Starting phenix.real_space_refine on Tue Jul 29 05:57:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0m_18797/07_2025/8r0m_18797_neut.cif" } resolution = 2.87 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= 0.005 sd= 0.207 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 35 5.16 5 C 7421 2.51 5 N 1709 2.21 5 O 1930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11095 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2107 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2108 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2102 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2118 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2118 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 99 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {'LFA': 3, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 7.13, per 1000 atoms: 0.64 Number of scatterers: 11095 At special positions: 0 Unit cell: (94.024, 90.958, 82.782, 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 35 16.00 O 1930 8.00 N 1709 7.00 C 7421 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 10 sheets defined 78.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 51 through 77 Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.863A pdb=" N ILE A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 removed outlier: 4.044A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.949A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 148 Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.904A pdb=" N ALA A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 263 removed outlier: 3.805A pdb=" N PHE A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 77 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 97 through 117 removed outlier: 4.001A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.946A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 removed outlier: 3.946A pdb=" N ARG B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 207 removed outlier: 3.581A pdb=" N LEU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.905A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'B' and resid 244 through 263 removed outlier: 3.678A pdb=" N HIS B 249 " --> pdb=" O CYS B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.703A pdb=" N ALA C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 97 through 117 removed outlier: 4.005A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.954A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 removed outlier: 3.921A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.902A pdb=" N ALA C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 243 Processing helix chain 'C' and resid 244 through 263 removed outlier: 3.663A pdb=" N HIS C 249 " --> pdb=" O CYS C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 removed outlier: 4.081A pdb=" N ALA D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 51 through 77 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 97 through 117 removed outlier: 4.096A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.931A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 148 Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 207 removed outlier: 3.592A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.936A pdb=" N ALA D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 263 removed outlier: 3.838A pdb=" N PHE D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 249 " --> pdb=" O CYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 51 through 77 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 97 through 117 removed outlier: 3.999A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.951A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 148 Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.902A pdb=" N ALA E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 243 Processing helix chain 'E' and resid 244 through 263 removed outlier: 3.671A pdb=" N HIS E 249 " --> pdb=" O CYS E 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.474A pdb=" N ILE A 271 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.477A pdb=" N ILE B 271 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.474A pdb=" N ILE C 271 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.644A pdb=" N LEU D 85 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.478A pdb=" N ILE D 271 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 272 removed outlier: 6.446A pdb=" N ILE E 271 " --> pdb=" O GLN E 278 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2484 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: 3.19 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1572 1.30 - 1.43: 3027 1.43 - 1.56: 6617 1.56 - 1.69: 0 1.69 - 1.82: 60 Bond restraints: 11276 Sorted by residual: bond pdb=" C GLU E 17 " pdb=" O GLU E 17 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.19e-02 7.06e+03 2.94e+01 bond pdb=" C GLY C 47 " pdb=" O GLY C 47 " ideal model delta sigma weight residual 1.232 1.183 0.049 9.40e-03 1.13e+04 2.68e+01 bond pdb=" C GLU D 17 " pdb=" O GLU D 17 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.26e-02 6.30e+03 2.18e+01 bond pdb=" CA SER E 275 " pdb=" CB SER E 275 " ideal model delta sigma weight residual 1.530 1.464 0.066 1.50e-02 4.44e+03 1.91e+01 bond pdb=" CA SER D 275 " pdb=" CB SER D 275 " ideal model delta sigma weight residual 1.530 1.467 0.062 1.50e-02 4.44e+03 1.72e+01 ... (remaining 11271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 12580 2.13 - 4.26: 2403 4.26 - 6.38: 294 6.38 - 8.51: 34 8.51 - 10.64: 11 Bond angle restraints: 15322 Sorted by residual: angle pdb=" C ALA A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta sigma weight residual 120.24 114.85 5.39 6.30e-01 2.52e+00 7.32e+01 angle pdb=" C ALA E 106 " pdb=" N VAL E 107 " pdb=" CA VAL E 107 " ideal model delta sigma weight residual 120.24 114.87 5.37 6.30e-01 2.52e+00 7.27e+01 angle pdb=" C ALA C 106 " pdb=" N VAL C 107 " pdb=" CA VAL C 107 " ideal model delta sigma weight residual 120.24 114.87 5.37 6.30e-01 2.52e+00 7.26e+01 angle pdb=" C ALA B 106 " pdb=" N VAL B 107 " pdb=" CA VAL B 107 " ideal model delta sigma weight residual 120.24 114.88 5.36 6.30e-01 2.52e+00 7.25e+01 angle pdb=" C ALA D 106 " pdb=" N VAL D 107 " pdb=" CA VAL D 107 " ideal model delta sigma weight residual 120.24 114.96 5.28 6.30e-01 2.52e+00 7.02e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 6212 16.72 - 33.44: 371 33.44 - 50.16: 94 50.16 - 66.88: 18 66.88 - 83.60: 3 Dihedral angle restraints: 6698 sinusoidal: 2658 harmonic: 4040 Sorted by residual: dihedral pdb=" C ILE C 150 " pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" CB ILE C 150 " ideal model delta harmonic sigma weight residual -122.00 -136.86 14.86 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" C ILE B 273 " pdb=" N ILE B 273 " pdb=" CA ILE B 273 " pdb=" CB ILE B 273 " ideal model delta harmonic sigma weight residual -122.00 -135.49 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CA ILE B 273 " pdb=" CB ILE B 273 " ideal model delta harmonic sigma weight residual 123.40 135.64 -12.24 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 6695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1514 0.096 - 0.193: 349 0.193 - 0.289: 35 0.289 - 0.386: 0 0.386 - 0.482: 2 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 1.95 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 1.96 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1897 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 49 " 0.568 9.50e-02 1.11e+02 2.55e-01 3.96e+01 pdb=" NE ARG C 49 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 49 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 49 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 49 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 50 " -0.048 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 50 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 50 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 50 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR E 50 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 50 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 50 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 126 " -0.366 9.50e-02 1.11e+02 1.65e-01 1.86e+01 pdb=" NE ARG E 126 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 126 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 126 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 126 " -0.005 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 807 2.70 - 3.25: 11090 3.25 - 3.80: 18645 3.80 - 4.35: 26171 4.35 - 4.90: 42185 Nonbonded interactions: 98898 Sorted by model distance: nonbonded pdb=" OH TYR D 79 " pdb=" O HOH D 501 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR A 79 " pdb=" O HOH A 501 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR E 79 " pdb=" O HOH E 501 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR B 79 " pdb=" O HOH B 501 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP C 80 " pdb=" ND2 ASN C 89 " model vdw 2.221 3.120 ... (remaining 98893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or resid 130 th \ rough 190 or (resid 191 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 284 or resid 401 through 402 or (resid 403 and \ (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or name C16)))) \ selection = (chain 'B' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or (resid 127 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or resid 128 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 284 \ or resid 401 or (resid 402 and (name C1 or name C10 or name C11 or name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or ( \ resid 403 and (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or \ name C16)))) selection = (chain 'C' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB )) or resid 183 through 284 or resid 401 or (resid 402 a \ nd (name C1 or name C10 or name C11 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 )) or (resid 403 and (name C7 )) or \ (resid 404 and (name C12 or name C13 or name C14 or name C15)))) selection = (chain 'D' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 151 or (resid 152 and (name N or \ name CA or name C or name O or name CB )) or resid 153 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 through \ 190 or (resid 191 through 194 and (name N or name CA or name C or name O or name \ CB )) or resid 195 through 249 or (resid 250 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE )) or resid 251 through 284 \ or resid 401 or (resid 402 and (name C1 or name C10 or name C11 or name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or ( \ resid 403 and (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or \ name C16)))) selection = (chain 'E' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or (resid 127 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or resid 128 through 151 or (resid 152 a \ nd (name N or name CA or name C or name O or name CB )) or resid 153 or (resid 1 \ 54 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE )) or resid 155 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB )) or resid 183 through 190 or (resid 191 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 28 \ 4 or resid 401 or (resid 402 and (name C1 or name C10 or name C11 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 403 and (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 o \ r name C16)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.013 0.090 11281 Z= 0.852 Angle : 1.687 10.638 15322 Z= 1.159 Chirality : 0.079 0.482 1900 Planarity : 0.016 0.255 1770 Dihedral : 12.083 83.598 4098 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.44 % Allowed : 2.72 % Favored : 94.84 % Cbeta Deviations : 0.62 % 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: -4.05 (0.16), residues: 1400 helix: -2.60 (0.11), residues: 990 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.009 TRP B 272 HIS 0.012 0.004 HIS E 183 PHE 0.034 0.009 PHE E 141 TYR 0.051 0.012 TYR E 50 ARG 0.025 0.004 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.23678 ( 846) hydrogen bonds : angle 9.06428 ( 2484) covalent geometry : bond 0.01264 (11276) covalent geometry : angle 1.68707 (15322) Misc. bond : bond 0.02664 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.155 Fit side-chains REVERT: A 43 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.8255 (ptt90) REVERT: A 82 VAL cc_start: 0.7863 (t) cc_final: 0.7599 (m) REVERT: A 191 GLU cc_start: 0.8378 (tt0) cc_final: 0.7316 (mp0) REVERT: A 247 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 259 ASP cc_start: 0.8605 (m-30) cc_final: 0.8373 (m-30) REVERT: A 280 ASP cc_start: 0.8762 (m-30) cc_final: 0.8559 (m-30) REVERT: B 82 VAL cc_start: 0.8212 (t) cc_final: 0.7998 (m) REVERT: B 259 ASP cc_start: 0.8574 (m-30) cc_final: 0.8340 (m-30) REVERT: C 82 VAL cc_start: 0.8458 (t) cc_final: 0.8235 (m) REVERT: C 259 ASP cc_start: 0.8579 (m-30) cc_final: 0.8350 (m-30) REVERT: D 259 ASP cc_start: 0.8408 (m-30) cc_final: 0.8167 (m-30) REVERT: E 43 ARG cc_start: 0.8587 (ptt-90) cc_final: 0.8358 (ptt90) REVERT: E 126 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6305 (mmt90) REVERT: E 247 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8174 (tt) outliers start: 26 outliers final: 7 residues processed: 165 average time/residue: 1.1150 time to fit residues: 200.0174 Evaluate side-chains 131 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 15 GLN B 230 HIS C 187 GLN C 230 HIS D 15 GLN D 230 HIS E 18 HIS E 230 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.092630 restraints weight = 12184.889| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 0.84 r_work: 0.2870 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11281 Z= 0.138 Angle : 0.570 5.521 15322 Z= 0.305 Chirality : 0.041 0.135 1900 Planarity : 0.005 0.034 1770 Dihedral : 9.630 59.255 2014 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.54 % Allowed : 5.26 % Favored : 92.21 % 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: 1.01 (0.21), residues: 1400 helix: 1.40 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 162 HIS 0.007 0.001 HIS B 18 PHE 0.012 0.002 PHE C 24 TYR 0.013 0.002 TYR A 68 ARG 0.008 0.001 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 846) hydrogen bonds : angle 3.82295 ( 2484) covalent geometry : bond 0.00299 (11276) covalent geometry : angle 0.56978 (15322) Misc. bond : bond 0.00032 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.070 Fit side-chains REVERT: A 191 GLU cc_start: 0.8122 (tt0) cc_final: 0.7460 (mp0) REVERT: A 204 MET cc_start: 0.9046 (mmp) cc_final: 0.8777 (mmp) REVERT: A 280 ASP cc_start: 0.8375 (m-30) cc_final: 0.8120 (m-30) REVERT: C 172 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8062 (mt) REVERT: D 259 ASP cc_start: 0.8087 (m-30) cc_final: 0.7870 (m-30) REVERT: D 271 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (mp) REVERT: E 49 ARG cc_start: 0.8745 (ttt180) cc_final: 0.8493 (ttt180) REVERT: E 126 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6609 (mmt90) REVERT: E 259 ASP cc_start: 0.7916 (m-30) cc_final: 0.7714 (m-30) outliers start: 27 outliers final: 10 residues processed: 146 average time/residue: 1.0492 time to fit residues: 167.5626 Evaluate side-chains 123 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN D 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092126 restraints weight = 12469.494| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.15 r_work: 0.2882 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11281 Z= 0.128 Angle : 0.509 5.187 15322 Z= 0.269 Chirality : 0.040 0.126 1900 Planarity : 0.004 0.035 1770 Dihedral : 8.816 59.426 2002 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.82 % Allowed : 6.29 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1400 helix: 2.82 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 162 HIS 0.005 0.001 HIS B 18 PHE 0.012 0.002 PHE E 34 TYR 0.014 0.002 TYR A 68 ARG 0.007 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 846) hydrogen bonds : angle 3.45660 ( 2484) covalent geometry : bond 0.00285 (11276) covalent geometry : angle 0.50913 (15322) Misc. bond : bond 0.00018 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.091 Fit side-chains REVERT: A 280 ASP cc_start: 0.8427 (m-30) cc_final: 0.8186 (m-30) REVERT: C 271 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 40 TRP cc_start: 0.7998 (t-100) cc_final: 0.7776 (t-100) REVERT: E 49 ARG cc_start: 0.8805 (ttt180) cc_final: 0.8551 (ttt180) REVERT: E 126 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6163 (mmt90) REVERT: E 268 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8573 (p) REVERT: E 269 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7934 (pt0) outliers start: 30 outliers final: 12 residues processed: 142 average time/residue: 1.0193 time to fit residues: 158.7989 Evaluate side-chains 125 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 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 = 0.3104 r_free = 0.3104 target = 0.105779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093226 restraints weight = 12386.168| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.15 r_work: 0.2874 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11281 Z= 0.114 Angle : 0.480 4.934 15322 Z= 0.252 Chirality : 0.040 0.142 1900 Planarity : 0.004 0.035 1770 Dihedral : 8.354 57.740 2002 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.16 % Allowed : 8.64 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.44 (0.22), residues: 1400 helix: 3.35 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 PHE 0.009 0.001 PHE A 137 TYR 0.013 0.002 TYR A 68 ARG 0.004 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 846) hydrogen bonds : angle 3.30404 ( 2484) covalent geometry : bond 0.00248 (11276) covalent geometry : angle 0.47964 (15322) Misc. bond : bond 0.00013 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.218 Fit side-chains REVERT: A 271 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 280 ASP cc_start: 0.8390 (m-30) cc_final: 0.8168 (m-30) REVERT: B 66 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7625 (mm) REVERT: C 172 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7850 (mt) REVERT: C 271 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 40 TRP cc_start: 0.8000 (t-100) cc_final: 0.7747 (t-100) REVERT: D 49 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8472 (ttt180) REVERT: D 269 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: E 49 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8596 (ttt180) REVERT: E 126 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6233 (mmt90) REVERT: E 268 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8517 (p) REVERT: E 269 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8002 (pt0) outliers start: 23 outliers final: 9 residues processed: 148 average time/residue: 1.0581 time to fit residues: 171.6317 Evaluate side-chains 135 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.105933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.093338 restraints weight = 12353.502| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.15 r_work: 0.2894 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11281 Z= 0.115 Angle : 0.475 5.783 15322 Z= 0.248 Chirality : 0.040 0.165 1900 Planarity : 0.004 0.035 1770 Dihedral : 7.997 58.004 2001 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.35 % Allowed : 9.30 % Favored : 88.36 % 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: 3.68 (0.22), residues: 1400 helix: 3.50 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.73 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.004 0.001 HIS D 18 PHE 0.010 0.001 PHE E 22 TYR 0.011 0.002 TYR A 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 846) hydrogen bonds : angle 3.23808 ( 2484) covalent geometry : bond 0.00253 (11276) covalent geometry : angle 0.47521 (15322) Misc. bond : bond 0.00020 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.151 Fit side-chains REVERT: A 271 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 280 ASP cc_start: 0.8397 (m-30) cc_final: 0.8143 (m-30) REVERT: B 66 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7673 (mm) REVERT: C 172 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 271 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 40 TRP cc_start: 0.8010 (t-100) cc_final: 0.7790 (t-100) REVERT: D 269 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: D 271 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8495 (mp) REVERT: E 49 ARG cc_start: 0.8813 (ttt180) cc_final: 0.8589 (ttt180) REVERT: E 268 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 269 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7892 (pt0) outliers start: 25 outliers final: 11 residues processed: 142 average time/residue: 1.0380 time to fit residues: 162.3375 Evaluate side-chains 135 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.103357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.090936 restraints weight = 12510.308| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.11 r_work: 0.2870 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11281 Z= 0.150 Angle : 0.508 5.410 15322 Z= 0.265 Chirality : 0.041 0.152 1900 Planarity : 0.004 0.036 1770 Dihedral : 8.167 58.179 1997 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.72 % Allowed : 9.30 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.55 (0.22), residues: 1400 helix: 3.36 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.68 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 PHE 0.016 0.002 PHE E 202 TYR 0.014 0.002 TYR A 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 846) hydrogen bonds : angle 3.33330 ( 2484) covalent geometry : bond 0.00356 (11276) covalent geometry : angle 0.50835 (15322) Misc. bond : bond 0.00049 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.240 Fit side-chains REVERT: A 271 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 280 ASP cc_start: 0.8447 (m-30) cc_final: 0.8183 (m-30) REVERT: C 271 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8599 (mp) REVERT: D 40 TRP cc_start: 0.8036 (t-100) cc_final: 0.7813 (t-100) REVERT: D 269 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: D 271 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8521 (mp) REVERT: E 49 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8607 (ttt180) REVERT: E 269 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8073 (pt0) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 1.0860 time to fit residues: 165.2621 Evaluate side-chains 142 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.102593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090149 restraints weight = 12708.666| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.11 r_work: 0.2853 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11281 Z= 0.160 Angle : 0.518 5.117 15322 Z= 0.270 Chirality : 0.042 0.144 1900 Planarity : 0.004 0.037 1770 Dihedral : 8.312 59.651 1997 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.72 % Allowed : 9.67 % Favored : 87.61 % 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: 3.49 (0.22), residues: 1400 helix: 3.32 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.70 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.004 0.001 HIS E 18 PHE 0.016 0.002 PHE E 202 TYR 0.014 0.002 TYR A 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 846) hydrogen bonds : angle 3.37318 ( 2484) covalent geometry : bond 0.00383 (11276) covalent geometry : angle 0.51762 (15322) Misc. bond : bond 0.00055 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.108 Fit side-chains REVERT: A 191 GLU cc_start: 0.8196 (tt0) cc_final: 0.7375 (mp0) REVERT: A 271 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 280 ASP cc_start: 0.8426 (m-30) cc_final: 0.8135 (m-30) REVERT: C 271 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8628 (mp) REVERT: D 40 TRP cc_start: 0.8043 (t-100) cc_final: 0.7823 (t-100) REVERT: D 269 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: E 49 ARG cc_start: 0.8834 (ttt180) cc_final: 0.8612 (ttt180) REVERT: E 269 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8083 (pt0) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 1.1249 time to fit residues: 159.8605 Evaluate side-chains 131 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.0670 chunk 97 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.107130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.094724 restraints weight = 12454.774| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.12 r_work: 0.2919 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11281 Z= 0.099 Angle : 0.448 4.805 15322 Z= 0.234 Chirality : 0.039 0.134 1900 Planarity : 0.004 0.037 1770 Dihedral : 7.557 59.994 1997 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.16 % Allowed : 10.05 % Favored : 87.79 % 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: 4.00 (0.22), residues: 1400 helix: 3.74 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.61 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS B 18 PHE 0.020 0.001 PHE E 202 TYR 0.010 0.001 TYR C 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 846) hydrogen bonds : angle 3.16231 ( 2484) covalent geometry : bond 0.00198 (11276) covalent geometry : angle 0.44750 (15322) Misc. bond : bond 0.00014 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.106 Fit side-chains REVERT: A 271 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 280 ASP cc_start: 0.8281 (m-30) cc_final: 0.8000 (m-30) REVERT: B 40 TRP cc_start: 0.7785 (t-100) cc_final: 0.7483 (t-100) REVERT: B 259 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: C 172 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7821 (mt) REVERT: C 271 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 283 ILE cc_start: 0.7945 (pt) cc_final: 0.7621 (pt) REVERT: D 40 TRP cc_start: 0.8046 (t-100) cc_final: 0.7814 (t-100) REVERT: D 269 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: E 49 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8556 (ttt180) REVERT: E 62 ILE cc_start: 0.8432 (mt) cc_final: 0.8219 (tt) REVERT: E 268 THR cc_start: 0.8785 (p) cc_final: 0.8546 (p) REVERT: E 269 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7993 (pt0) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 1.0764 time to fit residues: 162.4845 Evaluate side-chains 138 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 269 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 6.9990 chunk 99 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.108057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095245 restraints weight = 12449.793| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.18 r_work: 0.2925 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11281 Z= 0.100 Angle : 0.447 5.378 15322 Z= 0.233 Chirality : 0.039 0.145 1900 Planarity : 0.004 0.036 1770 Dihedral : 7.220 59.756 1997 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.16 % Allowed : 10.23 % Favored : 87.61 % 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: 4.08 (0.22), residues: 1400 helix: 3.81 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.59 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 PHE 0.021 0.001 PHE E 202 TYR 0.011 0.001 TYR C 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 846) hydrogen bonds : angle 3.12752 ( 2484) covalent geometry : bond 0.00207 (11276) covalent geometry : angle 0.44735 (15322) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.075 Fit side-chains REVERT: A 271 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 280 ASP cc_start: 0.8273 (m-30) cc_final: 0.8006 (m-30) REVERT: B 40 TRP cc_start: 0.7807 (t-100) cc_final: 0.7477 (t-100) REVERT: C 172 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7825 (mt) REVERT: C 271 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8528 (mp) REVERT: C 283 ILE cc_start: 0.8010 (pt) cc_final: 0.7692 (pt) REVERT: D 40 TRP cc_start: 0.8070 (t-100) cc_final: 0.7820 (t-100) REVERT: D 269 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: D 271 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8493 (mp) REVERT: E 49 ARG cc_start: 0.8840 (ttt180) cc_final: 0.8597 (ttt180) REVERT: E 268 THR cc_start: 0.8802 (p) cc_final: 0.8571 (p) REVERT: E 269 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8123 (pt0) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 1.0399 time to fit residues: 154.9259 Evaluate side-chains 139 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.092245 restraints weight = 12556.048| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.15 r_work: 0.2870 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11281 Z= 0.139 Angle : 0.490 5.700 15322 Z= 0.255 Chirality : 0.041 0.183 1900 Planarity : 0.004 0.036 1770 Dihedral : 7.543 59.625 1997 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.07 % Allowed : 10.52 % Favored : 87.42 % 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: 3.83 (0.22), residues: 1400 helix: 3.58 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 PHE 0.020 0.002 PHE E 202 TYR 0.013 0.002 TYR A 68 ARG 0.002 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 846) hydrogen bonds : angle 3.24737 ( 2484) covalent geometry : bond 0.00327 (11276) covalent geometry : angle 0.49020 (15322) Misc. bond : bond 0.00037 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.200 Fit side-chains REVERT: A 271 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 280 ASP cc_start: 0.8410 (m-30) cc_final: 0.8130 (m-30) REVERT: C 271 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 283 ILE cc_start: 0.8010 (pt) cc_final: 0.7662 (pt) REVERT: D 40 TRP cc_start: 0.8081 (t-100) cc_final: 0.7846 (t-100) REVERT: D 269 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: D 271 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8531 (mp) REVERT: E 49 ARG cc_start: 0.8852 (ttt180) cc_final: 0.8612 (ttt180) REVERT: E 268 THR cc_start: 0.8819 (p) cc_final: 0.8589 (p) REVERT: E 269 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8135 (pt0) outliers start: 22 outliers final: 15 residues processed: 132 average time/residue: 1.1039 time to fit residues: 160.3839 Evaluate side-chains 136 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3113 r_free = 0.3113 target = 0.106663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094217 restraints weight = 12384.191| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.11 r_work: 0.2927 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11281 Z= 0.106 Angle : 0.455 5.926 15322 Z= 0.238 Chirality : 0.040 0.152 1900 Planarity : 0.004 0.037 1770 Dihedral : 7.223 59.568 1997 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.78 % Allowed : 10.89 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.02 (0.22), residues: 1400 helix: 3.76 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 PHE 0.021 0.001 PHE E 202 TYR 0.011 0.001 TYR A 68 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 846) hydrogen bonds : angle 3.15886 ( 2484) covalent geometry : bond 0.00227 (11276) covalent geometry : angle 0.45543 (15322) Misc. bond : bond 0.00017 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6043.57 seconds wall clock time: 104 minutes 24.96 seconds (6264.96 seconds total)