVERT: G 147 GLU cc_start: 0.7261 (pt0) cc_final: 0.6553 (pm20) REVERT: H 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7680 (tmmt) REVERT: H 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6553 (pm20) REVERT: I 8 LYS cc_start: 0.8347 (tttt) cc_final: 0.7677 (tmmt) REVERT: I 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6560 (pm20) REVERT: J 8 LYS cc_start: 0.8346 (tttt) cc_final: 0.7677 (tmmt) REVERT: J 147 GLU cc_start: 0.7258 (pt0) cc_final: 0.6553 (pm20) REVERT: K 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7685 (tmmt) REVERT: K 147 GLU cc_start: 0.7258 (pt0) cc_final: 0.6557 (pm20) REVERT: L 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7672 (tmmt) REVERT: L 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6557 (pm20) REVERT: M 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7681 (tmmt) REVERT: M 147 GLU cc_start: 0.7253 (pt0) cc_final: 0.6554 (pm20) REVERT: N 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7681 (tmmt) REVERT: N 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6549 (pm20) REVERT: O 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7670 (tmmt) REVERT: O 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6562 (pm20) REVERT: P 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7670 (tmmt) REVERT: P 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6556 (pm20) REVERT: Q 8 LYS cc_start: 0.8336 (tttt) cc_final: 0.7669 (tmmt) REVERT: Q 147 GLU cc_start: 0.7270 (pt0) cc_final: 0.6561 (pm20) REVERT: R 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7669 (tmmt) REVERT: R 147 GLU cc_start: 0.7258 (pt0) cc_final: 0.6551 (pm20) REVERT: S 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7670 (tmmt) REVERT: S 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6556 (pm20) REVERT: T 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7671 (tmmt) REVERT: T 147 GLU cc_start: 0.7267 (pt0) cc_final: 0.6561 (pm20) REVERT: U 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7672 (tmmt) REVERT: U 147 GLU cc_start: 0.7261 (pt0) cc_final: 0.6561 (pm20) REVERT: V 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7676 (tmmt) REVERT: V 147 GLU cc_start: 0.7259 (pt0) cc_final: 0.6552 (pm20) REVERT: W 8 LYS cc_start: 0.8346 (tttt) cc_final: 0.7678 (tmmt) REVERT: W 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6553 (pm20) REVERT: X 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7684 (tmmt) REVERT: X 147 GLU cc_start: 0.7266 (pt0) cc_final: 0.6563 (pm20) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.8317 time to fit residues: 666.4997 Evaluate side-chains 696 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 284 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 chunk 286 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS A 88 GLN A 148 ASN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 78 HIS S 88 GLN S 148 ASN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117899 restraints weight = 24838.639| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.96 r_work: 0.3157 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 32508 Z= 0.197 Angle : 0.510 5.570 43872 Z= 0.293 Chirality : 0.039 0.135 4704 Planarity : 0.003 0.028 5664 Dihedral : 3.865 14.048 4056 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.03 % Allowed : 10.23 % Favored : 89.74 % 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: 5.00 (0.12), residues: 3840 helix: 3.73 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG H 165 TYR 0.012 0.002 TYR V 157 PHE 0.022 0.003 PHE O 87 TRP 0.007 0.002 TRP X 122 HIS 0.008 0.002 HIS R 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (32496) covalent geometry : angle 0.51016 / 0.29 (43848) SS BOND : bond 0.00306 / 0.20 ( 12) SS BOND : angle 0.87738 / 0.60 ( 24) hydrogen bonds : bond 0.07053 / 4.71 ( 2785) hydrogen bonds : angle 3.52937 / 2.62 ( 8355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 698 time to evaluate : 1.208 Fit side-chains REVERT: A 8 LYS cc_start: 0.8366 (tttt) cc_final: 0.7718 (tmmt) REVERT: A 147 GLU cc_start: 0.7275 (pt0) cc_final: 0.6584 (pm20) REVERT: B 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7732 (tmmt) REVERT: B 147 GLU cc_start: 0.7285 (pt0) cc_final: 0.6604 (pm20) REVERT: C 8 LYS cc_start: 0.8373 (tttt) cc_final: 0.7730 (tmmt) REVERT: C 147 GLU cc_start: 0.7269 (pt0) cc_final: 0.6640 (pm20) REVERT: D 8 LYS cc_start: 0.8374 (tttt) cc_final: 0.7726 (tmmt) REVERT: D 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6648 (pm20) REVERT: E 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7733 (tmmt) REVERT: E 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6656 (pm20) REVERT: F 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7733 (tmmt) REVERT: F 147 GLU cc_start: 0.7277 (pt0) cc_final: 0.6593 (pm20) REVERT: G 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7735 (tmmt) REVERT: G 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6600 (pm20) REVERT: H 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7727 (tmmt) REVERT: H 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6595 (pm20) REVERT: I 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7727 (tmmt) REVERT: I 147 GLU cc_start: 0.7282 (pt0) cc_final: 0.6596 (pm20) REVERT: J 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7731 (tmmt) REVERT: J 147 GLU cc_start: 0.7280 (pt0) cc_final: 0.6596 (pm20) REVERT: K 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7734 (tmmt) REVERT: K 147 GLU cc_start: 0.7284 (pt0) cc_final: 0.6604 (pm20) REVERT: L 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7730 (tmmt) REVERT: L 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6639 (pm20) REVERT: M 8 LYS cc_start: 0.8374 (tttt) cc_final: 0.7729 (tmmt) REVERT: M 147 GLU cc_start: 0.7270 (pt0) cc_final: 0.6584 (pm20) REVERT: N 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7732 (tmmt) REVERT: N 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6639 (pm20) REVERT: O 8 LYS cc_start: 0.8367 (tttt) cc_final: 0.7716 (tmmt) REVERT: O 147 GLU cc_start: 0.7289 (pt0) cc_final: 0.6657 (pm20) REVERT: P 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7725 (tmmt) REVERT: P 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6649 (pm20) REVERT: Q 8 LYS cc_start: 0.8368 (tttt) cc_final: 0.7720 (tmmt) REVERT: Q 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6604 (pm20) REVERT: R 8 LYS cc_start: 0.8374 (tttt) cc_final: 0.7719 (tmmt) REVERT: R 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6596 (pm20) REVERT: S 8 LYS cc_start: 0.8368 (tttt) cc_final: 0.7718 (tmmt) REVERT: S 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6595 (pm20) REVERT: T 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7720 (tmmt) REVERT: T 147 GLU cc_start: 0.7282 (pt0) cc_final: 0.6650 (pm20) REVERT: U 8 LYS cc_start: 0.8377 (tttt) cc_final: 0.7722 (tmmt) REVERT: U 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6581 (pm20) REVERT: V 8 LYS cc_start: 0.8373 (tttt) cc_final: 0.7728 (tmmt) REVERT: V 147 GLU cc_start: 0.7276 (pt0) cc_final: 0.6589 (pm20) REVERT: W 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7728 (tmmt) REVERT: W 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6595 (pm20) REVERT: X 8 LYS cc_start: 0.8373 (tttt) cc_final: 0.7732 (tmmt) REVERT: X 147 GLU cc_start: 0.7284 (pt0) cc_final: 0.6657 (pm20) outliers start: 1 outliers final: 0 residues processed: 698 average time/residue: 0.8294 time to fit residues: 666.7976 Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 293 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 289 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 65 ASN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117946 restraints weight = 24807.643| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.98 r_work: 0.3155 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 32508 Z= 0.193 Angle : 0.504 5.596 43872 Z= 0.289 Chirality : 0.039 0.134 4704 Planarity : 0.003 0.026 5664 Dihedral : 3.856 13.923 4056 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.66 % Allowed : 10.32 % Favored : 89.02 % 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: 5.03 (0.12), residues: 3840 helix: 3.74 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 165 TYR 0.012 0.002 TYR V 157 PHE 0.021 0.003 PHE L 87 TRP 0.007 0.002 TRP X 122 HIS 0.008 0.002 HIS Q 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (32496) covalent geometry : angle 0.50386 / 0.29 (43848) SS BOND : bond 0.00282 / 0.18 ( 12) SS BOND : angle 0.89943 / 0.62 ( 24) hydrogen bonds : bond 0.06992 / 4.67 ( 2785) hydrogen bonds : angle 3.52268 / 2.62 ( 8355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 722 time to evaluate : 1.359 Fit side-chains REVERT: A 8 LYS cc_start: 0.8320 (tttt) cc_final: 0.7663 (tmmt) REVERT: A 147 GLU cc_start: 0.7244 (pt0) cc_final: 0.6597 (pm20) REVERT: B 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7690 (tmmt) REVERT: B 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6623 (pm20) REVERT: C 8 LYS cc_start: 0.8344 (tttt) cc_final: 0.7681 (tmmt) REVERT: C 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6616 (pm20) REVERT: D 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7679 (tmmt) REVERT: D 147 GLU cc_start: 0.7266 (pt0) cc_final: 0.6620 (pm20) REVERT: E 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7681 (tmmt) REVERT: E 147 GLU cc_start: 0.7264 (pt0) cc_final: 0.6621 (pm20) REVERT: F 8 LYS cc_start: 0.8340 (tttt) cc_final: 0.7678 (tmmt) REVERT: F 147 GLU cc_start: 0.7258 (pt0) cc_final: 0.6617 (pm20) REVERT: G 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7678 (tmmt) REVERT: G 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6623 (pm20) REVERT: H 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7679 (tmmt) REVERT: H 147 GLU cc_start: 0.7268 (pt0) cc_final: 0.6627 (pm20) REVERT: I 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7675 (tmmt) REVERT: I 147 GLU cc_start: 0.7266 (pt0) cc_final: 0.6623 (pm20) REVERT: J 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7679 (tmmt) REVERT: J 147 GLU cc_start: 0.7252 (pt0) cc_final: 0.6611 (pm20) REVERT: K 8 LYS cc_start: 0.8346 (tttt) cc_final: 0.7688 (tmmt) REVERT: K 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6628 (pm20) REVERT: L 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7675 (tmmt) REVERT: L 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6630 (pm20) REVERT: M 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7679 (tmmt) REVERT: M 147 GLU cc_start: 0.7256 (pt0) cc_final: 0.6613 (pm20) REVERT: N 8 LYS cc_start: 0.8346 (tttt) cc_final: 0.7684 (tmmt) REVERT: N 147 GLU cc_start: 0.7263 (pt0) cc_final: 0.6617 (pm20) REVERT: O 8 LYS cc_start: 0.8335 (tttt) cc_final: 0.7669 (tmmt) REVERT: O 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6627 (pm20) REVERT: P 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7673 (tmmt) REVERT: P 147 GLU cc_start: 0.7263 (pt0) cc_final: 0.6618 (pm20) REVERT: Q 8 LYS cc_start: 0.8339 (tttt) cc_final: 0.7677 (tmmt) REVERT: Q 147 GLU cc_start: 0.7273 (pt0) cc_final: 0.6629 (pm20) REVERT: R 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7672 (tmmt) REVERT: R 147 GLU cc_start: 0.7269 (pt0) cc_final: 0.6625 (pm20) REVERT: S 8 LYS cc_start: 0.8337 (tttt) cc_final: 0.7673 (tmmt) REVERT: S 147 GLU cc_start: 0.7255 (pt0) cc_final: 0.6609 (pm20) REVERT: T 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7672 (tmmt) REVERT: T 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6620 (pm20) REVERT: U 8 LYS cc_start: 0.8339 (tttt) cc_final: 0.7671 (tmmt) REVERT: U 147 GLU cc_start: 0.7265 (pt0) cc_final: 0.6618 (pm20) REVERT: V 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7677 (tmmt) REVERT: V 147 GLU cc_start: 0.7257 (pt0) cc_final: 0.6612 (pm20) REVERT: W 8 LYS cc_start: 0.8342 (tttt) cc_final: 0.7680 (tmmt) REVERT: W 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6624 (pm20) REVERT: X 8 LYS cc_start: 0.8341 (tttt) cc_final: 0.7683 (tmmt) REVERT: X 147 GLU cc_start: 0.7260 (pt0) cc_final: 0.6621 (pm20) outliers start: 23 outliers final: 0 residues processed: 722 average time/residue: 0.8343 time to fit residues: 695.8429 Evaluate side-chains 674 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 53 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 380 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 65 ASN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118215 restraints weight = 24915.422| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.97 r_work: 0.3158 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 32508 Z= 0.190 Angle : 0.503 5.605 43872 Z= 0.288 Chirality : 0.039 0.134 4704 Planarity : 0.003 0.026 5664 Dihedral : 3.850 13.882 4056 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % 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: 5.04 (0.12), residues: 3840 helix: 3.74 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 165 TYR 0.012 0.002 TYR C 157 PHE 0.021 0.003 PHE O 87 TRP 0.007 0.002 TRP F 122 HIS 0.009 0.002 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (32496) covalent geometry : angle 0.50227 / 0.29 (43848) SS BOND : bond 0.00271 / 0.18 ( 12) SS BOND : angle 0.89588 / 0.61 ( 24) hydrogen bonds : bond 0.06943 / 4.63 ( 2785) hydrogen bonds : angle 3.52127 / 2.61 ( 8355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.376 Fit side-chains REVERT: A 8 LYS cc_start: 0.8357 (tttt) cc_final: 0.7712 (tmmt) REVERT: A 147 GLU cc_start: 0.7276 (pt0) cc_final: 0.6636 (pm20) REVERT: B 8 LYS cc_start: 0.8384 (tttt) cc_final: 0.7741 (tmmt) REVERT: B 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6659 (pm20) REVERT: C 8 LYS cc_start: 0.8372 (tttt) cc_final: 0.7725 (tmmt) REVERT: C 147 GLU cc_start: 0.7299 (pt0) cc_final: 0.6665 (pm20) REVERT: D 8 LYS cc_start: 0.8370 (tttt) cc_final: 0.7724 (tmmt) REVERT: D 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6665 (pm20) REVERT: E 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7726 (tmmt) REVERT: E 147 GLU cc_start: 0.7304 (pt0) cc_final: 0.6669 (pm20) REVERT: F 8 LYS cc_start: 0.8373 (tttt) cc_final: 0.7725 (tmmt) REVERT: F 147 GLU cc_start: 0.7303 (pt0) cc_final: 0.6670 (pm20) REVERT: G 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7727 (tmmt) REVERT: G 147 GLU cc_start: 0.7305 (pt0) cc_final: 0.6671 (pm20) REVERT: H 8 LYS cc_start: 0.8383 (tttt) cc_final: 0.7731 (tmmt) REVERT: H 147 GLU cc_start: 0.7295 (pt0) cc_final: 0.6661 (pm20) REVERT: I 8 LYS cc_start: 0.8374 (tttt) cc_final: 0.7724 (tmmt) REVERT: I 147 GLU cc_start: 0.7301 (pt0) cc_final: 0.6666 (pm20) REVERT: J 8 LYS cc_start: 0.8373 (tttt) cc_final: 0.7724 (tmmt) REVERT: J 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6653 (pm20) REVERT: K 8 LYS cc_start: 0.8386 (tttt) cc_final: 0.7744 (tmmt) REVERT: K 147 GLU cc_start: 0.7294 (pt0) cc_final: 0.6663 (pm20) REVERT: L 8 LYS cc_start: 0.8381 (tttt) cc_final: 0.7728 (tmmt) REVERT: L 147 GLU cc_start: 0.7303 (pt0) cc_final: 0.6663 (pm20) REVERT: M 8 LYS cc_start: 0.8374 (tttt) cc_final: 0.7727 (tmmt) REVERT: M 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6652 (pm20) REVERT: N 8 LYS cc_start: 0.8382 (tttt) cc_final: 0.7734 (tmmt) REVERT: N 147 GLU cc_start: 0.7303 (pt0) cc_final: 0.6665 (pm20) REVERT: O 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7726 (tmmt) REVERT: O 147 GLU cc_start: 0.7307 (pt0) cc_final: 0.6670 (pm20) REVERT: P 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7726 (tmmt) REVERT: P 147 GLU cc_start: 0.7305 (pt0) cc_final: 0.6669 (pm20) REVERT: Q 8 LYS cc_start: 0.8372 (tttt) cc_final: 0.7728 (tmmt) REVERT: Q 147 GLU cc_start: 0.7294 (pt0) cc_final: 0.6656 (pm20) REVERT: R 8 LYS cc_start: 0.8379 (tttt) cc_final: 0.7724 (tmmt) REVERT: R 147 GLU cc_start: 0.7305 (pt0) cc_final: 0.6669 (pm20) REVERT: S 8 LYS cc_start: 0.8376 (tttt) cc_final: 0.7728 (tmmt) REVERT: S 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6649 (pm20) REVERT: T 8 LYS cc_start: 0.8378 (tttt) cc_final: 0.7724 (tmmt) REVERT: T 147 GLU cc_start: 0.7306 (pt0) cc_final: 0.6670 (pm20) REVERT: U 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7723 (tmmt) REVERT: U 147 GLU cc_start: 0.7292 (pt0) cc_final: 0.6653 (pm20) REVERT: V 8 LYS cc_start: 0.8375 (tttt) cc_final: 0.7723 (tmmt) REVERT: V 147 GLU cc_start: 0.7296 (pt0) cc_final: 0.6660 (pm20) REVERT: W 8 LYS cc_start: 0.8379 (tttt) cc_final: 0.7731 (tmmt) REVERT: W 147 GLU cc_start: 0.7300 (pt0) cc_final: 0.6662 (pm20) REVERT: X 8 LYS cc_start: 0.8377 (tttt) cc_final: 0.7734 (tmmt) REVERT: X 147 GLU cc_start: 0.7299 (pt0) cc_final: 0.6668 (pm20) outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 0.8450 time to fit residues: 679.1999 Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 151 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 383 optimal weight: 2.9990 chunk 294 optimal weight: 0.1980 chunk 184 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 65 ASN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118177 restraints weight = 24889.320| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.98 r_work: 0.3158 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 32508 Z= 0.187 Angle : 0.502 5.738 43872 Z= 0.287 Chirality : 0.039 0.132 4704 Planarity : 0.003 0.025 5664 Dihedral : 3.841 13.805 4056 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % 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: 5.07 (0.12), residues: 3840 helix: 3.76 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 165 TYR 0.012 0.002 TYR F 157 PHE 0.021 0.003 PHE S 87 TRP 0.006 0.002 TRP O 122 HIS 0.008 0.002 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (32496) covalent geometry : angle 0.50204 / 0.29 (43848) SS BOND : bond 0.00263 / 0.17 ( 12) SS BOND : angle 0.89476 / 0.61 ( 24) hydrogen bonds : bond 0.06910 / 4.61 ( 2785) hydrogen bonds : angle 3.51488 / 2.61 ( 8355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.105 Fit side-chains REVERT: A 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7684 (tmmt) REVERT: A 147 GLU cc_start: 0.7222 (pt0) cc_final: 0.6585 (pm20) REVERT: B 8 LYS cc_start: 0.8355 (tttt) cc_final: 0.7698 (tmmt) REVERT: B 147 GLU cc_start: 0.7269 (pt0) cc_final: 0.6630 (pm20) REVERT: C 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7684 (tmmt) REVERT: C 147 GLU cc_start: 0.7282 (pt0) cc_final: 0.6637 (pm20) REVERT: D 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7683 (tmmt) REVERT: D 147 GLU cc_start: 0.7279 (pt0) cc_final: 0.6632 (pm20) REVERT: E 8 LYS cc_start: 0.8355 (tttt) cc_final: 0.7687 (tmmt) REVERT: E 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6637 (pm20) REVERT: F 8 LYS cc_start: 0.8347 (tttt) cc_final: 0.7684 (tmmt) REVERT: F 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6637 (pm20) REVERT: G 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7683 (tmmt) REVERT: G 147 GLU cc_start: 0.7279 (pt0) cc_final: 0.6636 (pm20) REVERT: H 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7687 (tmmt) REVERT: H 147 GLU cc_start: 0.7266 (pt0) cc_final: 0.6624 (pm20) REVERT: I 8 LYS cc_start: 0.8353 (tttt) cc_final: 0.7682 (tmmt) REVERT: I 147 GLU cc_start: 0.7282 (pt0) cc_final: 0.6638 (pm20) REVERT: J 8 LYS cc_start: 0.8346 (tttt) cc_final: 0.7682 (tmmt) REVERT: J 147 GLU cc_start: 0.7263 (pt0) cc_final: 0.6620 (pm20) REVERT: K 8 LYS cc_start: 0.8352 (tttt) cc_final: 0.7694 (tmmt) REVERT: K 147 GLU cc_start: 0.7262 (pt0) cc_final: 0.6623 (pm20) REVERT: L 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7685 (tmmt) REVERT: L 147 GLU cc_start: 0.7247 (pt0) cc_final: 0.6608 (pm20) REVERT: M 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7685 (tmmt) REVERT: M 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6634 (pm20) REVERT: N 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7685 (tmmt) REVERT: N 147 GLU cc_start: 0.7280 (pt0) cc_final: 0.6633 (pm20) REVERT: O 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7677 (tmmt) REVERT: O 147 GLU cc_start: 0.7285 (pt0) cc_final: 0.6640 (pm20) REVERT: P 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7679 (tmmt) REVERT: P 147 GLU cc_start: 0.7281 (pt0) cc_final: 0.6637 (pm20) REVERT: Q 8 LYS cc_start: 0.8343 (tttt) cc_final: 0.7680 (tmmt) REVERT: Q 147 GLU cc_start: 0.7270 (pt0) cc_final: 0.6625 (pm20) REVERT: R 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7679 (tmmt) REVERT: R 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6643 (pm20) REVERT: S 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7680 (tmmt) REVERT: S 147 GLU cc_start: 0.7232 (pt0) cc_final: 0.6596 (pm20) REVERT: T 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7678 (tmmt) REVERT: T 147 GLU cc_start: 0.7283 (pt0) cc_final: 0.6639 (pm20) REVERT: U 8 LYS cc_start: 0.8347 (tttt) cc_final: 0.7678 (tmmt) REVERT: U 147 GLU cc_start: 0.7279 (pt0) cc_final: 0.6632 (pm20) REVERT: V 8 LYS cc_start: 0.8347 (tttt) cc_final: 0.7680 (tmmt) REVERT: V 147 GLU cc_start: 0.7277 (pt0) cc_final: 0.6632 (pm20) REVERT: W 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7681 (tmmt) REVERT: W 147 GLU cc_start: 0.7269 (pt0) cc_final: 0.6621 (pm20) REVERT: X 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7691 (tmmt) REVERT: X 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6637 (pm20) outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 0.7774 time to fit residues: 624.9333 Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 238 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 275 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 354 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 88 GLN C 78 HIS ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 HIS H 88 GLN I 78 HIS ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 HIS J 88 GLN K 78 HIS ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 HIS L 88 GLN M 78 HIS ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 HIS ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS ** R 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN S 78 HIS ** S 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 HIS T 88 GLN U 78 HIS ** U 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 HIS V 88 GLN W 78 HIS ** W 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 HIS ** X 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119349 restraints weight = 24796.889| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 0.98 r_work: 0.3175 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 32508 Z= 0.160 Angle : 0.461 5.066 43872 Z= 0.265 Chirality : 0.037 0.128 4704 Planarity : 0.003 0.020 5664 Dihedral : 3.735 13.002 4056 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.40 % Allowed : 10.57 % Favored : 89.02 % 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: 5.19 (0.12), residues: 3840 helix: 3.85 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.010 0.002 TYR C 157 PHE 0.019 0.003 PHE A 44 TRP 0.006 0.002 TRP G 122 HIS 0.007 0.001 HIS F 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (32496) covalent geometry : angle 0.46097 / 0.27 (43848) SS BOND : bond 0.00168 / 0.11 ( 12) SS BOND : angle 0.84911 / 0.58 ( 24) hydrogen bonds : bond 0.06426 / 4.29 ( 2785) hydrogen bonds : angle 3.43514 / 2.55 ( 8355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 698 time to evaluate : 1.278 Fit side-chains REVERT: A 8 LYS cc_start: 0.8296 (tttt) cc_final: 0.7626 (tmmt) REVERT: A 147 GLU cc_start: 0.7284 (pt0) cc_final: 0.6618 (pm20) REVERT: B 8 LYS cc_start: 0.8307 (tttt) cc_final: 0.7660 (tmmt) REVERT: B 147 GLU cc_start: 0.7288 (pt0) cc_final: 0.6630 (pm20) REVERT: C 8 LYS cc_start: 0.8307 (tttt) cc_final: 0.7654 (tmmt) REVERT: C 147 GLU cc_start: 0.7288 (pt0) cc_final: 0.6631 (pm20) REVERT: D 8 LYS cc_start: 0.8304 (tttt) cc_final: 0.7650 (tmmt) REVERT: D 147 GLU cc_start: 0.7290 (pt0) cc_final: 0.6631 (pm20) REVERT: E 8 LYS cc_start: 0.8314 (tttt) cc_final: 0.7657 (tmmt) REVERT: E 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6632 (pm20) REVERT: F 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7655 (tmmt) REVERT: F 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6631 (pm20) REVERT: G 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7653 (tmmt) REVERT: G 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6638 (pm20) REVERT: H 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7658 (tmmt) REVERT: H 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6627 (pm20) REVERT: I 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7654 (tmmt) REVERT: I 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6633 (pm20) REVERT: J 8 LYS cc_start: 0.8311 (tttt) cc_final: 0.7658 (tmmt) REVERT: J 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6627 (pm20) REVERT: K 8 LYS cc_start: 0.8305 (tttt) cc_final: 0.7659 (tmmt) REVERT: K 147 GLU cc_start: 0.7288 (pt0) cc_final: 0.6631 (pm20) REVERT: L 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7651 (tmmt) REVERT: L 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6627 (pm20) REVERT: M 8 LYS cc_start: 0.8306 (tttt) cc_final: 0.7652 (tmmt) REVERT: M 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6633 (pm20) REVERT: N 8 LYS cc_start: 0.8306 (tttt) cc_final: 0.7652 (tmmt) REVERT: N 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6627 (pm20) REVERT: O 8 LYS cc_start: 0.8297 (tttt) cc_final: 0.7641 (tmmt) REVERT: O 147 GLU cc_start: 0.7297 (pt0) cc_final: 0.6637 (pm20) REVERT: P 8 LYS cc_start: 0.8303 (tttt) cc_final: 0.7643 (tmmt) REVERT: P 147 GLU cc_start: 0.7284 (pt0) cc_final: 0.6626 (pm20) REVERT: Q 8 LYS cc_start: 0.8300 (tttt) cc_final: 0.7643 (tmmt) REVERT: Q 147 GLU cc_start: 0.7297 (pt0) cc_final: 0.6635 (pm20) REVERT: R 8 LYS cc_start: 0.8302 (tttt) cc_final: 0.7643 (tmmt) REVERT: R 147 GLU cc_start: 0.7287 (pt0) cc_final: 0.6629 (pm20) REVERT: S 8 LYS cc_start: 0.8294 (tttt) cc_final: 0.7638 (tmmt) REVERT: S 147 GLU cc_start: 0.7293 (pt0) cc_final: 0.6630 (pm20) REVERT: T 8 LYS cc_start: 0.8302 (tttt) cc_final: 0.7645 (tmmt) REVERT: T 147 GLU cc_start: 0.7291 (pt0) cc_final: 0.6630 (pm20) REVERT: U 8 LYS cc_start: 0.8310 (tttt) cc_final: 0.7650 (tmmt) REVERT: U 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6625 (pm20) REVERT: V 8 LYS cc_start: 0.8303 (tttt) cc_final: 0.7647 (tmmt) REVERT: V 147 GLU cc_start: 0.7286 (pt0) cc_final: 0.6629 (pm20) REVERT: W 8 LYS cc_start: 0.8304 (tttt) cc_final: 0.7653 (tmmt) REVERT: W 147 GLU cc_start: 0.7292 (pt0) cc_final: 0.6628 (pm20) REVERT: X 8 LYS cc_start: 0.8305 (tttt) cc_final: 0.7656 (tmmt) REVERT: X 147 GLU cc_start: 0.7285 (pt0) cc_final: 0.6629 (pm20) outliers start: 14 outliers final: 0 residues processed: 712 average time/residue: 0.8131 time to fit residues: 668.2454 Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 303 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 316 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 65 ASN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118036 restraints weight = 24691.641| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.98 r_work: 0.3155 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 32508 Z= 0.194 Angle : 0.518 6.151 43872 Z= 0.294 Chirality : 0.039 0.139 4704 Planarity : 0.003 0.027 5664 Dihedral : 3.860 13.909 4056 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % 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: 5.01 (0.12), residues: 3840 helix: 3.73 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG U 165 TYR 0.012 0.002 TYR P 157 PHE 0.022 0.003 PHE O 87 TRP 0.007 0.002 TRP F 122 HIS 0.009 0.002 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (32496) covalent geometry : angle 0.51747 / 0.29 (43848) SS BOND : bond 0.00312 / 0.20 ( 12) SS BOND : angle 0.87983 / 0.60 ( 24) hydrogen bonds : bond 0.07033 / 4.69 ( 2785) hydrogen bonds : angle 3.52622 / 2.62 ( 8355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.368 Fit side-chains REVERT: A 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7685 (tmmt) REVERT: A 147 GLU cc_start: 0.7232 (pt0) cc_final: 0.6529 (pm20) REVERT: B 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7694 (tmmt) REVERT: B 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6565 (pm20) REVERT: C 8 LYS cc_start: 0.8353 (tttt) cc_final: 0.7688 (tmmt) REVERT: C 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6626 (pm20) REVERT: D 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7685 (tmmt) REVERT: D 147 GLU cc_start: 0.7275 (pt0) cc_final: 0.6628 (pm20) REVERT: E 8 LYS cc_start: 0.8356 (tttt) cc_final: 0.7690 (tmmt) REVERT: E 147 GLU cc_start: 0.7243 (pt0) cc_final: 0.6609 (pm20) REVERT: F 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7689 (tmmt) REVERT: F 147 GLU cc_start: 0.7269 (pt0) cc_final: 0.6628 (pm20) REVERT: G 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7688 (tmmt) REVERT: G 147 GLU cc_start: 0.7275 (pt0) cc_final: 0.6631 (pm20) REVERT: H 8 LYS cc_start: 0.8359 (tttt) cc_final: 0.7693 (tmmt) REVERT: H 147 GLU cc_start: 0.7272 (pt0) cc_final: 0.6564 (pm20) REVERT: I 8 LYS cc_start: 0.8353 (tttt) cc_final: 0.7686 (tmmt) REVERT: I 147 GLU cc_start: 0.7267 (pt0) cc_final: 0.6624 (pm20) REVERT: J 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7689 (tmmt) REVERT: J 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6563 (pm20) REVERT: K 8 LYS cc_start: 0.8355 (tttt) cc_final: 0.7697 (tmmt) REVERT: K 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6566 (pm20) REVERT: L 8 LYS cc_start: 0.8354 (tttt) cc_final: 0.7684 (tmmt) REVERT: L 147 GLU cc_start: 0.7237 (pt0) cc_final: 0.6596 (pm20) REVERT: M 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7687 (tmmt) REVERT: M 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6627 (pm20) REVERT: N 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7684 (tmmt) REVERT: N 147 GLU cc_start: 0.7270 (pt0) cc_final: 0.6623 (pm20) REVERT: O 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7680 (tmmt) REVERT: O 147 GLU cc_start: 0.7273 (pt0) cc_final: 0.6626 (pm20) REVERT: P 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7683 (tmmt) REVERT: P 147 GLU cc_start: 0.7277 (pt0) cc_final: 0.6630 (pm20) REVERT: Q 8 LYS cc_start: 0.8347 (tttt) cc_final: 0.7683 (tmmt) REVERT: Q 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6565 (pm20) REVERT: R 8 LYS cc_start: 0.8350 (tttt) cc_final: 0.7681 (tmmt) REVERT: R 147 GLU cc_start: 0.7273 (pt0) cc_final: 0.6627 (pm20) REVERT: S 8 LYS cc_start: 0.8345 (tttt) cc_final: 0.7680 (tmmt) REVERT: S 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6539 (pm20) REVERT: T 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7680 (tmmt) REVERT: T 147 GLU cc_start: 0.7278 (pt0) cc_final: 0.6631 (pm20) REVERT: U 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7679 (tmmt) REVERT: U 147 GLU cc_start: 0.7270 (pt0) cc_final: 0.6619 (pm20) REVERT: V 8 LYS cc_start: 0.8349 (tttt) cc_final: 0.7682 (tmmt) REVERT: V 147 GLU cc_start: 0.7273 (pt0) cc_final: 0.6629 (pm20) REVERT: W 8 LYS cc_start: 0.8348 (tttt) cc_final: 0.7683 (tmmt) REVERT: W 147 GLU cc_start: 0.7276 (pt0) cc_final: 0.6562 (pm20) REVERT: X 8 LYS cc_start: 0.8351 (tttt) cc_final: 0.7688 (tmmt) REVERT: X 147 GLU cc_start: 0.7271 (pt0) cc_final: 0.6628 (pm20) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.8392 time to fit residues: 649.6159 Evaluate side-chains 674 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 119 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 295 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 78 HIS A 88 GLN B 78 HIS B 88 GLN C 78 HIS C 88 GLN D 78 HIS D 88 GLN E 78 HIS E 88 GLN F 78 HIS F 88 GLN G 78 HIS G 88 GLN H 78 HIS H 88 GLN I 78 HIS I 88 GLN J 78 HIS J 88 GLN K 78 HIS K 88 GLN L 78 HIS L 88 GLN M 78 HIS M 88 GLN N 78 HIS N 88 GLN O 78 HIS O 88 GLN P 78 HIS P 88 GLN Q 78 HIS Q 88 GLN R 78 HIS R 88 GLN S 65 ASN S 78 HIS S 88 GLN T 78 HIS T 88 GLN U 78 HIS U 88 GLN V 78 HIS V 88 GLN W 78 HIS W 88 GLN X 78 HIS X 88 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119270 restraints weight = 25038.441| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.99 r_work: 0.3172 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 32508 Z= 0.161 Angle : 0.468 5.450 43872 Z= 0.267 Chirality : 0.037 0.132 4704 Planarity : 0.003 0.020 5664 Dihedral : 3.743 13.007 4056 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % 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: 5.16 (0.12), residues: 3840 helix: 3.83 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 165 TYR 0.010 0.002 TYR E 157 PHE 0.019 0.003 PHE G 44 TRP 0.006 0.002 TRP G 122 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (32496) covalent geometry : angle 0.46743 / 0.27 (43848) SS BOND : bond 0.00178 / 0.12 ( 12) SS BOND : angle 0.83663 / 0.57 ( 24) hydrogen bonds : bond 0.06428 / 4.29 ( 2785) hydrogen bonds : angle 3.43820 / 2.55 ( 8355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13306.74 seconds wall clock time: 227 minutes 16.38 seconds (13636.38 seconds total)