Starting phenix.real_space_refine on Sat Aug 23 11:41:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgs_40466/08_2025/8sgs_40466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgs_40466/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sgs_40466/08_2025/8sgs_40466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgs_40466/08_2025/8sgs_40466_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sgs_40466/08_2025/8sgs_40466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgs_40466/08_2025/8sgs_40466.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: 2.67, per 1000 atoms: 0.23 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: 0.69 Conformation dependent library (CDL) restraints added in 405.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.56 Time building geometry restraints manager: 0.91 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 4.430 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- 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 : 6.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG D 380 TYR 0.013 0.002 TYR C 382 PHE 0.008 0.001 PHE C 152 TRP 0.004 0.001 TRP C 190 HIS 0.002 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00991 (11948) covalent geometry : angle 0.84991 (16244) hydrogen bonds : bond 0.11471 ( 756) hydrogen bonds : angle 5.24641 ( 2196) *********************** 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 : 0.438 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: 0.0899 time to fit residues: 26.4311 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 278 GLN B 292 ASN C 119 ASN C 278 GLN C 292 ASN D 119 ASN D 292 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081661 restraints weight = 24732.426| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.82 r_work: 0.3044 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 11948 Z= 0.119 Angle : 0.459 4.774 16244 Z= 0.237 Chirality : 0.037 0.128 1836 Planarity : 0.004 0.033 2032 Dihedral : 13.118 94.978 2040 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.14 % Allowed : 7.48 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.22), residues: 1516 helix: 3.09 (0.17), residues: 812 sheet: -0.68 (0.33), residues: 216 loop : 0.64 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 380 TYR 0.011 0.002 TYR B 391 PHE 0.010 0.001 PHE B 152 TRP 0.003 0.001 TRP D 185 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00245 (11948) covalent geometry : angle 0.45915 (16244) hydrogen bonds : bond 0.04691 ( 756) hydrogen bonds : angle 4.10948 ( 2196) *********************** 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 143 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8889 (tpp) cc_final: 0.8601 (tpp) REVERT: B 370 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7950 (tmm) REVERT: C 102 MET cc_start: 0.8883 (tpp) cc_final: 0.8599 (tpp) REVERT: C 370 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: C 382 TYR cc_start: 0.8887 (t80) cc_final: 0.8670 (t80) REVERT: D 102 MET cc_start: 0.8903 (tpp) cc_final: 0.8618 (tpp) REVERT: D 370 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7954 (tmm) outliers start: 13 outliers final: 4 residues processed: 135 average time/residue: 0.0775 time to fit residues: 16.7320 Evaluate side-chains 126 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 95 TYR 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 104 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 C 278 GLN D 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078031 restraints weight = 25434.656| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.79 r_work: 0.2967 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 11948 Z= 0.177 Angle : 0.510 7.973 16244 Z= 0.259 Chirality : 0.038 0.125 1836 Planarity : 0.004 0.031 2032 Dihedral : 11.486 82.862 2040 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.46 % Allowed : 8.19 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.21), residues: 1516 helix: 3.08 (0.17), residues: 812 sheet: -0.67 (0.32), residues: 216 loop : 0.61 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.017 0.002 TYR B 391 PHE 0.009 0.001 PHE B 152 TRP 0.006 0.001 TRP B 185 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00401 (11948) covalent geometry : angle 0.51043 (16244) hydrogen bonds : bond 0.05048 ( 756) hydrogen bonds : angle 3.99124 ( 2196) *********************** 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 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8486 (p90) REVERT: B 102 MET cc_start: 0.9058 (tpp) cc_final: 0.8803 (tpp) REVERT: B 370 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8921 (tpt) REVERT: B 391 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8519 (p90) REVERT: C 102 MET cc_start: 0.9052 (tpp) cc_final: 0.8780 (tpp) REVERT: C 391 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8519 (p90) REVERT: D 102 MET cc_start: 0.9058 (tpp) cc_final: 0.8787 (tpp) outliers start: 28 outliers final: 6 residues processed: 140 average time/residue: 0.0754 time to fit residues: 16.4064 Evaluate side-chains 115 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 391 TYR 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 B residue 391 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 391 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 62 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.092691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075676 restraints weight = 25271.108| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.32 r_work: 0.2853 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2228 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= 0.136 Angle : 0.477 6.936 16244 Z= 0.243 Chirality : 0.037 0.127 1836 Planarity : 0.004 0.031 2032 Dihedral : 10.322 79.298 2040 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.11 % Allowed : 9.07 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.21), residues: 1516 helix: 3.11 (0.17), residues: 812 sheet: -0.55 (0.33), residues: 216 loop : 0.66 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 380 TYR 0.015 0.002 TYR A 410 PHE 0.009 0.001 PHE B 152 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00302 (11948) covalent geometry : angle 0.47739 (16244) hydrogen bonds : bond 0.04573 ( 756) hydrogen bonds : angle 3.88557 ( 2196) *********************** 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 144 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8829 (tpp) cc_final: 0.8537 (tpp) REVERT: B 102 MET cc_start: 0.8816 (tpp) cc_final: 0.8467 (tpp) REVERT: B 370 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8710 (tpt) REVERT: C 102 MET cc_start: 0.8824 (tpp) cc_final: 0.8460 (tpp) REVERT: D 102 MET cc_start: 0.8826 (tpp) cc_final: 0.8455 (tpp) REVERT: D 391 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8362 (p90) REVERT: D 392 GLU cc_start: 0.8772 (tp30) cc_final: 0.8312 (tp30) outliers start: 24 outliers final: 11 residues processed: 133 average time/residue: 0.1002 time to fit residues: 20.4960 Evaluate side-chains 117 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 B residue 95 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 391 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.093370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077465 restraints weight = 25242.611| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.87 r_work: 0.2971 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2380 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= 0.147 Angle : 0.476 6.334 16244 Z= 0.243 Chirality : 0.037 0.126 1836 Planarity : 0.004 0.031 2032 Dihedral : 9.912 80.837 2040 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.99 % Allowed : 8.63 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.21), residues: 1516 helix: 3.12 (0.17), residues: 812 sheet: -0.44 (0.34), residues: 216 loop : 0.59 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 325 TYR 0.014 0.002 TYR A 410 PHE 0.009 0.001 PHE B 152 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00331 (11948) covalent geometry : angle 0.47619 (16244) hydrogen bonds : bond 0.04659 ( 756) hydrogen bonds : angle 3.86756 ( 2196) *********************** 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 144 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.9035 (tpp) cc_final: 0.8718 (tpp) REVERT: A 391 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8493 (p90) REVERT: B 102 MET cc_start: 0.8996 (tpp) cc_final: 0.8735 (tpp) REVERT: B 370 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8922 (tpt) REVERT: B 391 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8488 (p90) REVERT: B 392 GLU cc_start: 0.8633 (tp30) cc_final: 0.8244 (tp30) REVERT: C 102 MET cc_start: 0.9002 (tpp) cc_final: 0.8729 (tpp) REVERT: C 392 GLU cc_start: 0.8622 (tp30) cc_final: 0.8179 (tp30) REVERT: D 102 MET cc_start: 0.9006 (tpp) cc_final: 0.8752 (tpp) REVERT: D 391 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8426 (p90) outliers start: 34 outliers final: 14 residues processed: 132 average time/residue: 0.0855 time to fit residues: 18.2291 Evaluate side-chains 121 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 370 MET 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 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 100 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.093960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077795 restraints weight = 25211.676| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.88 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2462 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= 0.147 Angle : 0.472 6.592 16244 Z= 0.240 Chirality : 0.037 0.127 1836 Planarity : 0.003 0.031 2032 Dihedral : 9.872 82.264 2040 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 9.60 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.21), residues: 1516 helix: 3.09 (0.17), residues: 816 sheet: -0.36 (0.35), residues: 216 loop : 0.61 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 380 TYR 0.014 0.002 TYR D 98 PHE 0.008 0.001 PHE B 152 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00333 (11948) covalent geometry : angle 0.47195 (16244) hydrogen bonds : bond 0.04615 ( 756) hydrogen bonds : angle 3.87268 ( 2196) *********************** 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 139 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8983 (tpp) cc_final: 0.8745 (tpp) REVERT: B 102 MET cc_start: 0.9030 (tpp) cc_final: 0.8758 (tpp) REVERT: B 298 MET cc_start: 0.9073 (mmm) cc_final: 0.8798 (tpp) REVERT: B 370 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8814 (tpt) REVERT: C 102 MET cc_start: 0.9003 (tpp) cc_final: 0.8744 (tpp) REVERT: C 298 MET cc_start: 0.9059 (mmm) cc_final: 0.8778 (tpp) REVERT: C 391 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8411 (p90) REVERT: C 392 GLU cc_start: 0.8660 (tp30) cc_final: 0.8294 (tp30) REVERT: D 102 MET cc_start: 0.9028 (tpp) cc_final: 0.8778 (tpp) REVERT: D 298 MET cc_start: 0.9070 (mmm) cc_final: 0.8788 (tpp) REVERT: D 391 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8542 (p90) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 0.0793 time to fit residues: 16.3157 Evaluate side-chains 122 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 370 MET 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 40 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3351 r_free = 0.3351 target = 0.091974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074912 restraints weight = 25180.520| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.32 r_work: 0.2832 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.027 11948 Z= 0.142 Angle : 0.479 5.715 16244 Z= 0.242 Chirality : 0.037 0.131 1836 Planarity : 0.003 0.031 2032 Dihedral : 9.904 83.384 2040 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.20 % Allowed : 10.12 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.21), residues: 1516 helix: 3.12 (0.17), residues: 812 sheet: -0.33 (0.36), residues: 216 loop : 0.56 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.016 0.002 TYR B 98 PHE 0.008 0.001 PHE B 152 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00324 (11948) covalent geometry : angle 0.47929 (16244) hydrogen bonds : bond 0.04571 ( 756) hydrogen bonds : angle 3.83976 ( 2196) *********************** 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 136 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8796 (tpp) cc_final: 0.8533 (tpp) REVERT: A 298 MET cc_start: 0.8905 (mmm) cc_final: 0.8581 (tpp) REVERT: A 391 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8346 (p90) REVERT: B 102 MET cc_start: 0.8836 (tpp) cc_final: 0.8540 (tpp) REVERT: B 391 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8503 (p90) REVERT: C 102 MET cc_start: 0.8827 (tpp) cc_final: 0.8536 (tpp) REVERT: C 391 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8419 (p90) REVERT: C 392 GLU cc_start: 0.8889 (tp30) cc_final: 0.8399 (tp30) REVERT: D 102 MET cc_start: 0.8829 (tpp) cc_final: 0.8525 (tpp) REVERT: D 391 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8359 (p90) outliers start: 25 outliers final: 16 residues processed: 126 average time/residue: 0.0815 time to fit residues: 16.4120 Evaluate side-chains 126 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 50 optimal weight: 0.0670 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.093500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.076655 restraints weight = 25138.533| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.32 r_work: 0.2867 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11948 Z= 0.110 Angle : 0.466 6.391 16244 Z= 0.232 Chirality : 0.036 0.127 1836 Planarity : 0.003 0.032 2032 Dihedral : 9.927 84.932 2040 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.02 % Allowed : 9.86 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.21), residues: 1516 helix: 3.12 (0.17), residues: 812 sheet: -0.28 (0.36), residues: 216 loop : 0.62 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 386 TYR 0.025 0.002 TYR A 382 PHE 0.007 0.001 PHE A 152 TRP 0.004 0.001 TRP C 329 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00239 (11948) covalent geometry : angle 0.46641 (16244) hydrogen bonds : bond 0.04247 ( 756) hydrogen bonds : angle 3.73939 ( 2196) *********************** 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 142 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8176 (p90) REVERT: B 102 MET cc_start: 0.8800 (tpp) cc_final: 0.8528 (tpp) REVERT: B 298 MET cc_start: 0.9005 (mmm) cc_final: 0.8714 (tpp) REVERT: C 102 MET cc_start: 0.8795 (tpp) cc_final: 0.8518 (tpp) REVERT: C 298 MET cc_start: 0.9018 (mmm) cc_final: 0.8733 (tpp) REVERT: C 391 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8328 (p90) REVERT: C 392 GLU cc_start: 0.8910 (tp30) cc_final: 0.8428 (tp30) REVERT: D 102 MET cc_start: 0.8791 (tpp) cc_final: 0.8499 (tpp) REVERT: D 298 MET cc_start: 0.9013 (mmm) cc_final: 0.8719 (tpp) REVERT: D 391 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8218 (p90) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.0748 time to fit residues: 14.9364 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 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 391 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 133 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.092201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075207 restraints weight = 24947.461| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.28 r_work: 0.2840 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2613 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= 0.142 Angle : 0.510 13.338 16244 Z= 0.253 Chirality : 0.037 0.128 1836 Planarity : 0.004 0.031 2032 Dihedral : 9.988 78.279 2040 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.11 % Allowed : 10.12 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.21), residues: 1516 helix: 3.08 (0.17), residues: 812 sheet: -0.34 (0.36), residues: 216 loop : 0.63 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 325 TYR 0.034 0.003 TYR A 382 PHE 0.008 0.001 PHE C 152 TRP 0.004 0.001 TRP A 190 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00325 (11948) covalent geometry : angle 0.51024 (16244) hydrogen bonds : bond 0.04482 ( 756) hydrogen bonds : angle 3.78636 ( 2196) *********************** 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: 24 poor density : 113 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9009 (mmm) cc_final: 0.8698 (tpp) REVERT: A 354 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8068 (mp0) REVERT: A 391 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8287 (p90) REVERT: A 392 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8578 (mm-30) REVERT: B 102 MET cc_start: 0.8817 (tpp) cc_final: 0.8505 (tpp) REVERT: B 298 MET cc_start: 0.8909 (mmm) cc_final: 0.8606 (tpp) REVERT: B 391 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8302 (p90) REVERT: C 102 MET cc_start: 0.8814 (tpp) cc_final: 0.8526 (tpp) REVERT: C 298 MET cc_start: 0.8913 (mmm) cc_final: 0.8611 (tpp) REVERT: C 391 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8331 (p90) REVERT: C 392 GLU cc_start: 0.8934 (tp30) cc_final: 0.8508 (tp30) REVERT: D 102 MET cc_start: 0.8796 (tpp) cc_final: 0.8484 (tpp) REVERT: D 298 MET cc_start: 0.8913 (mmm) cc_final: 0.8608 (tpp) REVERT: D 391 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8303 (p90) outliers start: 24 outliers final: 13 residues processed: 121 average time/residue: 0.0720 time to fit residues: 14.0511 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 : 0.402 ------------------------------------------------------------------------------- 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 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 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 151 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 148 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.094289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.077508 restraints weight = 25003.388| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.31 r_work: 0.2889 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2728 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= 0.106 Angle : 0.469 11.438 16244 Z= 0.233 Chirality : 0.036 0.125 1836 Planarity : 0.003 0.032 2032 Dihedral : 9.804 78.952 2040 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.02 % Allowed : 9.68 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.21), residues: 1516 helix: 3.10 (0.17), residues: 812 sheet: -0.30 (0.36), residues: 216 loop : 0.75 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 380 TYR 0.029 0.002 TYR C 382 PHE 0.007 0.001 PHE A 152 TRP 0.005 0.001 TRP C 329 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00228 (11948) covalent geometry : angle 0.46922 (16244) hydrogen bonds : bond 0.04092 ( 756) hydrogen bonds : angle 3.69123 ( 2196) ********************** 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 144 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.321 Fit side-chains REVERT: A 298 MET cc_start: 0.8973 (mmm) cc_final: 0.8682 (tpp) REVERT: A 354 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8033 (mp0) REVERT: A 391 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8187 (p90) REVERT: B 102 MET cc_start: 0.8798 (tpp) cc_final: 0.8530 (tpp) REVERT: B 298 MET cc_start: 0.8977 (mmm) cc_final: 0.8686 (tpp) REVERT: B 354 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8199 (mp0) REVERT: B 391 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8153 (p90) REVERT: C 102 MET cc_start: 0.8805 (tpp) cc_final: 0.8534 (tpp) REVERT: C 298 MET cc_start: 0.8982 (mmm) cc_final: 0.8693 (tpp) REVERT: C 354 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8226 (mp0) REVERT: C 391 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8289 (p90) REVERT: C 392 GLU cc_start: 0.8873 (tp30) cc_final: 0.8363 (tp30) REVERT: D 102 MET cc_start: 0.8805 (tpp) cc_final: 0.8525 (tpp) REVERT: D 298 MET cc_start: 0.8977 (mmm) cc_final: 0.8684 (tpp) REVERT: D 354 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8209 (mp0) REVERT: D 370 MET cc_start: 0.8423 (tpt) cc_final: 0.8085 (tpt) REVERT: D 391 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8211 (p90) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 0.0809 time to fit residues: 16.5111 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 : 0.461 ------------------------------------------------------------------------------- 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 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 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 87 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3378 r_free = 0.3378 target = 0.093323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076369 restraints weight = 24981.774| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.28 r_work: 0.2867 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11948 Z= 0.127 Angle : 0.491 11.527 16244 Z= 0.244 Chirality : 0.036 0.124 1836 Planarity : 0.003 0.031 2032 Dihedral : 9.870 79.248 2040 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.85 % Allowed : 10.12 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.21), residues: 1516 helix: 3.02 (0.17), residues: 812 sheet: -0.31 (0.36), residues: 216 loop : 0.73 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 380 TYR 0.040 0.002 TYR C 382 PHE 0.007 0.001 PHE C 152 TRP 0.004 0.001 TRP D 329 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00285 (11948) covalent geometry : angle 0.49111 (16244) hydrogen bonds : bond 0.04266 ( 756) hydrogen bonds : angle 3.74951 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.12 seconds wall clock time: 35 minutes 19.44 seconds (2119.44 seconds total)