Starting phenix.real_space_refine on Sat Aug 23 23:50:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amx_15528/08_2025/8amx_15528.map" } resolution = 2.55 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= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10336 2.51 5 N 2536 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15633 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "G" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 3.84, per 1000 atoms: 0.25 Number of scatterers: 15633 At special positions: 0 Unit cell: (93.104, 92.2576, 120.189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2657 8.00 N 2536 7.00 C 10336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 708.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 31 through 61 Processing helix chain 'A' and resid 66 through 86 Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.817A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.631A pdb=" N SER A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 61 Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 167 through 190 Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.818A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.636A pdb=" N SER B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 31 through 61 Processing helix chain 'C' and resid 66 through 86 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 167 through 190 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.631A pdb=" N SER C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 31 through 61 Processing helix chain 'D' and resid 66 through 86 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 167 through 190 Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.635A pdb=" N SER D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.571A pdb=" N GLN E 30 " --> pdb=" O GLN E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 26 through 30' Processing helix chain 'E' and resid 31 through 61 Processing helix chain 'E' and resid 66 through 86 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 167 through 190 Processing helix chain 'E' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.634A pdb=" N SER E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 61 Processing helix chain 'F' and resid 66 through 86 Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 167 through 190 Processing helix chain 'F' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 218 " --> pdb=" O GLY F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.634A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU F 251 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 26 through 30 removed outlier: 3.507A pdb=" N GLN G 30 " --> pdb=" O GLN G 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 26 through 30' Processing helix chain 'G' and resid 31 through 61 Processing helix chain 'G' and resid 66 through 86 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 167 through 190 Processing helix chain 'G' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 241 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 253 removed outlier: 3.630A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU G 251 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 252 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 61 Processing helix chain 'H' and resid 66 through 86 Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 Processing helix chain 'H' and resid 167 through 190 Processing helix chain 'H' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix Processing helix chain 'H' and resid 244 through 253 removed outlier: 3.627A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU H 251 " --> pdb=" O PHE H 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN H 252 " --> pdb=" O SER H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1100 hydrogen bonds defined for protein. 3252 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: 2.29 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4726 1.34 - 1.46: 2818 1.46 - 1.57: 8296 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16032 Sorted by residual: bond pdb=" CA LEU B 231 " pdb=" C LEU B 231 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.09e-01 bond pdb=" CA LEU H 231 " pdb=" C LEU H 231 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.43e-01 bond pdb=" CB PRO C 233 " pdb=" CG PRO C 233 " ideal model delta sigma weight residual 1.492 1.449 0.043 5.00e-02 4.00e+02 7.23e-01 bond pdb=" CB PRO E 233 " pdb=" CG PRO E 233 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 7.21e-01 bond pdb=" CB PRO G 233 " pdb=" CG PRO G 233 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 7.19e-01 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 20641 1.14 - 2.28: 905 2.28 - 3.42: 189 3.42 - 4.56: 68 4.56 - 5.70: 37 Bond angle restraints: 21840 Sorted by residual: angle pdb=" CA TYR G 223 " pdb=" CB TYR G 223 " pdb=" CG TYR G 223 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 119.52 -5.62 1.80e+00 3.09e-01 9.75e+00 angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 119.50 -5.60 1.80e+00 3.09e-01 9.68e+00 angle pdb=" CA TYR F 223 " pdb=" CB TYR F 223 " pdb=" CG TYR F 223 " ideal model delta sigma weight residual 113.90 119.37 -5.47 1.80e+00 3.09e-01 9.23e+00 angle pdb=" CA TYR B 223 " pdb=" CB TYR B 223 " pdb=" CG TYR B 223 " ideal model delta sigma weight residual 113.90 119.34 -5.44 1.80e+00 3.09e-01 9.14e+00 ... (remaining 21835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8440 17.35 - 34.69: 412 34.69 - 52.04: 120 52.04 - 69.39: 12 69.39 - 86.73: 8 Dihedral angle restraints: 8992 sinusoidal: 3344 harmonic: 5648 Sorted by residual: dihedral pdb=" CA PHE B 76 " pdb=" C PHE B 76 " pdb=" N GLY B 77 " pdb=" CA GLY B 77 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE C 76 " pdb=" C PHE C 76 " pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE H 76 " pdb=" C PHE H 76 " pdb=" N GLY H 77 " pdb=" CA GLY H 77 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.067: 855 0.067 - 0.101: 212 0.101 - 0.134: 52 0.134 - 0.168: 18 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CA TYR G 223 " pdb=" N TYR G 223 " pdb=" C TYR G 223 " pdb=" CB TYR G 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA TYR A 223 " pdb=" N TYR A 223 " pdb=" C TYR A 223 " pdb=" CB TYR A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 2445 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 232 " -0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO H 233 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 233 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 232 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 233 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 232 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO D 233 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.022 5.00e-02 4.00e+02 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6160 2.91 - 3.41: 15448 3.41 - 3.91: 26498 3.91 - 4.40: 30277 4.40 - 4.90: 51861 Nonbonded interactions: 130244 Sorted by model distance: nonbonded pdb=" NH2 ARG G 229 " pdb=" O HOH G 401 " model vdw 2.414 3.120 nonbonded pdb=" OD2 ASP A 230 " pdb=" O HOH A 401 " model vdw 2.414 3.040 nonbonded pdb=" NH2 ARG D 229 " pdb=" O HOH D 401 " model vdw 2.417 3.120 nonbonded pdb=" NH2 ARG F 229 " pdb=" O HOH F 401 " model vdw 2.418 3.120 nonbonded pdb=" NH2 ARG B 229 " pdb=" O HOH B 401 " model vdw 2.419 3.120 ... (remaining 130239 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.420 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.560 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.004 0.043 16032 Z= 0.194 Angle : 0.627 5.699 21840 Z= 0.344 Chirality : 0.045 0.168 2448 Planarity : 0.006 0.040 2712 Dihedral : 11.934 86.732 5440 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 2008 helix: 2.09 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.022 0.003 TYR G 223 PHE 0.013 0.002 PHE C 236 TRP 0.011 0.002 TRP D 169 HIS 0.005 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00438 (16032) covalent geometry : angle 0.62731 (21840) hydrogen bonds : bond 0.16785 ( 1100) hydrogen bonds : angle 4.76826 ( 3252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.620 Fit side-chains REVERT: A 147 MET cc_start: 0.8306 (mmm) cc_final: 0.8087 (mmp) REVERT: A 244 LYS cc_start: 0.8411 (pttt) cc_final: 0.8049 (pttm) REVERT: B 147 MET cc_start: 0.8305 (mmm) cc_final: 0.8088 (mmp) REVERT: B 175 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8074 (pttm) REVERT: C 147 MET cc_start: 0.8311 (mmm) cc_final: 0.8097 (mmp) REVERT: C 175 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8062 (pttm) REVERT: D 147 MET cc_start: 0.8312 (mmm) cc_final: 0.8095 (mmp) REVERT: D 175 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7853 (mm-30) REVERT: D 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8064 (pttm) REVERT: E 147 MET cc_start: 0.8313 (mmm) cc_final: 0.8095 (mmp) REVERT: E 175 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8064 (pttm) REVERT: F 147 MET cc_start: 0.8309 (mmm) cc_final: 0.8093 (mmp) REVERT: F 244 LYS cc_start: 0.8447 (pttt) cc_final: 0.8063 (pttm) REVERT: G 147 MET cc_start: 0.8304 (mmm) cc_final: 0.8086 (mmp) REVERT: G 175 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7843 (mm-30) REVERT: G 244 LYS cc_start: 0.8437 (pttt) cc_final: 0.8056 (pttm) REVERT: H 147 MET cc_start: 0.8305 (mmm) cc_final: 0.8087 (mmp) REVERT: H 175 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7862 (mm-30) REVERT: H 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8059 (pttm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.7482 time to fit residues: 167.9790 Evaluate side-chains 197 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 245 GLN B 245 GLN C 245 GLN D 245 GLN E 245 GLN F 165 HIS F 245 GLN G 165 HIS G 245 GLN H 245 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102011 restraints weight = 16261.403| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.60 r_work: 0.3050 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16032 Z= 0.160 Angle : 0.595 5.474 21840 Z= 0.331 Chirality : 0.042 0.152 2448 Planarity : 0.005 0.038 2712 Dihedral : 4.764 18.311 2160 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.29 % Favored : 96.36 % Rotamer: Outliers : 1.01 % Allowed : 7.85 % Favored : 91.14 % 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 aren not related in a simple way. whole: 2.46 (0.19), residues: 2008 helix: 2.32 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.13 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.021 0.002 TYR G 223 PHE 0.013 0.002 PHE D 236 TRP 0.012 0.001 TRP E 169 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00330 (16032) covalent geometry : angle 0.59547 (21840) hydrogen bonds : bond 0.07851 ( 1100) hydrogen bonds : angle 3.87977 ( 3252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.492 Fit side-chains REVERT: A 244 LYS cc_start: 0.8658 (pttt) cc_final: 0.8252 (pttm) REVERT: B 244 LYS cc_start: 0.8699 (pttt) cc_final: 0.8282 (pttm) REVERT: C 244 LYS cc_start: 0.8678 (pttt) cc_final: 0.8264 (pttm) REVERT: D 244 LYS cc_start: 0.8688 (pttt) cc_final: 0.8263 (pttm) REVERT: E 244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8277 (pttm) REVERT: F 244 LYS cc_start: 0.8695 (pttt) cc_final: 0.8275 (pttm) REVERT: G 244 LYS cc_start: 0.8658 (pttt) cc_final: 0.8255 (pttm) REVERT: H 244 LYS cc_start: 0.8650 (pttt) cc_final: 0.8241 (pttm) outliers start: 16 outliers final: 7 residues processed: 185 average time/residue: 0.7639 time to fit residues: 153.5311 Evaluate side-chains 186 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN H 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099524 restraints weight = 16366.361| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.60 r_work: 0.3015 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16032 Z= 0.193 Angle : 0.640 5.666 21840 Z= 0.354 Chirality : 0.045 0.163 2448 Planarity : 0.006 0.040 2712 Dihedral : 4.909 18.525 2160 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.74 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 8.92 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.19), residues: 2008 helix: 2.23 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.20 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 35 TYR 0.022 0.002 TYR G 223 PHE 0.015 0.002 PHE F 236 TRP 0.010 0.002 TRP G 169 HIS 0.005 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00432 (16032) covalent geometry : angle 0.64002 (21840) hydrogen bonds : bond 0.08970 ( 1100) hydrogen bonds : angle 3.90921 ( 3252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.563 Fit side-chains REVERT: A 244 LYS cc_start: 0.8690 (pttt) cc_final: 0.8290 (pttm) REVERT: B 29 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7160 (tp) REVERT: B 33 MET cc_start: 0.7476 (mmm) cc_final: 0.7228 (tpt) REVERT: B 244 LYS cc_start: 0.8703 (pttt) cc_final: 0.8287 (pttm) REVERT: C 244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8303 (pttm) REVERT: D 244 LYS cc_start: 0.8689 (pttt) cc_final: 0.8282 (pttm) REVERT: E 244 LYS cc_start: 0.8698 (pttt) cc_final: 0.8289 (pttm) REVERT: F 244 LYS cc_start: 0.8696 (pttt) cc_final: 0.8293 (pttm) REVERT: G 244 LYS cc_start: 0.8683 (pttt) cc_final: 0.8287 (pttm) REVERT: H 244 LYS cc_start: 0.8680 (pttt) cc_final: 0.8274 (pttm) outliers start: 28 outliers final: 8 residues processed: 197 average time/residue: 0.6646 time to fit residues: 142.7690 Evaluate side-chains 197 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN H 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105946 restraints weight = 16157.145| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.60 r_work: 0.3111 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16032 Z= 0.132 Angle : 0.542 5.514 21840 Z= 0.301 Chirality : 0.040 0.144 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.550 17.747 2160 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.49 % Favored : 97.16 % Rotamer: Outliers : 0.75 % Allowed : 10.99 % Favored : 88.25 % 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 aren not related in a simple way. whole: 2.78 (0.20), residues: 2008 helix: 2.59 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.019 0.001 TYR G 223 PHE 0.010 0.001 PHE B 236 TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00247 (16032) covalent geometry : angle 0.54248 (21840) hydrogen bonds : bond 0.06287 ( 1100) hydrogen bonds : angle 3.73799 ( 3252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.681 Fit side-chains REVERT: A 244 LYS cc_start: 0.8627 (pttt) cc_final: 0.8238 (pttm) REVERT: B 244 LYS cc_start: 0.8663 (pttt) cc_final: 0.8271 (pttm) REVERT: C 244 LYS cc_start: 0.8654 (pttt) cc_final: 0.8261 (pttm) REVERT: D 244 LYS cc_start: 0.8665 (pttt) cc_final: 0.8272 (pttm) REVERT: E 244 LYS cc_start: 0.8668 (pttt) cc_final: 0.8277 (pttm) REVERT: F 244 LYS cc_start: 0.8677 (pttt) cc_final: 0.8285 (pttm) REVERT: G 244 LYS cc_start: 0.8624 (pttt) cc_final: 0.8243 (pttm) REVERT: H 244 LYS cc_start: 0.8616 (pttt) cc_final: 0.8228 (pttm) outliers start: 12 outliers final: 1 residues processed: 168 average time/residue: 0.6424 time to fit residues: 118.5044 Evaluate side-chains 159 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 131 optimal weight: 0.0060 chunk 167 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105164 restraints weight = 16334.685| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.61 r_work: 0.3100 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16032 Z= 0.138 Angle : 0.548 5.516 21840 Z= 0.303 Chirality : 0.040 0.144 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.531 17.681 2160 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.19 % Favored : 96.46 % Rotamer: Outliers : 1.38 % Allowed : 10.87 % Favored : 87.75 % 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 aren not related in a simple way. whole: 2.79 (0.19), residues: 2008 helix: 2.61 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 35 TYR 0.019 0.002 TYR G 223 PHE 0.012 0.001 PHE B 236 TRP 0.009 0.001 TRP E 169 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00268 (16032) covalent geometry : angle 0.54847 (21840) hydrogen bonds : bond 0.06661 ( 1100) hydrogen bonds : angle 3.72557 ( 3252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.681 Fit side-chains REVERT: A 244 LYS cc_start: 0.8608 (pttt) cc_final: 0.8229 (pttm) REVERT: B 29 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7240 (tp) REVERT: B 244 LYS cc_start: 0.8650 (pttt) cc_final: 0.8269 (pttm) REVERT: C 244 LYS cc_start: 0.8640 (pttt) cc_final: 0.8251 (pttm) REVERT: D 244 LYS cc_start: 0.8646 (pttt) cc_final: 0.8255 (pttm) REVERT: D 251 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: E 244 LYS cc_start: 0.8666 (pttt) cc_final: 0.8275 (pttm) REVERT: F 244 LYS cc_start: 0.8662 (pttt) cc_final: 0.8267 (pttm) REVERT: F 251 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: G 244 LYS cc_start: 0.8624 (pttt) cc_final: 0.8246 (pttm) REVERT: G 251 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: H 244 LYS cc_start: 0.8612 (pttt) cc_final: 0.8230 (pttm) REVERT: H 251 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7882 (pt0) outliers start: 22 outliers final: 3 residues processed: 172 average time/residue: 0.6336 time to fit residues: 119.6172 Evaluate side-chains 168 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100111 restraints weight = 16287.435| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.60 r_work: 0.3016 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16032 Z= 0.191 Angle : 0.629 5.759 21840 Z= 0.347 Chirality : 0.045 0.161 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.852 18.504 2160 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.49 % Favored : 96.17 % Rotamer: Outliers : 2.07 % Allowed : 9.61 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.19), residues: 2008 helix: 2.51 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.69 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 35 TYR 0.021 0.002 TYR G 223 PHE 0.016 0.002 PHE B 236 TRP 0.009 0.002 TRP D 169 HIS 0.005 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00428 (16032) covalent geometry : angle 0.62926 (21840) hydrogen bonds : bond 0.08745 ( 1100) hydrogen bonds : angle 3.83854 ( 3252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.572 Fit side-chains REVERT: A 244 LYS cc_start: 0.8641 (pttt) cc_final: 0.8251 (pttm) REVERT: B 29 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7228 (tp) REVERT: B 244 LYS cc_start: 0.8668 (pttt) cc_final: 0.8273 (pttm) REVERT: C 32 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6427 (tttt) REVERT: C 244 LYS cc_start: 0.8681 (pttt) cc_final: 0.8286 (pttm) REVERT: D 244 LYS cc_start: 0.8662 (pttt) cc_final: 0.8262 (pttm) REVERT: E 32 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6441 (mtpt) REVERT: E 244 LYS cc_start: 0.8690 (pttt) cc_final: 0.8289 (pttm) REVERT: F 244 LYS cc_start: 0.8676 (pttt) cc_final: 0.8273 (pttm) REVERT: G 244 LYS cc_start: 0.8654 (pttt) cc_final: 0.8265 (pttm) REVERT: H 244 LYS cc_start: 0.8657 (pttt) cc_final: 0.8260 (pttm) outliers start: 33 outliers final: 12 residues processed: 201 average time/residue: 0.6919 time to fit residues: 151.7871 Evaluate side-chains 200 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 197 optimal weight: 0.0070 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113381 restraints weight = 16340.244| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.43 r_work: 0.3228 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16032 Z= 0.125 Angle : 0.527 5.521 21840 Z= 0.291 Chirality : 0.039 0.141 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.460 17.443 2160 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.49 % Favored : 97.16 % Rotamer: Outliers : 0.57 % Allowed : 11.93 % Favored : 87.50 % 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 aren not related in a simple way. whole: 2.84 (0.19), residues: 2008 helix: 2.68 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.22 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 35 TYR 0.018 0.001 TYR G 223 PHE 0.010 0.001 PHE B 236 TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00227 (16032) covalent geometry : angle 0.52724 (21840) hydrogen bonds : bond 0.05770 ( 1100) hydrogen bonds : angle 3.68609 ( 3252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.644 Fit side-chains REVERT: B 29 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7362 (tp) REVERT: B 244 LYS cc_start: 0.8566 (pttt) cc_final: 0.8294 (pttm) outliers start: 9 outliers final: 5 residues processed: 166 average time/residue: 0.5874 time to fit residues: 107.0536 Evaluate side-chains 166 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain F residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 156 optimal weight: 6.9990 chunk 78 optimal weight: 0.0980 chunk 143 optimal weight: 0.7980 chunk 137 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116760 restraints weight = 16428.854| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.44 r_work: 0.3275 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16032 Z= 0.115 Angle : 0.504 5.624 21840 Z= 0.276 Chirality : 0.038 0.135 2448 Planarity : 0.005 0.034 2712 Dihedral : 4.244 16.853 2160 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.02 % Rotamer: Outliers : 0.63 % Allowed : 12.31 % Favored : 87.06 % 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 aren not related in a simple way. whole: 3.10 (0.20), residues: 2008 helix: 2.89 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 35 TYR 0.016 0.001 TYR G 223 PHE 0.008 0.001 PHE B 236 TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00209 (16032) covalent geometry : angle 0.50442 (21840) hydrogen bonds : bond 0.05060 ( 1100) hydrogen bonds : angle 3.63675 ( 3252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.576 Fit side-chains REVERT: B 244 LYS cc_start: 0.8532 (pttt) cc_final: 0.8279 (pttm) outliers start: 10 outliers final: 4 residues processed: 191 average time/residue: 0.5811 time to fit residues: 122.3271 Evaluate side-chains 185 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain F residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 81 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 141 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113719 restraints weight = 16504.219| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.42 r_work: 0.3195 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16032 Z= 0.125 Angle : 0.523 5.553 21840 Z= 0.286 Chirality : 0.039 0.140 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.323 16.866 2160 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.19 % Favored : 96.51 % Rotamer: Outliers : 0.44 % Allowed : 12.75 % Favored : 86.81 % 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 aren not related in a simple way. whole: 2.96 (0.19), residues: 2008 helix: 2.98 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.55 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 31 TYR 0.019 0.001 TYR G 223 PHE 0.011 0.001 PHE F 236 TRP 0.009 0.001 TRP G 169 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00236 (16032) covalent geometry : angle 0.52268 (21840) hydrogen bonds : bond 0.05787 ( 1100) hydrogen bonds : angle 3.65251 ( 3252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.506 Fit side-chains REVERT: B 244 LYS cc_start: 0.8557 (pttt) cc_final: 0.8313 (pttm) outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.6503 time to fit residues: 122.1541 Evaluate side-chains 172 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 148 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117494 restraints weight = 16378.514| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.42 r_work: 0.3257 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16032 Z= 0.112 Angle : 0.499 5.611 21840 Z= 0.273 Chirality : 0.038 0.135 2448 Planarity : 0.004 0.034 2712 Dihedral : 4.187 16.450 2160 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.54 % Favored : 96.17 % Rotamer: Outliers : 0.38 % Allowed : 12.81 % Favored : 86.81 % 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 aren not related in a simple way. whole: 3.15 (0.20), residues: 2008 helix: 2.96 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.24 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.017 0.001 TYR G 223 PHE 0.008 0.001 PHE B 236 TRP 0.009 0.001 TRP G 169 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00205 (16032) covalent geometry : angle 0.49907 (21840) hydrogen bonds : bond 0.04867 ( 1100) hydrogen bonds : angle 3.61028 ( 3252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.589 Fit side-chains REVERT: B 244 LYS cc_start: 0.8502 (pttt) cc_final: 0.8295 (pttm) outliers start: 6 outliers final: 2 residues processed: 180 average time/residue: 0.5616 time to fit residues: 111.1787 Evaluate side-chains 175 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 149 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN D 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109360 restraints weight = 16510.454| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.42 r_work: 0.3138 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16032 Z= 0.150 Angle : 0.567 5.506 21840 Z= 0.311 Chirality : 0.041 0.147 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.506 17.449 2160 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.29 % Favored : 96.41 % Rotamer: Outliers : 0.19 % Allowed : 13.13 % Favored : 86.68 % 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 aren not related in a simple way. whole: 2.75 (0.19), residues: 2008 helix: 2.81 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.60 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 234 TYR 0.021 0.002 TYR G 223 PHE 0.013 0.002 PHE B 236 TRP 0.007 0.001 TRP G 169 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00311 (16032) covalent geometry : angle 0.56725 (21840) hydrogen bonds : bond 0.07162 ( 1100) hydrogen bonds : angle 3.73928 ( 3252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.93 seconds wall clock time: 75 minutes 22.37 seconds (4522.37 seconds total)