Starting phenix.real_space_refine on Wed May 14 13:10:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgs_40466/05_2025/8sgs_40466_trim.cif" } resolution = 3.15 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= 0.002 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 80 5.16 5 C 7364 2.51 5 N 2000 2.21 5 O 2256 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-5687/modules/chem_data/mon_lib" Total number of atoms: 11720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.64, per 1000 atoms: 0.65 Number of scatterers: 11720 At special positions: 0 Unit cell: (96.5835, 99.8855, 94.9325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 20 15.00 O 2256 8.00 N 2000 7.00 C 7364 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: 2.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 63.8% alpha, 9.2% 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 35 through 64 removed outlier: 4.979A pdb=" N PHE A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix removed outlier: 4.886A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.869A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 140 Processing helix chain 'A' and resid 140 through 145 removed outlier: 4.351A pdb=" N SER A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.614A pdb=" N ALA A 166 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 259 through 297 Processing helix chain 'A' and resid 307 through 337 Processing helix chain 'A' and resid 341 through 368 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.758A pdb=" N TYR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.058A pdb=" N ILE A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'B' and resid 35 through 64 removed outlier: 4.979A pdb=" N PHE B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Proline residue: B 55 - end of helix removed outlier: 4.886A pdb=" N ALA B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.870A pdb=" N ILE B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.352A pdb=" N SER B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.614A pdb=" N ALA B 166 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 259 through 297 Processing helix chain 'B' and resid 307 through 337 Processing helix chain 'B' and resid 341 through 368 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.758A pdb=" N TYR B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 377 through 387 removed outlier: 4.058A pdb=" N ILE B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'C' and resid 35 through 64 removed outlier: 4.979A pdb=" N PHE C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Proline residue: C 55 - end of helix removed outlier: 4.886A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 94 through 109 Processing helix chain 'C' and resid 109 through 121 Processing helix chain 'C' and resid 123 through 131 removed outlier: 3.869A pdb=" N ILE C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 140 through 145 removed outlier: 4.350A pdb=" N SER C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.615A pdb=" N ALA C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 259 through 297 Processing helix chain 'C' and resid 307 through 337 Processing helix chain 'C' and resid 341 through 368 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.758A pdb=" N TYR C 372 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 377 through 387 removed outlier: 4.059A pdb=" N ILE C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 394 through 411 Processing helix chain 'D' and resid 35 through 64 removed outlier: 4.980A pdb=" N PHE D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Proline residue: D 55 - end of helix removed outlier: 4.887A pdb=" N ALA D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN D 59 " --> pdb=" O PRO D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 77 Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 123 through 131 removed outlier: 3.869A pdb=" N ILE D 127 " --> pdb=" O TYR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 4.351A pdb=" N SER D 145 " --> pdb=" O THR D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.614A pdb=" N ALA D 166 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 259 through 297 Processing helix chain 'D' and resid 307 through 337 Processing helix chain 'D' and resid 341 through 368 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.757A pdb=" N TYR D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 377 through 387 removed outlier: 4.058A pdb=" N ILE D 387 " --> pdb=" O ARG D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 394 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 removed outlier: 7.748A pdb=" N GLY A 181 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU A 244 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 171 removed outlier: 7.749A pdb=" N GLY B 181 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU B 244 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 171 removed outlier: 7.748A pdb=" N GLY C 181 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU C 244 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'D' and resid 169 through 171 removed outlier: 7.748A pdb=" N GLY D 181 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU D 244 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'D' and resid 298 through 299 756 hydrogen bonds defined for protein. 2196 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: 4.31 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 3812 1.35 - 1.48: 2840 1.48 - 1.61: 5140 1.61 - 1.74: 12 1.74 - 1.88: 144 Bond restraints: 11948 Sorted by residual: bond pdb=" O6A COA D1002 " pdb=" P2A COA D1002 " ideal model delta sigma weight residual 1.620 1.869 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" O6A COA A1002 " pdb=" P2A COA A1002 " ideal model delta sigma weight residual 1.620 1.868 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O6A COA B1002 " pdb=" P2A COA B1002 " ideal model delta sigma weight residual 1.620 1.868 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O6A COA C1002 " pdb=" P2A COA C1002 " ideal model delta sigma weight residual 1.620 1.868 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O3B COA A1002 " pdb=" P3B COA A1002 " ideal model delta sigma weight residual 1.683 1.868 -0.185 2.00e-02 2.50e+03 8.53e+01 ... (remaining 11943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 16025 2.82 - 5.65: 155 5.65 - 8.47: 47 8.47 - 11.29: 9 11.29 - 14.12: 8 Bond angle restraints: 16244 Sorted by residual: angle pdb=" O4A COA D1002 " pdb=" P2A COA D1002 " pdb=" O6A COA D1002 " ideal model delta sigma weight residual 110.27 96.15 14.12 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O4A COA A1002 " pdb=" P2A COA A1002 " pdb=" O6A COA A1002 " ideal model delta sigma weight residual 110.27 96.17 14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O4A COA C1002 " pdb=" P2A COA C1002 " pdb=" O6A COA C1002 " ideal model delta sigma weight residual 110.27 96.18 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O4A COA B1002 " pdb=" P2A COA B1002 " pdb=" O6A COA B1002 " ideal model delta sigma weight residual 110.27 96.19 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" CAP COA A1002 " pdb=" C9P COA A1002 " pdb=" N8P COA A1002 " ideal model delta sigma weight residual 114.91 127.64 -12.73 3.00e+00 1.11e-01 1.80e+01 ... (remaining 16239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.95: 7003 22.95 - 45.90: 293 45.90 - 68.85: 64 68.85 - 91.80: 8 91.80 - 114.75: 4 Dihedral angle restraints: 7372 sinusoidal: 3044 harmonic: 4328 Sorted by residual: dihedral pdb=" CA SER C 121 " pdb=" C SER C 121 " pdb=" N LEU C 122 " pdb=" CA LEU C 122 " ideal model delta harmonic sigma weight residual 180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LEU A 122 " pdb=" CA LEU A 122 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA SER D 121 " pdb=" C SER D 121 " pdb=" N LEU D 122 " pdb=" CA LEU D 122 " ideal model delta harmonic sigma weight residual 180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 7369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1756 0.094 - 0.188: 68 0.188 - 0.282: 8 0.282 - 0.376: 0 0.376 - 0.470: 4 Chirality restraints: 1836 Sorted by residual: chirality pdb=" C2B COA C1002 " pdb=" C1B COA C1002 " pdb=" C3B COA C1002 " pdb=" O2B COA C1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C2B COA A1002 " pdb=" C1B COA A1002 " pdb=" C3B COA A1002 " pdb=" O2B COA A1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C2B COA D1002 " pdb=" C1B COA D1002 " pdb=" C3B COA D1002 " pdb=" O2B COA D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 1833 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 220 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 219 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO D 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 220 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 220 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " -0.022 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2610 2.78 - 3.31: 11393 3.31 - 3.84: 20536 3.84 - 4.37: 23491 4.37 - 4.90: 41540 Nonbonded interactions: 99570 Sorted by model distance: nonbonded pdb=" OH TYR A 410 " pdb=" OD1 ASP C 288 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 410 " pdb=" OD1 ASP D 288 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP B 288 " pdb=" OH TYR D 410 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP A 288 " pdb=" OH TYR C 410 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU C 191 " pdb=" OG SER C 237 " model vdw 2.327 3.040 ... (remaining 99565 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 3.770 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: 0.080 Set scattering table: 0.100 Process input model: 29.750 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.010 0.249 11948 Z= 0.498 Angle : 0.850 14.116 16244 Z= 0.397 Chirality : 0.048 0.470 1836 Planarity : 0.005 0.040 2032 Dihedral : 13.569 114.748 4596 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.41 % Allowed : 4.23 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.80 (0.21), residues: 1516 helix: 2.34 (0.17), residues: 812 sheet: -1.12 (0.36), residues: 184 loop : 0.35 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 190 HIS 0.002 0.001 HIS D 64 PHE 0.008 0.001 PHE C 152 TYR 0.013 0.002 TYR C 382 ARG 0.003 0.000 ARG D 380 Details of bonding type rmsd hydrogen bonds : bond 0.11471 ( 756) hydrogen bonds : angle 5.24641 ( 2196) covalent geometry : bond 0.00991 (11948) covalent geometry : angle 0.84991 (16244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 202 average time/residue: 0.2401 time to fit residues: 69.0803 Evaluate side-chains 105 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 292 ASN B 119 ASN B 292 ASN C 119 ASN C 292 ASN D 119 ASN D 292 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081556 restraints weight = 24822.592| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.73 r_work: 0.3035 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 11948 Z= 0.133 Angle : 0.469 4.757 16244 Z= 0.241 Chirality : 0.037 0.132 1836 Planarity : 0.004 0.033 2032 Dihedral : 12.799 92.124 2040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.23 % Allowed : 8.01 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.63 (0.22), residues: 1516 helix: 3.10 (0.17), residues: 812 sheet: -0.69 (0.33), residues: 216 loop : 0.63 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 185 HIS 0.003 0.001 HIS D 38 PHE 0.011 0.001 PHE B 152 TYR 0.013 0.002 TYR B 391 ARG 0.003 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 756) hydrogen bonds : angle 4.04795 ( 2196) covalent geometry : bond 0.00282 (11948) covalent geometry : angle 0.46920 (16244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8613 (tpt) REVERT: B 102 MET cc_start: 0.8931 (tpp) cc_final: 0.8659 (tpp) REVERT: B 370 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8553 (tpt) REVERT: C 102 MET cc_start: 0.8934 (tpp) cc_final: 0.8641 (tpp) REVERT: C 370 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8547 (tpt) REVERT: C 382 TYR cc_start: 0.8885 (t80) cc_final: 0.8665 (t80) REVERT: D 102 MET cc_start: 0.8949 (tpp) cc_final: 0.8657 (tpp) REVERT: D 370 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8544 (tpt) outliers start: 14 outliers final: 6 residues processed: 134 average time/residue: 0.1883 time to fit residues: 39.5123 Evaluate side-chains 123 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 370 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.0170 chunk 133 optimal weight: 4.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 159 ASN C 159 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078178 restraints weight = 25210.567| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.27 r_work: 0.2902 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11948 Z= 0.112 Angle : 0.456 8.574 16244 Z= 0.229 Chirality : 0.036 0.125 1836 Planarity : 0.004 0.032 2032 Dihedral : 11.041 81.738 2040 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.50 % Allowed : 8.80 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.75 (0.22), residues: 1516 helix: 3.14 (0.17), residues: 816 sheet: -0.61 (0.33), residues: 216 loop : 0.76 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 185 HIS 0.003 0.001 HIS B 64 PHE 0.009 0.001 PHE A 152 TYR 0.009 0.002 TYR A 391 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 756) hydrogen bonds : angle 3.83762 ( 2196) covalent geometry : bond 0.00237 (11948) covalent geometry : angle 0.45569 (16244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.375 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 136 average time/residue: 0.2008 time to fit residues: 41.8890 Evaluate side-chains 116 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 159 ASN C 159 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077685 restraints weight = 24753.414| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.32 r_work: 0.2890 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11948 Z= 0.113 Angle : 0.463 8.521 16244 Z= 0.230 Chirality : 0.036 0.124 1836 Planarity : 0.003 0.031 2032 Dihedral : 10.153 81.736 2040 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.76 % Allowed : 9.33 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.80 (0.21), residues: 1516 helix: 3.22 (0.17), residues: 812 sheet: -0.50 (0.33), residues: 216 loop : 0.67 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 185 HIS 0.003 0.001 HIS D 64 PHE 0.009 0.001 PHE A 152 TYR 0.014 0.002 TYR A 410 ARG 0.002 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 756) hydrogen bonds : angle 3.79390 ( 2196) covalent geometry : bond 0.00241 (11948) covalent geometry : angle 0.46254 (16244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.314 Fit side-chains REVERT: B 102 MET cc_start: 0.8716 (tpp) cc_final: 0.8429 (tpp) REVERT: B 354 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8239 (mp0) REVERT: C 354 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8266 (mp0) REVERT: D 354 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8260 (mp0) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 0.2005 time to fit residues: 40.1754 Evaluate side-chains 125 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 364 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 159 ASN C 159 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.094042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077100 restraints weight = 24894.932| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.33 r_work: 0.2876 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11948 Z= 0.116 Angle : 0.452 7.459 16244 Z= 0.226 Chirality : 0.036 0.126 1836 Planarity : 0.003 0.030 2032 Dihedral : 9.908 82.924 2040 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.82 % Allowed : 8.63 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.82 (0.21), residues: 1516 helix: 3.23 (0.17), residues: 812 sheet: -0.44 (0.34), residues: 216 loop : 0.66 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 185 HIS 0.003 0.001 HIS B 64 PHE 0.009 0.001 PHE A 152 TYR 0.012 0.002 TYR C 98 ARG 0.002 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 756) hydrogen bonds : angle 3.77434 ( 2196) covalent geometry : bond 0.00251 (11948) covalent geometry : angle 0.45200 (16244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.240 Fit side-chains REVERT: A 391 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8207 (p90) REVERT: B 298 MET cc_start: 0.8913 (mmm) cc_final: 0.8612 (tpp) REVERT: B 354 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8238 (mp0) REVERT: C 298 MET cc_start: 0.8950 (mmm) cc_final: 0.8658 (tpp) REVERT: C 334 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8511 (tt) REVERT: C 354 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8244 (mp0) REVERT: D 298 MET cc_start: 0.8950 (mmm) cc_final: 0.8648 (tpp) REVERT: D 334 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8478 (tt) REVERT: D 354 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8254 (mp0) outliers start: 32 outliers final: 12 residues processed: 135 average time/residue: 0.1821 time to fit residues: 38.6778 Evaluate side-chains 126 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 364 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 148 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 159 ASN C 159 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076201 restraints weight = 25284.505| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.30 r_work: 0.2859 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11948 Z= 0.133 Angle : 0.482 9.359 16244 Z= 0.238 Chirality : 0.037 0.123 1836 Planarity : 0.003 0.030 2032 Dihedral : 9.833 83.891 2040 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.29 % Allowed : 10.12 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.78 (0.21), residues: 1516 helix: 3.17 (0.17), residues: 812 sheet: -0.43 (0.34), residues: 216 loop : 0.70 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 190 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE B 152 TYR 0.013 0.002 TYR B 98 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 756) hydrogen bonds : angle 3.80444 ( 2196) covalent geometry : bond 0.00298 (11948) covalent geometry : angle 0.48215 (16244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.321 Fit side-chains REVERT: A 298 MET cc_start: 0.8966 (mmm) cc_final: 0.8658 (tpp) REVERT: A 391 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8299 (p90) REVERT: B 354 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8249 (mp0) REVERT: B 391 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8343 (p90) REVERT: C 354 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8257 (mp0) REVERT: C 391 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8319 (p90) REVERT: D 354 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8262 (mp0) REVERT: D 391 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8231 (p90) outliers start: 26 outliers final: 13 residues processed: 126 average time/residue: 0.1905 time to fit residues: 37.6779 Evaluate side-chains 129 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 391 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 207 ASN B 159 ASN C 159 ASN D 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076468 restraints weight = 25486.269| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.31 r_work: 0.2868 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11948 Z= 0.120 Angle : 0.471 6.823 16244 Z= 0.233 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.030 2032 Dihedral : 9.801 85.278 2040 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.38 % Allowed : 10.39 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.76 (0.21), residues: 1516 helix: 3.12 (0.17), residues: 812 sheet: -0.36 (0.35), residues: 216 loop : 0.71 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 190 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE B 152 TYR 0.016 0.002 TYR A 98 ARG 0.002 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 756) hydrogen bonds : angle 3.79076 ( 2196) covalent geometry : bond 0.00266 (11948) covalent geometry : angle 0.47063 (16244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.355 Fit side-chains REVERT: A 391 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8364 (p90) REVERT: B 298 MET cc_start: 0.9006 (mmm) cc_final: 0.8725 (tpp) REVERT: B 391 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8219 (p90) REVERT: C 298 MET cc_start: 0.9014 (mmm) cc_final: 0.8733 (tpp) REVERT: C 376 MET cc_start: 0.8675 (mmm) cc_final: 0.8315 (mmt) REVERT: C 391 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8189 (p90) REVERT: D 298 MET cc_start: 0.9004 (mmm) cc_final: 0.8721 (tpp) REVERT: D 391 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8186 (p90) outliers start: 27 outliers final: 15 residues processed: 135 average time/residue: 0.1917 time to fit residues: 40.8118 Evaluate side-chains 133 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076775 restraints weight = 25212.432| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.29 r_work: 0.2872 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11948 Z= 0.119 Angle : 0.471 6.234 16244 Z= 0.235 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.030 2032 Dihedral : 9.760 85.860 2040 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.11 % Allowed : 10.48 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.80 (0.21), residues: 1516 helix: 3.14 (0.17), residues: 812 sheet: -0.29 (0.35), residues: 216 loop : 0.72 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 185 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE B 152 TYR 0.026 0.002 TYR C 382 ARG 0.002 0.000 ARG C 386 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 756) hydrogen bonds : angle 3.74654 ( 2196) covalent geometry : bond 0.00263 (11948) covalent geometry : angle 0.47150 (16244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.394 Fit side-chains REVERT: A 298 MET cc_start: 0.9034 (mmm) cc_final: 0.8739 (tpp) REVERT: A 391 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8260 (p90) REVERT: B 298 MET cc_start: 0.8910 (mmm) cc_final: 0.8621 (tpp) REVERT: B 391 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8316 (p90) REVERT: C 298 MET cc_start: 0.8934 (mmm) cc_final: 0.8649 (tpp) REVERT: C 376 MET cc_start: 0.8641 (mmm) cc_final: 0.8328 (mmt) REVERT: C 391 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8200 (p90) REVERT: D 298 MET cc_start: 0.8926 (mmm) cc_final: 0.8637 (tpp) REVERT: D 391 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8202 (p90) outliers start: 24 outliers final: 16 residues processed: 127 average time/residue: 0.1947 time to fit residues: 38.8407 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 159 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075058 restraints weight = 25358.137| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.25 r_work: 0.2836 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11948 Z= 0.154 Angle : 0.503 7.031 16244 Z= 0.252 Chirality : 0.037 0.125 1836 Planarity : 0.004 0.029 2032 Dihedral : 9.819 83.772 2040 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.02 % Allowed : 10.39 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.21), residues: 1516 helix: 3.09 (0.17), residues: 812 sheet: -0.23 (0.35), residues: 216 loop : 0.73 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 190 HIS 0.003 0.001 HIS D 64 PHE 0.009 0.001 PHE D 152 TYR 0.030 0.003 TYR A 382 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 756) hydrogen bonds : angle 3.84952 ( 2196) covalent geometry : bond 0.00351 (11948) covalent geometry : angle 0.50309 (16244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.205 Fit side-chains REVERT: A 298 MET cc_start: 0.8891 (mmm) cc_final: 0.8582 (tpp) REVERT: A 391 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8381 (p90) REVERT: B 391 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8404 (p90) REVERT: C 354 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8328 (mp0) REVERT: C 376 MET cc_start: 0.8657 (mmm) cc_final: 0.8331 (mmt) REVERT: C 391 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8325 (p90) REVERT: D 354 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8328 (mp0) REVERT: D 391 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8316 (p90) outliers start: 23 outliers final: 14 residues processed: 121 average time/residue: 0.1835 time to fit residues: 34.8869 Evaluate side-chains 124 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.094070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.077495 restraints weight = 24978.891| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.27 r_work: 0.2886 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11948 Z= 0.109 Angle : 0.487 7.287 16244 Z= 0.240 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.031 2032 Dihedral : 9.697 85.400 2040 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.50 % Allowed : 10.56 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.86 (0.21), residues: 1516 helix: 3.13 (0.17), residues: 812 sheet: -0.14 (0.36), residues: 216 loop : 0.80 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE D 152 TYR 0.027 0.002 TYR C 382 ARG 0.002 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 756) hydrogen bonds : angle 3.74346 ( 2196) covalent geometry : bond 0.00238 (11948) covalent geometry : angle 0.48676 (16244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.286 Fit side-chains REVERT: A 298 MET cc_start: 0.8965 (mmm) cc_final: 0.8665 (tpp) REVERT: A 391 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8234 (p90) REVERT: B 298 MET cc_start: 0.9070 (mmm) cc_final: 0.8807 (tpp) REVERT: B 391 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8271 (p90) REVERT: C 298 MET cc_start: 0.9081 (mmm) cc_final: 0.8819 (tpp) REVERT: C 354 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8255 (mp0) REVERT: D 298 MET cc_start: 0.9078 (mmm) cc_final: 0.8809 (tpp) REVERT: D 354 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8254 (mp0) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 0.1980 time to fit residues: 39.2595 Evaluate side-chains 128 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 364 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN D 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075402 restraints weight = 25431.721| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.26 r_work: 0.2848 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11948 Z= 0.146 Angle : 0.519 8.318 16244 Z= 0.256 Chirality : 0.037 0.126 1836 Planarity : 0.004 0.030 2032 Dihedral : 9.741 84.661 2040 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.20 % Allowed : 10.74 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.74 (0.21), residues: 1516 helix: 2.98 (0.17), residues: 812 sheet: -0.09 (0.36), residues: 216 loop : 0.80 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 190 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE B 152 TYR 0.041 0.003 TYR C 382 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 756) hydrogen bonds : angle 3.86437 ( 2196) covalent geometry : bond 0.00333 (11948) covalent geometry : angle 0.51879 (16244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4201.88 seconds wall clock time: 74 minutes 32.98 seconds (4472.98 seconds total)