Starting phenix.real_space_refine on Wed Jul 30 00:47:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgs_40466/07_2025/8sgs_40466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgs_40466/07_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_40466/07_2025/8sgs_40466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgs_40466/07_2025/8sgs_40466.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgs_40466/07_2025/8sgs_40466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgs_40466/07_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-5711/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: 9.79, per 1000 atoms: 0.84 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 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: 1.23 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: 3.77 Time building geometry restraints manager: 3.64 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: 0.08 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: 1.970 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.980 Find NCS groups from input model: 0.230 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- 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 : 1.148 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: 0.2352 time to fit residues: 67.9260 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 : 1.179 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081558 restraints weight = 24822.592| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.73 r_work: 0.3034 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- 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 : 2.055 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: 0.8612 (tpt) REVERT: B 102 MET cc_start: 0.8933 (tpp) cc_final: 0.8659 (tpp) REVERT: B 370 MET cc_start: 0.8897 (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: 0.8664 (t80) REVERT: D 102 MET cc_start: 0.8949 (tpp) cc_final: 0.8657 (tpp) REVERT: D 370 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8544 (tpt) outliers start: 14 outliers final: 6 residues processed: 134 average time/residue: 0.2090 time to fit residues: 43.9468 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 : 1.222 ------------------------------------------------------------------------------- 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: 0.6980 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.094519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077998 restraints weight = 25203.150| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.25 r_work: 0.2897 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1947 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= 0.115 Angle : 0.457 8.527 16244 Z= 0.230 Chirality : 0.036 0.124 1836 Planarity : 0.004 0.031 2032 Dihedral : 11.069 81.822 2040 Min Nonbonded Distance : 2.353 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: 2.74 (0.21), residues: 1516 helix: 3.17 (0.17), residues: 812 sheet: -0.61 (0.33), residues: 216 loop : 0.71 (0.29), residues: 488 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 0.010 0.002 TYR A 391 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 756) hydrogen bonds : angle 3.84789 ( 2196) covalent geometry : bond 0.00248 (11948) covalent geometry : angle 0.45730 (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 145 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 133 average time/residue: 0.1987 time to fit residues: 40.6814 Evaluate side-chains 113 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.093434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076462 restraints weight = 24826.136| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.30 r_work: 0.2865 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11948 Z= 0.133 Angle : 0.477 8.346 16244 Z= 0.239 Chirality : 0.037 0.126 1836 Planarity : 0.004 0.031 2032 Dihedral : 10.206 80.990 2040 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.85 % Allowed : 9.51 % Favored : 88.64 % 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 (0.21), residues: 1516 helix: 3.17 (0.17), residues: 812 sheet: -0.51 (0.33), residues: 216 loop : 0.67 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 185 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE A 152 TYR 0.015 0.002 TYR A 410 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 756) hydrogen bonds : angle 3.84927 ( 2196) covalent geometry : bond 0.00294 (11948) covalent geometry : angle 0.47726 (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 135 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.272 Fit side-chains REVERT: A 391 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8295 (p90) REVERT: B 354 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8221 (mp0) REVERT: C 354 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8254 (mp0) REVERT: D 354 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8245 (mp0) outliers start: 21 outliers final: 8 residues processed: 125 average time/residue: 0.1922 time to fit residues: 37.6005 Evaluate side-chains 116 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 391 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU 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: 0.7980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076045 restraints weight = 25031.755| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.30 r_work: 0.2859 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11948 Z= 0.129 Angle : 0.466 7.496 16244 Z= 0.234 Chirality : 0.037 0.126 1836 Planarity : 0.004 0.030 2032 Dihedral : 10.082 82.581 2040 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.43 % Allowed : 8.71 % Favored : 87.85 % 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: 2.79 (0.21), residues: 1516 helix: 3.19 (0.17), residues: 812 sheet: -0.43 (0.34), residues: 216 loop : 0.66 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 185 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE A 152 TYR 0.013 0.002 TYR B 410 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 756) hydrogen bonds : angle 3.82419 ( 2196) covalent geometry : bond 0.00287 (11948) covalent geometry : angle 0.46629 (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 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.224 Fit side-chains REVERT: B 354 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8263 (mp0) REVERT: B 391 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8453 (p90) REVERT: C 354 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8267 (mp0) REVERT: C 391 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8338 (p90) REVERT: D 354 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8271 (mp0) REVERT: D 391 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8349 (p90) outliers start: 39 outliers final: 14 residues processed: 143 average time/residue: 0.1922 time to fit residues: 43.1080 Evaluate side-chains 125 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 149 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 148 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.093611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076664 restraints weight = 25225.621| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.34 r_work: 0.2866 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11948 Z= 0.117 Angle : 0.462 8.386 16244 Z= 0.230 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.031 2032 Dihedral : 10.012 84.579 2040 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.55 % Allowed : 10.12 % Favored : 87.32 % 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 (0.21), residues: 1516 helix: 3.14 (0.17), residues: 812 sheet: -0.34 (0.35), residues: 216 loop : 0.64 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 177 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE B 152 TYR 0.014 0.002 TYR C 98 ARG 0.002 0.000 ARG D 380 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 756) hydrogen bonds : angle 3.79521 ( 2196) covalent geometry : bond 0.00258 (11948) covalent geometry : angle 0.46250 (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 152 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.323 Fit side-chains REVERT: A 298 MET cc_start: 0.8946 (mmm) cc_final: 0.8630 (tpp) REVERT: A 334 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 391 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8458 (p90) REVERT: B 298 MET cc_start: 0.8945 (mmm) cc_final: 0.8646 (tpp) REVERT: B 354 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8225 (mp0) REVERT: B 391 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8225 (p90) REVERT: C 298 MET cc_start: 0.8951 (mmm) cc_final: 0.8651 (tpp) REVERT: C 354 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8218 (mp0) REVERT: C 391 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8260 (p90) REVERT: D 298 MET cc_start: 0.8959 (mmm) cc_final: 0.8660 (tpp) REVERT: D 354 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8233 (mp0) REVERT: D 391 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8265 (p90) outliers start: 29 outliers final: 16 residues processed: 135 average time/residue: 0.1950 time to fit residues: 41.0872 Evaluate side-chains 132 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 334 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 278 GLN B 159 ASN B 278 GLN C 159 ASN C 278 GLN D 159 ASN D 278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.074990 restraints weight = 25536.290| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.63 r_work: 0.2929 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 11948 Z= 0.345 Angle : 0.669 10.634 16244 Z= 0.336 Chirality : 0.043 0.131 1836 Planarity : 0.004 0.040 2032 Dihedral : 10.544 79.782 2040 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.64 % Allowed : 11.18 % Favored : 86.18 % 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: 2.34 (0.21), residues: 1516 helix: 2.83 (0.17), residues: 808 sheet: -0.43 (0.35), residues: 216 loop : 0.37 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 190 HIS 0.005 0.002 HIS D 405 PHE 0.012 0.002 PHE A 213 TYR 0.025 0.003 TYR B 391 ARG 0.006 0.001 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.05978 ( 756) hydrogen bonds : angle 4.37100 ( 2196) covalent geometry : bond 0.00797 (11948) covalent geometry : angle 0.66924 (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 131 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 1.324 Fit side-chains REVERT: D 102 MET cc_start: 0.8845 (tpp) cc_final: 0.8572 (tpp) outliers start: 30 outliers final: 15 residues processed: 120 average time/residue: 0.1943 time to fit residues: 37.1863 Evaluate side-chains 117 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 278 GLN B 159 ASN B 278 GLN C 159 ASN C 278 GLN D 159 ASN D 278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079832 restraints weight = 25194.995| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.63 r_work: 0.3028 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2624 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= 0.120 Angle : 0.510 11.006 16244 Z= 0.251 Chirality : 0.037 0.128 1836 Planarity : 0.003 0.031 2032 Dihedral : 10.165 84.497 2040 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.67 % Allowed : 11.97 % Favored : 86.36 % 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: 2.49 (0.21), residues: 1516 helix: 2.92 (0.17), residues: 812 sheet: -0.37 (0.36), residues: 216 loop : 0.47 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 329 HIS 0.003 0.001 HIS B 64 PHE 0.007 0.001 PHE A 152 TYR 0.018 0.002 TYR A 98 ARG 0.002 0.000 ARG C 386 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 756) hydrogen bonds : angle 3.99294 ( 2196) covalent geometry : bond 0.00263 (11948) covalent geometry : angle 0.51038 (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 131 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.494 Fit side-chains REVERT: A 298 MET cc_start: 0.9045 (mmm) cc_final: 0.8819 (tpp) REVERT: A 382 TYR cc_start: 0.8778 (t80) cc_final: 0.8540 (t80) REVERT: A 391 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8415 (p90) REVERT: B 298 MET cc_start: 0.9053 (mmm) cc_final: 0.8836 (tpp) REVERT: B 376 MET cc_start: 0.8987 (mmt) cc_final: 0.8765 (mmt) REVERT: B 382 TYR cc_start: 0.8789 (t80) cc_final: 0.8570 (t80) REVERT: B 391 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8309 (p90) REVERT: C 298 MET cc_start: 0.9054 (mmm) cc_final: 0.8838 (tpp) REVERT: C 382 TYR cc_start: 0.8794 (t80) cc_final: 0.8539 (t80) REVERT: C 391 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8310 (p90) REVERT: D 298 MET cc_start: 0.9042 (mmm) cc_final: 0.8831 (tpp) REVERT: D 382 TYR cc_start: 0.8803 (t80) cc_final: 0.8557 (t80) REVERT: D 391 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8283 (p90) outliers start: 19 outliers final: 8 residues processed: 120 average time/residue: 0.2004 time to fit residues: 37.5439 Evaluate side-chains 122 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU 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 391 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 147 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076549 restraints weight = 25230.974| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.30 r_work: 0.2865 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2693 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= 0.111 Angle : 0.494 7.930 16244 Z= 0.241 Chirality : 0.036 0.127 1836 Planarity : 0.003 0.031 2032 Dihedral : 9.988 86.753 2040 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.67 % Allowed : 11.00 % Favored : 87.32 % 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: 2.66 (0.21), residues: 1516 helix: 3.02 (0.17), residues: 812 sheet: -0.33 (0.36), residues: 216 loop : 0.65 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 329 HIS 0.003 0.001 HIS C 64 PHE 0.007 0.001 PHE B 152 TYR 0.022 0.002 TYR B 98 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 756) hydrogen bonds : angle 3.84128 ( 2196) covalent geometry : bond 0.00241 (11948) covalent geometry : angle 0.49359 (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 137 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.200 Fit side-chains REVERT: A 298 MET cc_start: 0.8891 (mmm) cc_final: 0.8581 (tpp) REVERT: A 354 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8220 (mp0) REVERT: A 391 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8187 (p90) REVERT: B 298 MET cc_start: 0.8911 (mmm) cc_final: 0.8616 (tpp) REVERT: B 370 MET cc_start: 0.8412 (tpt) cc_final: 0.8199 (tpt) REVERT: B 376 MET cc_start: 0.8571 (mmt) cc_final: 0.8285 (mmt) REVERT: B 391 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8313 (p90) REVERT: C 298 MET cc_start: 0.8908 (mmm) cc_final: 0.8608 (tpp) REVERT: C 370 MET cc_start: 0.8405 (tpt) cc_final: 0.8198 (tpt) REVERT: C 376 MET cc_start: 0.8560 (mmt) cc_final: 0.8264 (mmt) REVERT: C 391 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8204 (p90) REVERT: D 298 MET cc_start: 0.8903 (mmm) cc_final: 0.8601 (tpp) REVERT: D 370 MET cc_start: 0.8416 (tpt) cc_final: 0.8207 (tpt) REVERT: D 376 MET cc_start: 0.8552 (mmt) cc_final: 0.8266 (mmt) REVERT: D 391 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8197 (p90) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.1883 time to fit residues: 36.1954 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 364 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 392 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 50 optimal weight: 0.0370 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- 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 B 278 GLN 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 = 0.3407 r_free = 0.3407 target = 0.094765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078456 restraints weight = 24823.087| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.23 r_work: 0.2916 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11948 Z= 0.097 Angle : 0.495 8.363 16244 Z= 0.237 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.033 2032 Dihedral : 9.802 81.211 2040 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.58 % Allowed : 11.62 % Favored : 86.80 % 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: 2.70 (0.21), residues: 1516 helix: 3.02 (0.17), residues: 812 sheet: -0.38 (0.36), residues: 216 loop : 0.79 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 329 HIS 0.002 0.001 HIS D 381 PHE 0.007 0.001 PHE D 261 TYR 0.019 0.002 TYR C 98 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 756) hydrogen bonds : angle 3.74533 ( 2196) covalent geometry : bond 0.00199 (11948) covalent geometry : angle 0.49516 (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 150 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.363 Fit side-chains REVERT: A 298 MET cc_start: 0.8986 (mmm) cc_final: 0.8703 (tpp) REVERT: A 391 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8104 (p90) REVERT: B 298 MET cc_start: 0.8996 (mmm) cc_final: 0.8720 (tpp) REVERT: B 354 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8223 (mp0) REVERT: B 376 MET cc_start: 0.8614 (mmt) cc_final: 0.8331 (mmt) REVERT: B 391 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8202 (p90) REVERT: C 298 MET cc_start: 0.8992 (mmm) cc_final: 0.8710 (tpp) REVERT: C 354 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8216 (mp0) REVERT: C 370 MET cc_start: 0.8442 (tpt) cc_final: 0.8240 (tpt) REVERT: C 376 MET cc_start: 0.8607 (mmt) cc_final: 0.8392 (mmt) REVERT: D 298 MET cc_start: 0.8986 (mmm) cc_final: 0.8704 (tpp) REVERT: D 354 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8230 (mp0) REVERT: D 376 MET cc_start: 0.8622 (mmt) cc_final: 0.8339 (mmt) outliers start: 18 outliers final: 7 residues processed: 135 average time/residue: 0.2046 time to fit residues: 43.2247 Evaluate side-chains 120 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 149 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS B 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076786 restraints weight = 25236.776| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.24 r_work: 0.2883 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11948 Z= 0.122 Angle : 0.525 9.399 16244 Z= 0.254 Chirality : 0.036 0.126 1836 Planarity : 0.003 0.033 2032 Dihedral : 9.811 82.301 2040 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.32 % Allowed : 12.85 % Favored : 85.83 % 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: 2.59 (0.21), residues: 1516 helix: 2.89 (0.17), residues: 812 sheet: -0.34 (0.36), residues: 216 loop : 0.78 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 329 HIS 0.003 0.001 HIS B 64 PHE 0.009 0.001 PHE D 152 TYR 0.023 0.002 TYR D 98 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 756) hydrogen bonds : angle 3.80476 ( 2196) covalent geometry : bond 0.00275 (11948) covalent geometry : angle 0.52543 (16244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5203.91 seconds wall clock time: 93 minutes 32.40 seconds (5612.40 seconds total)