Starting phenix.real_space_refine on Mon Jul 6 01:01:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4u_37270/07_2026/8w4u_37270.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 10460 2.51 5 N 2692 2.21 5 O 2892 1.98 5 F 4 1.80 5 H 15620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ARG 87": not complete - not flipped Residue "B ARG 87": not complete - not flipped Residue "D ARG 87": not complete - not flipped Residue "G ARG 87": not complete - not flipped Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.67, per 1000 atoms: 0.18 Number of scatterers: 31768 At special positions: 0 Unit cell: (128.34, 128.34, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 88 16.00 P 12 15.00 F 4 9.00 O 2892 8.00 N 2692 7.00 C 10460 6.00 H 15620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 885.3 milliseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 115 removed outlier: 3.582A pdb=" N ILE A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.050A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.603A pdb=" N PHE A 261 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 348 removed outlier: 4.252A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.542A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 563 through 600 Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 90 through 115 removed outlier: 3.578A pdb=" N ILE B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.042A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.630A pdb=" N PHE B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 348 removed outlier: 4.173A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.542A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 559 Processing helix chain 'B' and resid 563 through 600 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.608A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 90 through 115 removed outlier: 3.573A pdb=" N ILE D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.953A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.673A pdb=" N PHE D 261 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 262' Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 348 removed outlier: 4.216A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 356 through 367 removed outlier: 4.484A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 563 through 600 Proline residue: D 597 - end of helix Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.518A pdb=" N THR F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.627A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 90 through 115 removed outlier: 3.558A pdb=" N ILE G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.981A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 254 Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.657A pdb=" N PHE G 261 " --> pdb=" O ASN G 258 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP G 262 " --> pdb=" O ASP G 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 262' Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 348 removed outlier: 4.289A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 356 through 367 removed outlier: 4.540A pdb=" N TYR G 362 " --> pdb=" O SER G 358 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 363 " --> pdb=" O THR G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 559 Processing helix chain 'G' and resid 563 through 600 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.648A pdb=" N LEU H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 148 Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 76 through 81 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.549A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 148 1244 hydrogen bonds defined for protein. 3732 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: 7.28 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15592 1.03 - 1.23: 47 1.23 - 1.42: 7001 1.42 - 1.62: 9300 1.62 - 1.81: 164 Bond restraints: 32104 Sorted by residual: bond pdb=" C09 9MF A 801 " pdb=" N08 9MF A 801 " ideal model delta sigma weight residual 1.352 1.449 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C09 9MF G 801 " pdb=" N08 9MF G 801 " ideal model delta sigma weight residual 1.352 1.449 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C09 9MF B 801 " pdb=" N08 9MF B 801 " ideal model delta sigma weight residual 1.352 1.448 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C09 9MF D 801 " pdb=" N08 9MF D 801 " ideal model delta sigma weight residual 1.352 1.447 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O41 PIO A 802 " pdb=" P4 PIO A 802 " ideal model delta sigma weight residual 1.528 1.459 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 32099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 57497 3.97 - 7.95: 116 7.95 - 11.92: 47 11.92 - 15.90: 8 15.90 - 19.87: 4 Bond angle restraints: 57672 Sorted by residual: angle pdb=" O11 PIO B 802 " pdb=" P1 PIO B 802 " pdb=" O12 PIO B 802 " ideal model delta sigma weight residual 121.09 101.22 19.87 3.00e+00 1.11e-01 4.39e+01 angle pdb=" O11 PIO G 802 " pdb=" P1 PIO G 802 " pdb=" O12 PIO G 802 " ideal model delta sigma weight residual 121.09 101.43 19.66 3.00e+00 1.11e-01 4.30e+01 angle pdb=" O11 PIO A 802 " pdb=" P1 PIO A 802 " pdb=" O12 PIO A 802 " ideal model delta sigma weight residual 121.09 101.46 19.63 3.00e+00 1.11e-01 4.28e+01 angle pdb=" O11 PIO D 802 " pdb=" P1 PIO D 802 " pdb=" O12 PIO D 802 " ideal model delta sigma weight residual 121.09 101.46 19.63 3.00e+00 1.11e-01 4.28e+01 angle pdb=" O1 PIO D 802 " pdb=" P1 PIO D 802 " pdb=" O13 PIO D 802 " ideal model delta sigma weight residual 97.64 111.20 -13.56 3.00e+00 1.11e-01 2.04e+01 ... (remaining 57667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 14335 35.81 - 71.62: 533 71.62 - 107.43: 24 107.43 - 143.24: 0 143.24 - 179.05: 4 Dihedral angle restraints: 14896 sinusoidal: 7956 harmonic: 6940 Sorted by residual: dihedral pdb=" CD ARG B 87 " pdb=" NE ARG B 87 " pdb=" CZ ARG B 87 " pdb=" NH1 ARG B 87 " ideal model delta sinusoidal sigma weight residual 0.00 179.05 -179.05 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG A 87 " pdb=" NE ARG A 87 " pdb=" CZ ARG A 87 " pdb=" NH1 ARG A 87 " ideal model delta sinusoidal sigma weight residual 0.00 178.99 -178.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG G 87 " pdb=" NE ARG G 87 " pdb=" CZ ARG G 87 " pdb=" NH1 ARG G 87 " ideal model delta sinusoidal sigma weight residual 0.00 178.98 -178.98 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 14893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.999: 2452 0.999 - 1.998: 0 1.998 - 2.997: 0 2.997 - 3.996: 0 3.996 - 4.995: 4 Chirality restraints: 2456 Sorted by residual: chirality pdb=" C4 PIO D 802 " pdb=" C3 PIO D 802 " pdb=" C5 PIO D 802 " pdb=" O4 PIO D 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" C4 PIO A 802 " pdb=" C3 PIO A 802 " pdb=" C5 PIO A 802 " pdb=" O4 PIO A 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.23e+02 chirality pdb=" C4 PIO G 802 " pdb=" C3 PIO G 802 " pdb=" C5 PIO G 802 " pdb=" O4 PIO G 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.23e+02 ... (remaining 2453 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 43 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.83e+00 pdb=" C ASN H 43 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN H 43 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO H 44 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 43 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C ASN F 43 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN F 43 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO F 44 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 43 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO H 44 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " -0.024 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1206 2.13 - 2.75: 58820 2.75 - 3.36: 97396 3.36 - 3.98: 114130 3.98 - 4.60: 180770 Nonbonded interactions: 452322 Sorted by model distance: nonbonded pdb="HE22 GLN A 341 " pdb=" O LEU E 113 " model vdw 1.512 2.450 nonbonded pdb=" OE1 GLU C 46 " pdb=" H GLU C 46 " model vdw 1.524 2.450 nonbonded pdb="HE22 GLN D 341 " pdb=" O LEU F 113 " model vdw 1.546 2.450 nonbonded pdb="HE22 GLN G 341 " pdb=" O LEU H 113 " model vdw 1.550 2.450 nonbonded pdb="HE22 GLN B 341 " pdb=" O LEU C 113 " model vdw 1.564 2.450 ... (remaining 452317 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } 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: 0.940 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: 0.190 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16484 Z= 0.270 Angle : 0.903 19.871 22200 Z= 0.401 Chirality : 0.204 4.995 2456 Planarity : 0.005 0.058 2780 Dihedral : 17.819 179.049 5932 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.60 % Allowed : 25.78 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1956 helix: 1.82 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.23 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 588 TYR 0.010 0.001 TYR G 362 PHE 0.016 0.001 PHE C 13 TRP 0.015 0.001 TRP D 288 HIS 0.002 0.001 HIS G 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.27 (16484) covalent geometry : angle 0.90264 / 0.40 (22200) hydrogen bonds : bond 0.10723 / 7.15 ( 1244) hydrogen bonds : angle 5.14991 / 3.86 ( 3732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 258 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.6469 (mmm) cc_final: 0.4870 (mmm) REVERT: H 31 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8209 (mppt) REVERT: E 31 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8144 (mppt) REVERT: E 87 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8770 (mmm-85) outliers start: 10 outliers final: 9 residues processed: 263 average time/residue: 0.3791 time to fit residues: 138.4075 Evaluate side-chains 228 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 570 GLN F 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.146783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100008 restraints weight = 113890.244| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.13 r_work: 0.3442 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16484 Z= 0.177 Angle : 0.572 7.630 22200 Z= 0.314 Chirality : 0.035 0.164 2456 Planarity : 0.004 0.050 2780 Dihedral : 10.417 176.899 2226 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.33 % Allowed : 24.16 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1956 helix: 1.74 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.21 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 91 TYR 0.008 0.001 TYR G 251 PHE 0.016 0.001 PHE E 13 TRP 0.010 0.001 TRP D 288 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (16484) covalent geometry : angle 0.57158 / 0.31 (22200) hydrogen bonds : bond 0.04939 / 3.26 ( 1244) hydrogen bonds : angle 4.69137 / 3.51 ( 3732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6747 (tp) REVERT: B 183 LEU cc_start: -0.0409 (OUTLIER) cc_final: -0.0716 (tp) REVERT: H 31 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8224 (mppt) REVERT: E 31 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8258 (mppt) outliers start: 39 outliers final: 25 residues processed: 260 average time/residue: 0.3201 time to fit residues: 118.1827 Evaluate side-chains 243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099209 restraints weight = 114343.632| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.12 r_work: 0.3428 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16484 Z= 0.186 Angle : 0.543 5.515 22200 Z= 0.304 Chirality : 0.034 0.162 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.353 177.631 2222 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.16 % Allowed : 22.43 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1956 helix: 1.72 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.21 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 91 TYR 0.008 0.001 TYR D 251 PHE 0.011 0.001 PHE E 13 TRP 0.015 0.001 TRP G 344 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (16484) covalent geometry : angle 0.54282 / 0.30 (22200) hydrogen bonds : bond 0.04812 / 3.19 ( 1244) hydrogen bonds : angle 4.58126 / 3.44 ( 3732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6721 (tp) REVERT: B 183 LEU cc_start: -0.0606 (OUTLIER) cc_final: -0.0891 (tp) REVERT: C 8 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: C 31 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8015 (mppt) REVERT: C 51 ASP cc_start: 0.9015 (m-30) cc_final: 0.8805 (m-30) REVERT: C 73 MET cc_start: 0.8193 (mmm) cc_final: 0.7843 (mmm) REVERT: H 31 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8312 (mppt) REVERT: E 23 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7448 (t0) REVERT: E 31 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8325 (mppt) REVERT: E 43 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7630 (t0) outliers start: 53 outliers final: 40 residues processed: 266 average time/residue: 0.3386 time to fit residues: 127.3638 Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 0.0370 chunk 181 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.147240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101521 restraints weight = 113442.350| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.26 r_work: 0.3443 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16484 Z= 0.134 Angle : 0.511 5.618 22200 Z= 0.281 Chirality : 0.033 0.204 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.032 177.977 2216 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.98 % Allowed : 22.61 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.19), residues: 1956 helix: 1.87 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.007 0.001 TYR G 362 PHE 0.010 0.001 PHE E 13 TRP 0.013 0.001 TRP A 344 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16484) covalent geometry : angle 0.51056 / 0.28 (22200) hydrogen bonds : bond 0.04448 / 2.93 ( 1244) hydrogen bonds : angle 4.38291 / 3.29 ( 3732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6714 (tp) REVERT: B 183 LEU cc_start: -0.0724 (OUTLIER) cc_final: -0.1026 (tp) REVERT: C 8 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 31 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8027 (mppt) REVERT: C 51 ASP cc_start: 0.8968 (m-30) cc_final: 0.8728 (m-30) REVERT: C 72 MET cc_start: 0.8505 (tmm) cc_final: 0.8234 (tmm) REVERT: F 43 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7320 (m-40) REVERT: H 31 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8364 (mppt) REVERT: E 31 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8400 (mppt) outliers start: 50 outliers final: 41 residues processed: 273 average time/residue: 0.3081 time to fit residues: 120.5656 Evaluate side-chains 267 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 43 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.145537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.098519 restraints weight = 114683.311| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.12 r_work: 0.3416 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16484 Z= 0.208 Angle : 0.541 6.682 22200 Z= 0.305 Chirality : 0.034 0.207 2456 Planarity : 0.004 0.054 2780 Dihedral : 10.297 178.072 2216 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.64 % Allowed : 22.79 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1956 helix: 1.80 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.009 0.001 TYR D 251 PHE 0.011 0.001 PHE C 93 TRP 0.009 0.001 TRP A 344 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (16484) covalent geometry : angle 0.54107 / 0.30 (22200) hydrogen bonds : bond 0.04686 / 3.10 ( 1244) hydrogen bonds : angle 4.44525 / 3.33 ( 3732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6772 (tp) REVERT: B 183 LEU cc_start: -0.0579 (OUTLIER) cc_final: -0.0852 (tp) REVERT: C 31 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8071 (mppt) REVERT: C 51 ASP cc_start: 0.9042 (m-30) cc_final: 0.8772 (m-30) REVERT: C 72 MET cc_start: 0.8525 (tmm) cc_final: 0.8324 (tmm) REVERT: C 73 MET cc_start: 0.7745 (mmm) cc_final: 0.7127 (mmm) REVERT: F 14 LYS cc_start: 0.8895 (tppt) cc_final: 0.8480 (mmtm) REVERT: F 73 MET cc_start: 0.6366 (mmm) cc_final: 0.5536 (mmm) REVERT: H 31 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8394 (mppt) REVERT: H 73 MET cc_start: 0.8194 (mmm) cc_final: 0.7299 (mmm) REVERT: E 31 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8422 (mppt) REVERT: E 43 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7662 (t0) outliers start: 61 outliers final: 47 residues processed: 276 average time/residue: 0.3079 time to fit residues: 121.4317 Evaluate side-chains 271 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.143713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096602 restraints weight = 114550.455| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.07 r_work: 0.3380 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16484 Z= 0.270 Angle : 0.582 6.746 22200 Z= 0.332 Chirality : 0.037 0.205 2456 Planarity : 0.004 0.046 2780 Dihedral : 10.401 178.615 2216 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.24 % Allowed : 22.37 % Favored : 73.39 % 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: 1.93 (0.19), residues: 1956 helix: 1.61 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 87 TYR 0.012 0.001 TYR D 251 PHE 0.012 0.002 PHE G 104 TRP 0.007 0.001 TRP A 344 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.27 (16484) covalent geometry : angle 0.58238 / 0.33 (22200) hydrogen bonds : bond 0.04975 / 3.30 ( 1244) hydrogen bonds : angle 4.57601 / 3.42 ( 3732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6823 (tp) REVERT: B 183 LEU cc_start: -0.0709 (OUTLIER) cc_final: -0.0960 (tp) REVERT: C 51 ASP cc_start: 0.9019 (m-30) cc_final: 0.8819 (m-30) REVERT: C 72 MET cc_start: 0.8561 (tmm) cc_final: 0.8323 (tmm) REVERT: F 14 LYS cc_start: 0.8831 (tppt) cc_final: 0.8451 (mptt) REVERT: H 31 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8400 (mppt) REVERT: H 72 MET cc_start: 0.8359 (tmm) cc_final: 0.8106 (tmm) REVERT: H 73 MET cc_start: 0.7832 (mmm) cc_final: 0.7468 (mmm) REVERT: E 23 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7441 (t0) REVERT: E 31 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8430 (mppt) REVERT: E 87 ARG cc_start: 0.9134 (mmm-85) cc_final: 0.8765 (tmm-80) outliers start: 71 outliers final: 52 residues processed: 277 average time/residue: 0.2976 time to fit residues: 119.8687 Evaluate side-chains 265 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 344 TRP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100435 restraints weight = 114345.704| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.17 r_work: 0.3450 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16484 Z= 0.126 Angle : 0.519 7.970 22200 Z= 0.284 Chirality : 0.034 0.205 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.003 178.280 2216 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.10 % Allowed : 23.03 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1956 helix: 1.81 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.007 0.001 TYR G 251 PHE 0.012 0.001 PHE H 66 TRP 0.013 0.001 TRP A 344 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (16484) covalent geometry : angle 0.51931 / 0.28 (22200) hydrogen bonds : bond 0.04415 / 2.91 ( 1244) hydrogen bonds : angle 4.28431 / 3.21 ( 3732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6786 (tp) REVERT: B 183 LEU cc_start: -0.0624 (OUTLIER) cc_final: -0.0924 (tp) REVERT: B 268 LEU cc_start: 0.9173 (tp) cc_final: 0.8891 (mt) REVERT: C 72 MET cc_start: 0.8524 (tmm) cc_final: 0.8320 (tmm) REVERT: H 31 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8387 (mppt) REVERT: H 73 MET cc_start: 0.7793 (mmm) cc_final: 0.7570 (mmm) REVERT: E 31 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8367 (mppt) outliers start: 52 outliers final: 45 residues processed: 268 average time/residue: 0.3309 time to fit residues: 127.1432 Evaluate side-chains 265 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.144838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097922 restraints weight = 114865.835| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.11 r_work: 0.3403 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16484 Z= 0.206 Angle : 0.556 7.487 22200 Z= 0.312 Chirality : 0.035 0.190 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.088 178.690 2216 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.16 % Allowed : 23.21 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1956 helix: 1.76 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.009 0.001 TYR D 251 PHE 0.018 0.001 PHE C 142 TRP 0.010 0.001 TRP A 344 HIS 0.005 0.001 HIS G 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (16484) covalent geometry : angle 0.55614 / 0.31 (22200) hydrogen bonds : bond 0.04676 / 3.10 ( 1244) hydrogen bonds : angle 4.40682 / 3.30 ( 3732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8974 (tpt) cc_final: 0.8766 (tpt) REVERT: B 109 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6768 (tp) REVERT: B 183 LEU cc_start: -0.0643 (OUTLIER) cc_final: -0.0912 (tp) REVERT: B 546 MET cc_start: 0.8521 (tpt) cc_final: 0.8319 (tpt) REVERT: F 72 MET cc_start: 0.8494 (tmm) cc_final: 0.8217 (tmm) REVERT: H 31 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8424 (mppt) REVERT: E 31 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8422 (mppt) outliers start: 53 outliers final: 51 residues processed: 257 average time/residue: 0.3108 time to fit residues: 115.2625 Evaluate side-chains 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 344 TRP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.145035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098370 restraints weight = 114128.995| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.08 r_work: 0.3418 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16484 Z= 0.180 Angle : 0.548 7.876 22200 Z= 0.305 Chirality : 0.035 0.204 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.045 178.770 2216 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.34 % Allowed : 23.27 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 1956 helix: 1.75 (0.12), residues: 1612 sheet: None (None), residues: 0 loop : -0.16 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 75 TYR 0.008 0.001 TYR D 251 PHE 0.015 0.001 PHE C 142 TRP 0.010 0.001 TRP A 344 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (16484) covalent geometry : angle 0.54779 / 0.30 (22200) hydrogen bonds : bond 0.04628 / 3.06 ( 1244) hydrogen bonds : angle 4.38783 / 3.29 ( 3732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8974 (tpt) cc_final: 0.8750 (tpt) REVERT: B 109 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6783 (tp) REVERT: B 183 LEU cc_start: -0.0693 (OUTLIER) cc_final: -0.0981 (tp) REVERT: H 31 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8412 (mppt) REVERT: E 31 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8412 (mppt) outliers start: 56 outliers final: 54 residues processed: 263 average time/residue: 0.3235 time to fit residues: 122.2168 Evaluate side-chains 274 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 344 TRP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.145371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098751 restraints weight = 114293.221| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.14 r_work: 0.3422 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16484 Z= 0.158 Angle : 0.545 8.156 22200 Z= 0.300 Chirality : 0.034 0.200 2456 Planarity : 0.004 0.045 2780 Dihedral : 10.036 178.551 2216 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.52 % Allowed : 23.03 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 1956 helix: 1.77 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -0.16 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 75 TYR 0.007 0.001 TYR A 251 PHE 0.023 0.001 PHE E 142 TRP 0.011 0.001 TRP A 344 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (16484) covalent geometry : angle 0.54512 / 0.30 (22200) hydrogen bonds : bond 0.04554 / 3.01 ( 1244) hydrogen bonds : angle 4.35749 / 3.26 ( 3732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8959 (tpt) cc_final: 0.8735 (tpt) REVERT: B 109 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6838 (tp) REVERT: B 183 LEU cc_start: -0.0705 (OUTLIER) cc_final: -0.1011 (tp) REVERT: F 72 MET cc_start: 0.8357 (tmm) cc_final: 0.8046 (ppp) REVERT: H 31 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8409 (mppt) REVERT: E 31 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8407 (mppt) outliers start: 59 outliers final: 56 residues processed: 262 average time/residue: 0.3405 time to fit residues: 128.4205 Evaluate side-chains 276 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 344 TRP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.145509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098936 restraints weight = 114904.551| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.14 r_work: 0.3425 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16484 Z= 0.157 Angle : 0.543 8.213 22200 Z= 0.299 Chirality : 0.034 0.198 2456 Planarity : 0.004 0.045 2780 Dihedral : 9.953 178.767 2216 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.64 % Allowed : 22.79 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.19), residues: 1956 helix: 1.79 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 75 TYR 0.007 0.001 TYR A 251 PHE 0.014 0.001 PHE H 142 TRP 0.011 0.001 TRP D 288 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (16484) covalent geometry : angle 0.54314 / 0.30 (22200) hydrogen bonds : bond 0.04509 / 2.98 ( 1244) hydrogen bonds : angle 4.33401 / 3.25 ( 3732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8420.82 seconds wall clock time: 143 minutes 22.42 seconds (8602.42 seconds total)