Starting phenix.real_space_refine on Fri Jun 13 22:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amx_15528/06_2025/8amx_15528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amx_15528/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8amx_15528/06_2025/8amx_15528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amx_15528/06_2025/8amx_15528.map" model { file = "/net/cci-nas-00/data/ceres_data/8amx_15528/06_2025/8amx_15528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amx_15528/06_2025/8amx_15528.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.91, per 1000 atoms: 0.63 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: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.25 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: 4.52 Time building geometry restraints manager: 4.77 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: 0.02 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: 10.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.310 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP D 169 HIS 0.005 0.001 HIS E 57 PHE 0.013 0.002 PHE C 236 TYR 0.022 0.003 TYR G 223 ARG 0.002 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.16785 ( 1100) hydrogen bonds : angle 4.76826 ( 3252) covalent geometry : bond 0.00438 (16032) covalent geometry : angle 0.62731 (21840) *********************** 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 : 1.694 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: 1.5917 time to fit residues: 357.0403 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 : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 E 245 GLN F 165 HIS G 165 HIS G 245 GLN H 245 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101011 restraints weight = 16343.518| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.60 r_work: 0.3032 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16032 Z= 0.170 Angle : 0.614 5.466 21840 Z= 0.342 Chirality : 0.043 0.155 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.826 18.460 2160 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.29 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 8.23 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.19), residues: 2008 helix: 2.26 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.16 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 169 HIS 0.005 0.001 HIS B 57 PHE 0.014 0.002 PHE C 236 TYR 0.021 0.002 TYR G 223 ARG 0.002 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.08283 ( 1100) hydrogen bonds : angle 3.91037 ( 3252) covalent geometry : bond 0.00362 (16032) covalent geometry : angle 0.61446 (21840) *********************** 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 206 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.772 Fit side-chains REVERT: A 244 LYS cc_start: 0.8653 (pttt) cc_final: 0.8256 (pttm) REVERT: B 244 LYS cc_start: 0.8721 (pttt) cc_final: 0.8302 (pttm) REVERT: C 244 LYS cc_start: 0.8684 (pttt) cc_final: 0.8270 (pttm) REVERT: D 244 LYS cc_start: 0.8695 (pttt) cc_final: 0.8268 (pttm) REVERT: E 244 LYS cc_start: 0.8707 (pttt) cc_final: 0.8281 (pttm) REVERT: F 244 LYS cc_start: 0.8706 (pttt) cc_final: 0.8288 (pttm) REVERT: G 244 LYS cc_start: 0.8675 (pttt) cc_final: 0.8266 (pttm) REVERT: H 244 LYS cc_start: 0.8665 (pttt) cc_final: 0.8253 (pttm) outliers start: 17 outliers final: 8 residues processed: 189 average time/residue: 1.6918 time to fit residues: 346.9182 Evaluate side-chains 191 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 21 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 245 GLN E 245 GLN G 245 GLN H 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105827 restraints weight = 15964.293| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.59 r_work: 0.3098 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16032 Z= 0.134 Angle : 0.546 5.526 21840 Z= 0.303 Chirality : 0.040 0.144 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.544 17.624 2160 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 0.57 % Allowed : 10.18 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.20), residues: 2008 helix: 2.57 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.07 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.004 0.001 HIS E 57 PHE 0.011 0.001 PHE D 236 TYR 0.019 0.002 TYR G 223 ARG 0.001 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.06443 ( 1100) hydrogen bonds : angle 3.76331 ( 3252) covalent geometry : bond 0.00256 (16032) covalent geometry : angle 0.54649 (21840) *********************** 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 170 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 1.580 Fit side-chains REVERT: A 244 LYS cc_start: 0.8643 (pttt) cc_final: 0.8235 (pttm) REVERT: B 244 LYS cc_start: 0.8672 (pttt) cc_final: 0.8269 (pttm) REVERT: C 244 LYS cc_start: 0.8682 (pttt) cc_final: 0.8269 (pttm) REVERT: C 251 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: D 244 LYS cc_start: 0.8686 (pttt) cc_final: 0.8271 (pttm) REVERT: D 251 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: E 244 LYS cc_start: 0.8711 (pttt) cc_final: 0.8298 (pttm) REVERT: E 251 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: F 244 LYS cc_start: 0.8688 (pttt) cc_final: 0.8275 (pttm) REVERT: F 251 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: G 244 LYS cc_start: 0.8641 (pttt) cc_final: 0.8239 (pttm) REVERT: G 251 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: H 244 LYS cc_start: 0.8649 (pttt) cc_final: 0.8233 (pttm) outliers start: 9 outliers final: 0 residues processed: 162 average time/residue: 1.6070 time to fit residues: 283.8252 Evaluate side-chains 166 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 251 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN F 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099261 restraints weight = 16287.087| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.60 r_work: 0.3000 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16032 Z= 0.203 Angle : 0.648 5.699 21840 Z= 0.358 Chirality : 0.046 0.162 2448 Planarity : 0.006 0.041 2712 Dihedral : 4.923 18.579 2160 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.59 % Favored : 96.07 % Rotamer: Outliers : 1.57 % Allowed : 9.99 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 2008 helix: 2.51 (0.13), residues: 1376 sheet: None (None), residues: 0 loop : -0.76 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 169 HIS 0.005 0.001 HIS D 57 PHE 0.016 0.002 PHE F 236 TYR 0.021 0.002 TYR G 223 ARG 0.002 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.09177 ( 1100) hydrogen bonds : angle 3.89236 ( 3252) covalent geometry : bond 0.00463 (16032) covalent geometry : angle 0.64762 (21840) *********************** 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 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.501 Fit side-chains REVERT: A 244 LYS cc_start: 0.8673 (pttt) cc_final: 0.8284 (pttm) REVERT: B 29 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7163 (tp) REVERT: B 33 MET cc_start: 0.7452 (mmm) cc_final: 0.7203 (tpt) REVERT: B 244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8287 (pttm) REVERT: C 244 LYS cc_start: 0.8696 (pttt) cc_final: 0.8299 (pttm) REVERT: D 244 LYS cc_start: 0.8683 (pttt) cc_final: 0.8276 (pttm) REVERT: E 244 LYS cc_start: 0.8700 (pttt) cc_final: 0.8300 (pttm) REVERT: F 244 LYS cc_start: 0.8690 (pttt) cc_final: 0.8285 (pttm) REVERT: G 244 LYS cc_start: 0.8679 (pttt) cc_final: 0.8290 (pttm) REVERT: H 244 LYS cc_start: 0.8667 (pttt) cc_final: 0.8264 (pttm) outliers start: 25 outliers final: 8 residues processed: 197 average time/residue: 1.6749 time to fit residues: 359.2266 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 : 1.514 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 30 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.130768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108160 restraints weight = 16286.865| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.60 r_work: 0.3142 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1204 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= 0.122 Angle : 0.523 5.541 21840 Z= 0.290 Chirality : 0.039 0.140 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.466 17.463 2160 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.82 % Allowed : 11.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.20), residues: 2008 helix: 2.68 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS E 57 PHE 0.009 0.001 PHE B 236 TYR 0.018 0.001 TYR G 223 ARG 0.001 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.05644 ( 1100) hydrogen bonds : angle 3.69721 ( 3252) covalent geometry : bond 0.00219 (16032) covalent geometry : angle 0.52319 (21840) *********************** 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 174 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 1.913 Fit side-chains REVERT: B 244 LYS cc_start: 0.8655 (pttt) cc_final: 0.8265 (pttm) outliers start: 13 outliers final: 2 residues processed: 172 average time/residue: 1.4258 time to fit residues: 268.4801 Evaluate side-chains 163 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 170 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.128417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105707 restraints weight = 16279.928| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.60 r_work: 0.3112 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16032 Z= 0.135 Angle : 0.543 5.526 21840 Z= 0.299 Chirality : 0.040 0.142 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.483 17.536 2160 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.44 % Favored : 96.22 % Rotamer: Outliers : 1.26 % Allowed : 11.37 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.19), residues: 2008 helix: 2.66 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS D 57 PHE 0.012 0.001 PHE B 236 TYR 0.019 0.002 TYR G 223 ARG 0.001 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.06498 ( 1100) hydrogen bonds : angle 3.71034 ( 3252) covalent geometry : bond 0.00262 (16032) covalent geometry : angle 0.54254 (21840) *********************** 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 181 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.510 Fit side-chains REVERT: B 29 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7141 (tp) REVERT: B 244 LYS cc_start: 0.8659 (pttt) cc_final: 0.8294 (pttm) outliers start: 20 outliers final: 4 residues processed: 178 average time/residue: 1.3944 time to fit residues: 271.9419 Evaluate side-chains 166 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain F residue 217 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.130326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107677 restraints weight = 16262.280| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.61 r_work: 0.3140 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1244 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= 0.126 Angle : 0.525 5.568 21840 Z= 0.289 Chirality : 0.039 0.141 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.393 17.340 2160 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.79 % Favored : 96.86 % Rotamer: Outliers : 1.95 % Allowed : 10.68 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.20), residues: 2008 helix: 2.75 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS G 57 PHE 0.010 0.001 PHE B 236 TYR 0.019 0.001 TYR G 223 ARG 0.001 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.05880 ( 1100) hydrogen bonds : angle 3.66790 ( 3252) covalent geometry : bond 0.00236 (16032) covalent geometry : angle 0.52525 (21840) *********************** 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 194 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.551 Fit side-chains REVERT: B 29 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7192 (tp) REVERT: B 244 LYS cc_start: 0.8640 (pttt) cc_final: 0.8281 (pttm) REVERT: D 251 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: F 251 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: G 251 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7896 (pt0) outliers start: 31 outliers final: 15 residues processed: 181 average time/residue: 1.4537 time to fit residues: 289.4797 Evaluate side-chains 182 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 32 LYS 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 D residue 149 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 251 GLU 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 F residue 251 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 136 optimal weight: 0.0270 chunk 128 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.128273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105622 restraints weight = 16174.815| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.60 r_work: 0.3117 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16032 Z= 0.137 Angle : 0.545 5.535 21840 Z= 0.300 Chirality : 0.040 0.144 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.474 17.442 2160 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.29 % Favored : 96.36 % Rotamer: Outliers : 1.32 % Allowed : 11.43 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.19), residues: 2008 helix: 2.84 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.54 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.004 0.001 HIS E 57 PHE 0.012 0.001 PHE B 236 TYR 0.020 0.002 TYR G 223 ARG 0.001 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.06552 ( 1100) hydrogen bonds : angle 3.69760 ( 3252) covalent geometry : bond 0.00268 (16032) covalent geometry : angle 0.54465 (21840) *********************** 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 184 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.727 Fit side-chains REVERT: B 29 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7173 (tp) REVERT: B 244 LYS cc_start: 0.8664 (pttt) cc_final: 0.8299 (pttm) outliers start: 21 outliers final: 17 residues processed: 172 average time/residue: 1.9061 time to fit residues: 359.3461 Evaluate side-chains 181 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 32 LYS 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 D residue 149 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 217 LEU 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 G residue 217 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.3980 chunk 129 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.133799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113379 restraints weight = 16440.717| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.44 r_work: 0.3226 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1267 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= 0.126 Angle : 0.525 5.570 21840 Z= 0.289 Chirality : 0.039 0.141 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.378 17.137 2160 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.04 % Favored : 96.61 % Rotamer: Outliers : 1.19 % Allowed : 11.62 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.20), residues: 2008 helix: 2.76 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS E 57 PHE 0.011 0.001 PHE E 236 TYR 0.019 0.001 TYR G 223 ARG 0.001 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.05882 ( 1100) hydrogen bonds : angle 3.66400 ( 3252) covalent geometry : bond 0.00237 (16032) covalent geometry : angle 0.52533 (21840) *********************** 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 182 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.608 Fit side-chains REVERT: B 244 LYS cc_start: 0.8572 (pttt) cc_final: 0.8316 (pttm) outliers start: 19 outliers final: 12 residues processed: 173 average time/residue: 1.4721 time to fit residues: 278.8217 Evaluate side-chains 175 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 32 LYS 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 F residue 217 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.123687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.100900 restraints weight = 16361.619| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.60 r_work: 0.3031 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16032 Z= 0.181 Angle : 0.618 5.528 21840 Z= 0.339 Chirality : 0.044 0.154 2448 Planarity : 0.005 0.038 2712 Dihedral : 4.765 18.433 2160 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.88 % Favored : 95.77 % Rotamer: Outliers : 0.69 % Allowed : 12.12 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 2008 helix: 2.60 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.64 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 169 HIS 0.004 0.001 HIS H 57 PHE 0.015 0.002 PHE C 236 TYR 0.022 0.002 TYR G 223 ARG 0.002 0.000 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.08368 ( 1100) hydrogen bonds : angle 3.79743 ( 3252) covalent geometry : bond 0.00400 (16032) covalent geometry : angle 0.61758 (21840) ********************** 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 191 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.587 Fit side-chains REVERT: B 244 LYS cc_start: 0.8663 (pttt) cc_final: 0.8285 (pttm) outliers start: 11 outliers final: 11 residues processed: 183 average time/residue: 1.5269 time to fit residues: 304.3504 Evaluate side-chains 190 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 32 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 0.0050 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 163 optimal weight: 0.0670 chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.135458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115192 restraints weight = 16409.792| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.43 r_work: 0.3225 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1370 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= 0.119 Angle : 0.515 5.582 21840 Z= 0.283 Chirality : 0.039 0.139 2448 Planarity : 0.005 0.034 2712 Dihedral : 4.367 17.299 2160 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.79 % Favored : 96.86 % Rotamer: Outliers : 0.44 % Allowed : 12.94 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.20), residues: 2008 helix: 2.77 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.21 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 169 HIS 0.004 0.001 HIS E 57 PHE 0.009 0.001 PHE B 236 TYR 0.017 0.001 TYR G 223 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 1100) hydrogen bonds : angle 3.66237 ( 3252) covalent geometry : bond 0.00218 (16032) covalent geometry : angle 0.51461 (21840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.51 seconds wall clock time: 187 minutes 7.36 seconds (11227.36 seconds total)