Starting phenix.real_space_refine on Fri Oct 23 16:57:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbw_52032/10_2026/9hbw_52032.map" } resolution = 3.59 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= -0.000 sd= 0.007 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 54 5.49 5 S 68 5.16 5 C 6572 2.51 5 N 1919 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10702 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 546 Classifications: {'RNA': 28} Modifications used: {'rna2p': 1, 'rna3p': 27} Link IDs: {'rna2p': 1, 'rna3p': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'RNA': 8} Modifications used: {'rna2p': 2, 'rna3p': 6} Link IDs: {'rna2p': 1, 'rna3p': 6} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'RNA': 10} Modifications used: {'rna2p': 2, 'rna3p': 8} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2403 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'RNA': 8} Modifications used: {'rna2p': 1, 'rna3p': 7} Link IDs: {'rna2p': 1, 'rna3p': 6} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 2.61, per 1000 atoms: 0.24 Number of scatterers: 10702 At special positions: 0 Unit cell: (115.902, 120.012, 78.912, 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 68 16.00 P 54 15.00 O 2089 8.00 N 1919 7.00 C 6572 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: 0.86 Conformation dependent library (CDL) restraints added in 322.3 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 10 sheets defined 51.2% alpha, 5.1% beta 0 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.505A pdb=" N PHE A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 143 through 173 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.523A pdb=" N LEU A 266 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 58 through 74 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.655A pdb=" N VAL B 128 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 143 through 173 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 263 through 270 removed outlier: 3.685A pdb=" N LEU B 266 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.667A pdb=" N GLY B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.511A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 73 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.449A pdb=" N GLU C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.698A pdb=" N LEU C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.921A pdb=" N GLY C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.566A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 175 removed outlier: 4.224A pdb=" N VAL D 174 " --> pdb=" O TYR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.761A pdb=" N ALA D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.640A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.903A pdb=" N GLY D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 removed outlier: 3.515A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA5, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.703A pdb=" N LEU C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AA8, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'D' and resid 270 through 273 removed outlier: 4.071A pdb=" N SER D 273 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE D 279 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 285 through 287 removed outlier: 4.477A pdb=" N ALA D 324 " --> pdb=" O LEU D 287 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3346 1.34 - 1.46: 2495 1.46 - 1.58: 4967 1.58 - 1.69: 103 1.69 - 1.81: 92 Bond restraints: 11003 Sorted by residual: bond pdb=" N3 Y5P O 12 " pdb=" C4 Y5P O 12 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" N3 Y5P O 26 " pdb=" C4 Y5P O 26 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" N3 Y5P O 19 " pdb=" C4 Y5P O 19 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" N3 Y5P O 16 " pdb=" C4 Y5P O 16 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" N3 Y5P O 14 " pdb=" C4 Y5P O 14 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 10998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 14650 2.39 - 4.79: 253 4.79 - 7.18: 74 7.18 - 9.57: 27 9.57 - 11.96: 19 Bond angle restraints: 15023 Sorted by residual: angle pdb=" N1 Y5P O 39 " pdb=" C2 Y5P O 39 " pdb=" N3 Y5P O 39 " ideal model delta sigma weight residual 126.68 114.72 11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 Y5P R 9 " pdb=" C2 Y5P R 9 " pdb=" N3 Y5P R 9 " ideal model delta sigma weight residual 126.68 114.79 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P P 8 " pdb=" C2 Y5P P 8 " pdb=" N3 Y5P P 8 " ideal model delta sigma weight residual 126.68 114.81 11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P Q 9 " pdb=" C2 Y5P Q 9 " pdb=" N3 Y5P Q 9 " ideal model delta sigma weight residual 126.68 114.84 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P O 18 " pdb=" C2 Y5P O 18 " pdb=" N3 Y5P O 18 " ideal model delta sigma weight residual 126.68 114.88 11.80 3.00e+00 1.11e-01 1.55e+01 ... (remaining 15018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 7099 34.42 - 68.84: 272 68.84 - 103.26: 174 103.26 - 137.68: 2 137.68 - 172.10: 1 Dihedral angle restraints: 7548 sinusoidal: 3970 harmonic: 3578 Sorted by residual: dihedral pdb=" P Y5P O 37 " pdb=" O5' Y5P O 37 " pdb=" C5' Y5P O 37 " pdb=" C4' Y5P O 37 " ideal model delta sinusoidal sigma weight residual -111.10 61.00 -172.10 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" P Y5P O 19 " pdb=" O5' Y5P O 19 " pdb=" C5' Y5P O 19 " pdb=" C4' Y5P O 19 " ideal model delta sinusoidal sigma weight residual 248.90 141.35 107.55 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" P Y5P Q 8 " pdb=" O5' Y5P Q 8 " pdb=" C5' Y5P Q 8 " pdb=" C4' Y5P Q 8 " ideal model delta sinusoidal sigma weight residual 248.90 144.03 104.87 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 7545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1219 0.031 - 0.063: 342 0.063 - 0.094: 68 0.094 - 0.126: 51 0.126 - 0.157: 5 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA ILE B 230 " pdb=" N ILE B 230 " pdb=" C ILE B 230 " pdb=" CB ILE B 230 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA VAL C 248 " pdb=" N VAL C 248 " pdb=" C VAL C 248 " pdb=" CB VAL C 248 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1682 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' P5P O 34 " 0.006 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" N9 P5P O 34 " 0.005 2.00e-02 2.50e+03 pdb=" C8 P5P O 34 " -0.003 2.00e-02 2.50e+03 pdb=" N7 P5P O 34 " -0.006 2.00e-02 2.50e+03 pdb=" C5 P5P O 34 " -0.002 2.00e-02 2.50e+03 pdb=" C6 P5P O 34 " -0.011 2.00e-02 2.50e+03 pdb=" N1 P5P O 34 " 0.039 2.00e-02 2.50e+03 pdb=" C2 P5P O 34 " -0.033 2.00e-02 2.50e+03 pdb=" N3 P5P O 34 " 0.001 2.00e-02 2.50e+03 pdb=" C4 P5P O 34 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 285 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO D 286 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' P5P Q 11 " -0.015 2.00e-02 2.50e+03 8.15e-03 1.66e+00 pdb=" N9 P5P Q 11 " 0.020 2.00e-02 2.50e+03 pdb=" C8 P5P Q 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 P5P Q 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 P5P Q 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 P5P Q 11 " -0.004 2.00e-02 2.50e+03 pdb=" N1 P5P Q 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 P5P Q 11 " 0.000 2.00e-02 2.50e+03 pdb=" N3 P5P Q 11 " 0.003 2.00e-02 2.50e+03 pdb=" C4 P5P Q 11 " 0.002 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 70 2.55 - 3.14: 8417 3.14 - 3.73: 16718 3.73 - 4.31: 22356 4.31 - 4.90: 36562 Nonbonded interactions: 84123 Sorted by model distance: nonbonded pdb=" O2' P5P Q 11 " pdb=" O4' Y5P Q 12 " model vdw 1.965 3.040 nonbonded pdb=" OG SER A 308 " pdb=" O GLY D 338 " model vdw 1.973 3.040 nonbonded pdb=" OG1 THR A 182 " pdb=" OD2 ASP A 185 " model vdw 1.995 3.040 nonbonded pdb=" O2' P5P O 33 " pdb=" OP1 P5P O 34 " model vdw 2.004 3.040 nonbonded pdb=" O ASP C 185 " pdb=" OH TYR C 191 " model vdw 2.066 3.040 ... (remaining 84118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 34 through 288 or resid 291 through 312 or resid 317 throu \ gh 350)) selection = (chain 'C' and (resid 34 through 288 or resid 291 through 312 or resid 317 throu \ gh 350)) selection = (chain 'D' and (resid 34 through 288 or resid 291 through 312 or resid 317 throu \ gh 350)) } ncs_group { reference = chain 'P' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 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 : 0.009 0.123 11003 Z= 0.472 Angle : 0.943 11.965 15023 Z= 0.382 Chirality : 0.035 0.157 1685 Planarity : 0.003 0.034 1748 Dihedral : 21.323 172.099 5250 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.57 % Allowed : 15.82 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.18 (0.26), residues: 1245 helix: 1.69 (0.22), residues: 596 sheet: -0.52 (0.77), residues: 56 loop : 0.07 (0.29), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 112 TYR 0.006 0.001 TYR B 197 PHE 0.013 0.001 PHE C 189 TRP 0.015 0.001 TRP C 259 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.47 (11003) covalent geometry : angle 0.94291 / 0.38 (15023) hydrogen bonds : bond 0.14574 / 9.79 ( 437) hydrogen bonds : angle 4.94025 / 3.48 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 339 time to evaluate : 0.403 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7110 (tm-30) REVERT: B 76 SER cc_start: 0.8317 (m) cc_final: 0.8005 (p) REVERT: B 197 TYR cc_start: 0.8129 (t80) cc_final: 0.7924 (t80) REVERT: C 134 LYS cc_start: 0.6259 (mptt) cc_final: 0.5632 (tttt) REVERT: C 326 GLN cc_start: 0.6364 (tm-30) cc_final: 0.6001 (tm-30) REVERT: C 340 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7373 (p) REVERT: D 135 MET cc_start: 0.0818 (tpp) cc_final: 0.0506 (ppp) REVERT: D 166 TRP cc_start: 0.7206 (t60) cc_final: 0.6838 (t60) REVERT: D 231 PRO cc_start: 0.6757 (Cg_exo) cc_final: 0.6150 (Cg_endo) outliers start: 16 outliers final: 6 residues processed: 350 average time/residue: 0.1272 time to fit residues: 57.9653 Evaluate side-chains 180 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 343 HIS B 240 HIS C 59 ASN C 154 ASN D 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.283894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.242016 restraints weight = 11983.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.243375 restraints weight = 18884.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.237405 restraints weight = 11961.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.239003 restraints weight = 9469.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.239641 restraints weight = 6154.537| |-----------------------------------------------------------------------------| r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11003 Z= 0.148 Angle : 0.682 9.876 15023 Z= 0.328 Chirality : 0.040 0.166 1685 Planarity : 0.005 0.066 1748 Dihedral : 22.769 178.664 2977 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.63 % Allowed : 21.91 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.97 (0.25), residues: 1245 helix: 1.27 (0.21), residues: 629 sheet: -0.66 (0.71), residues: 56 loop : 0.19 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.020 0.002 TYR A 170 PHE 0.020 0.002 PHE C 208 TRP 0.016 0.002 TRP C 259 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11003) covalent geometry : angle 0.68184 / 0.33 (15023) hydrogen bonds : bond 0.04545 / 3.05 ( 437) hydrogen bonds : angle 4.66002 / 3.33 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4968 (pm20) REVERT: A 150 MET cc_start: 0.6466 (ptm) cc_final: 0.6259 (ptt) REVERT: A 166 TRP cc_start: 0.6217 (t60) cc_final: 0.5907 (t60) REVERT: A 197 TYR cc_start: 0.4670 (t80) cc_final: 0.4232 (t80) REVERT: A 265 VAL cc_start: 0.7341 (p) cc_final: 0.7045 (p) REVERT: B 57 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6976 (tm-30) REVERT: B 76 SER cc_start: 0.8283 (m) cc_final: 0.7848 (p) REVERT: C 203 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7033 (mp) REVERT: D 166 TRP cc_start: 0.7465 (t60) cc_final: 0.5865 (t60) outliers start: 37 outliers final: 15 residues processed: 206 average time/residue: 0.1145 time to fit residues: 32.2361 Evaluate side-chains 159 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [59, 106, 103, 26, 82, 85, 41, 124, 2, 107, 18] chunk 59 optimal weight: 0.0030 chunk 106 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 107 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS B 247 GLN B 343 HIS D 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.277914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.232891 restraints weight = 12255.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.240032 restraints weight = 18259.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.237642 restraints weight = 8167.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.239254 restraints weight = 7128.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.239626 restraints weight = 5685.354| |-----------------------------------------------------------------------------| r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11003 Z= 0.120 Angle : 0.643 7.230 15023 Z= 0.307 Chirality : 0.039 0.155 1685 Planarity : 0.004 0.031 1748 Dihedral : 22.582 179.580 2965 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.83 % Allowed : 21.51 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.87 (0.25), residues: 1245 helix: 1.15 (0.21), residues: 638 sheet: -0.48 (0.72), residues: 52 loop : 0.15 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.020 0.002 TYR B 197 PHE 0.015 0.001 PHE A 294 TRP 0.016 0.002 TRP D 270 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11003) covalent geometry : angle 0.64328 / 0.31 (15023) hydrogen bonds : bond 0.03905 / 2.58 ( 437) hydrogen bonds : angle 4.51291 / 3.24 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: B 76 SER cc_start: 0.8197 (m) cc_final: 0.7809 (p) REVERT: B 326 GLN cc_start: 0.6770 (tm-30) cc_final: 0.6278 (tm-30) outliers start: 39 outliers final: 21 residues processed: 191 average time/residue: 0.1027 time to fit residues: 26.9501 Evaluate side-chains 170 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [104, 56, 69, 40, 6, 71, 22, 109, 35, 5, 4] chunk 104 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS B 181 GLN B 247 GLN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.264544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.202809 restraints weight = 11960.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 92)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.187421 restraints weight = 13125.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 92)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171913 restraints weight = 12188.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170156 restraints weight = 10547.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173105 restraints weight = 9255.067| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 11003 Z= 0.388 Angle : 0.900 16.562 15023 Z= 0.446 Chirality : 0.049 0.231 1685 Planarity : 0.006 0.072 1748 Dihedral : 22.909 174.439 2965 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.89 % Allowed : 21.61 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -0.14 (0.24), residues: 1245 helix: 0.25 (0.20), residues: 629 sheet: -0.51 (0.79), residues: 50 loop : -0.28 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 162 TYR 0.025 0.004 TYR B 197 PHE 0.037 0.003 PHE C 189 TRP 0.039 0.005 TRP D 166 HIS 0.010 0.002 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00915 / 0.39 (11003) covalent geometry : angle 0.89974 / 0.45 (15023) hydrogen bonds : bond 0.05568 / 3.75 ( 437) hydrogen bonds : angle 5.46312 / 3.91 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6983 (ttp80) REVERT: B 341 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8333 (tt) REVERT: C 197 TYR cc_start: 0.7931 (t80) cc_final: 0.7404 (t80) REVERT: C 321 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: D 164 GLU cc_start: 0.7163 (tp30) cc_final: 0.6609 (pt0) REVERT: D 166 TRP cc_start: 0.7378 (t60) cc_final: 0.6939 (t60) outliers start: 60 outliers final: 39 residues processed: 200 average time/residue: 0.0973 time to fit residues: 27.4575 Evaluate side-chains 184 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [11, 85, 103, 43, 4, 95, 27, 36, 33, 76, 101] chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 chunk 43 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 27 optimal weight: 0.0050 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 76 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS B 247 GLN D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.275910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.230993 restraints weight = 12276.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.237279 restraints weight = 19227.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.236659 restraints weight = 8382.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.237679 restraints weight = 7102.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.238443 restraints weight = 5770.575| |-----------------------------------------------------------------------------| r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11003 Z= 0.116 Angle : 0.647 8.519 15023 Z= 0.306 Chirality : 0.038 0.167 1685 Planarity : 0.004 0.042 1748 Dihedral : 22.723 171.214 2965 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.14 % Allowed : 24.26 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.49 (0.24), residues: 1245 helix: 0.85 (0.21), residues: 635 sheet: -0.22 (0.76), residues: 52 loop : -0.10 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 217 TYR 0.013 0.002 TYR D 342 PHE 0.016 0.002 PHE A 208 TRP 0.028 0.002 TRP D 166 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (11003) covalent geometry : angle 0.64672 / 0.31 (15023) hydrogen bonds : bond 0.03773 / 2.52 ( 437) hydrogen bonds : angle 4.74695 / 3.43 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: B 76 SER cc_start: 0.8245 (m) cc_final: 0.7877 (p) REVERT: B 326 GLN cc_start: 0.6743 (tm-30) cc_final: 0.6269 (tm-30) REVERT: C 197 TYR cc_start: 0.7569 (t80) cc_final: 0.6775 (t80) REVERT: C 234 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7365 (ptp90) REVERT: D 162 ARG cc_start: 0.6599 (mmm-85) cc_final: 0.6135 (mmm-85) outliers start: 32 outliers final: 19 residues processed: 184 average time/residue: 0.1067 time to fit residues: 27.3833 Evaluate side-chains 160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [48, 85, 112, 20, 109, 74, 31, 87, 22, 35, 113] chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.273192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.235560 restraints weight = 12313.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.237256 restraints weight = 21330.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.237323 restraints weight = 9354.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.241943 restraints weight = 6982.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.239987 restraints weight = 4614.928| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11003 Z= 0.146 Angle : 0.678 10.821 15023 Z= 0.320 Chirality : 0.039 0.155 1685 Planarity : 0.004 0.039 1748 Dihedral : 22.638 168.171 2965 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.24 % Allowed : 24.07 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.51 (0.24), residues: 1245 helix: 0.91 (0.21), residues: 623 sheet: -0.11 (0.76), residues: 52 loop : -0.14 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 217 TYR 0.013 0.002 TYR A 197 PHE 0.017 0.002 PHE A 208 TRP 0.058 0.003 TRP D 166 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (11003) covalent geometry : angle 0.67818 / 0.32 (15023) hydrogen bonds : bond 0.03988 / 2.67 ( 437) hydrogen bonds : angle 4.69965 / 3.39 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6794 (t) REVERT: A 184 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: B 76 SER cc_start: 0.8374 (m) cc_final: 0.7933 (p) REVERT: B 326 GLN cc_start: 0.6650 (tm-30) cc_final: 0.6233 (tm-30) REVERT: B 333 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7505 (mttt) REVERT: C 197 TYR cc_start: 0.7759 (t80) cc_final: 0.7118 (t80) REVERT: C 234 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7438 (ptp90) outliers start: 33 outliers final: 22 residues processed: 171 average time/residue: 0.1060 time to fit residues: 25.5920 Evaluate side-chains 163 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [67, 8, 0, 39, 68, 84, 113, 65, 13, 11, 9] chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.0060 chunk 113 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.273983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.236207 restraints weight = 12226.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.237913 restraints weight = 20286.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.238187 restraints weight = 9292.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.241763 restraints weight = 7115.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.240763 restraints weight = 5169.547| |-----------------------------------------------------------------------------| r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11003 Z= 0.134 Angle : 0.651 9.496 15023 Z= 0.308 Chirality : 0.039 0.159 1685 Planarity : 0.004 0.039 1748 Dihedral : 22.572 165.582 2965 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.05 % Allowed : 24.56 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.49 (0.24), residues: 1245 helix: 0.87 (0.21), residues: 623 sheet: -0.21 (0.74), residues: 52 loop : -0.12 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.020 0.002 TYR A 170 PHE 0.017 0.002 PHE A 208 TRP 0.080 0.003 TRP D 166 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11003) covalent geometry : angle 0.65096 / 0.31 (15023) hydrogen bonds : bond 0.03769 / 2.52 ( 437) hydrogen bonds : angle 4.66741 / 3.37 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.2567 (ptt-90) cc_final: 0.1548 (mtp180) REVERT: A 184 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: B 76 SER cc_start: 0.8322 (m) cc_final: 0.7897 (p) REVERT: B 326 GLN cc_start: 0.6694 (tm-30) cc_final: 0.6212 (tm-30) REVERT: C 197 TYR cc_start: 0.7701 (t80) cc_final: 0.7075 (t80) REVERT: C 234 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7401 (ptp90) REVERT: D 73 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4011 (m-70) REVERT: D 162 ARG cc_start: 0.6553 (mmm-85) cc_final: 0.6290 (mmm-85) REVERT: D 169 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7482 (mtt-85) REVERT: D 197 TYR cc_start: 0.6541 (t80) cc_final: 0.6286 (t80) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 0.1010 time to fit residues: 24.1577 Evaluate side-chains 160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [91, 24, 64, 108, 46, 62, 71, 116, 8, 44, 104] chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 116 optimal weight: 0.0570 chunk 8 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.270746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209775 restraints weight = 12093.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 95)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193352 restraints weight = 14352.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.190466 restraints weight = 12716.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.191039 restraints weight = 10357.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.193003 restraints weight = 8169.304| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11003 Z= 0.205 Angle : 0.705 9.857 15023 Z= 0.339 Chirality : 0.041 0.175 1685 Planarity : 0.004 0.039 1748 Dihedral : 22.595 162.542 2965 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.34 % Allowed : 24.85 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.22 (0.24), residues: 1245 helix: 0.63 (0.21), residues: 623 sheet: -0.33 (0.74), residues: 52 loop : -0.23 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 92 TYR 0.015 0.002 TYR B 197 PHE 0.024 0.002 PHE C 189 TRP 0.074 0.004 TRP D 166 HIS 0.007 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (11003) covalent geometry : angle 0.70469 / 0.34 (15023) hydrogen bonds : bond 0.04276 / 2.87 ( 437) hydrogen bonds : angle 4.85332 / 3.50 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 SER cc_start: 0.5754 (t) cc_final: 0.5217 (m) REVERT: A 119 ARG cc_start: 0.3051 (ptt-90) cc_final: 0.1722 (mtp180) REVERT: A 166 TRP cc_start: 0.6818 (t60) cc_final: 0.6569 (t60) REVERT: A 184 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: B 76 SER cc_start: 0.8265 (m) cc_final: 0.7814 (p) REVERT: C 197 TYR cc_start: 0.7865 (t80) cc_final: 0.7221 (t80) REVERT: C 234 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7641 (ptp90) REVERT: D 73 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.5228 (m-70) REVERT: D 162 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6667 (mmm-85) REVERT: D 169 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: D 197 TYR cc_start: 0.6794 (t80) cc_final: 0.6440 (t80) outliers start: 34 outliers final: 23 residues processed: 173 average time/residue: 0.0974 time to fit residues: 24.2307 Evaluate side-chains 160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [92, 59, 105, 79, 38, 126, 70, 31, 52, 67, 35] chunk 92 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.274084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.230144 restraints weight = 12222.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.237536 restraints weight = 19892.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.235625 restraints weight = 8733.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.237034 restraints weight = 7365.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.238655 restraints weight = 5610.291| |-----------------------------------------------------------------------------| r_work (final): 0.4655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11003 Z= 0.121 Angle : 0.658 11.626 15023 Z= 0.310 Chirality : 0.039 0.179 1685 Planarity : 0.004 0.040 1748 Dihedral : 22.484 160.414 2965 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.95 % Allowed : 25.25 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.40 (0.24), residues: 1245 helix: 0.81 (0.21), residues: 626 sheet: -0.28 (0.72), residues: 52 loop : -0.18 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 217 TYR 0.012 0.002 TYR A 191 PHE 0.013 0.001 PHE D 42 TRP 0.075 0.003 TRP D 166 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11003) covalent geometry : angle 0.65840 / 0.31 (15023) hydrogen bonds : bond 0.03830 / 2.58 ( 437) hydrogen bonds : angle 4.68493 / 3.40 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.2457 (ptt-90) cc_final: 0.1657 (mtp180) REVERT: A 149 MET cc_start: 0.6283 (tmm) cc_final: 0.6036 (tmm) REVERT: A 184 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: B 76 SER cc_start: 0.8308 (m) cc_final: 0.7875 (p) REVERT: B 326 GLN cc_start: 0.6711 (tm-30) cc_final: 0.6414 (tm-30) REVERT: B 333 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7062 (mmmm) REVERT: C 197 TYR cc_start: 0.7601 (t80) cc_final: 0.6960 (t80) REVERT: C 234 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7410 (ptp90) REVERT: D 50 PHE cc_start: 0.5685 (m-80) cc_final: 0.5347 (m-80) REVERT: D 73 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.4343 (m-70) REVERT: D 162 ARG cc_start: 0.6717 (mmm-85) cc_final: 0.6352 (mmm-85) REVERT: D 169 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7627 (mtt180) REVERT: D 197 TYR cc_start: 0.6710 (t80) cc_final: 0.6492 (t80) outliers start: 30 outliers final: 20 residues processed: 165 average time/residue: 0.1007 time to fit residues: 23.6648 Evaluate side-chains 160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [31, 38, 85, 69, 22, 121, 51, 53, 83, 92, 80] chunk 31 optimal weight: 30.0000 chunk 38 optimal weight: 0.0570 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 53 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.275531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.232234 restraints weight = 12395.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.239026 restraints weight = 19767.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.236922 restraints weight = 8816.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.238536 restraints weight = 7627.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.238732 restraints weight = 5863.480| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11003 Z= 0.117 Angle : 0.655 10.744 15023 Z= 0.308 Chirality : 0.039 0.190 1685 Planarity : 0.004 0.042 1748 Dihedral : 22.367 159.032 2965 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.36 % Allowed : 26.03 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.44 (0.25), residues: 1245 helix: 0.88 (0.21), residues: 632 sheet: -0.31 (0.71), residues: 52 loop : -0.20 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.011 0.001 TYR A 191 PHE 0.036 0.002 PHE D 42 TRP 0.076 0.003 TRP D 166 HIS 0.010 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11003) covalent geometry : angle 0.65487 / 0.31 (15023) hydrogen bonds : bond 0.03680 / 2.51 ( 437) hydrogen bonds : angle 4.68342 / 3.40 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.2517 (ptt-90) cc_final: 0.1789 (mtp180) REVERT: A 143 ASP cc_start: 0.7064 (p0) cc_final: 0.6771 (p0) REVERT: A 184 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: A 197 TYR cc_start: 0.4933 (t80) cc_final: 0.4571 (t80) REVERT: B 76 SER cc_start: 0.8228 (m) cc_final: 0.7822 (p) REVERT: B 326 GLN cc_start: 0.6780 (tm-30) cc_final: 0.6349 (tm-30) REVERT: B 333 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7110 (mmmm) REVERT: C 197 TYR cc_start: 0.7627 (t80) cc_final: 0.6955 (t80) REVERT: C 234 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7388 (ptp90) REVERT: D 162 ARG cc_start: 0.6739 (mmm-85) cc_final: 0.6358 (mmm-85) REVERT: D 169 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7645 (mtt180) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.1037 time to fit residues: 23.8498 Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 292 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [13, 88, 24, 71, 76, 107, 9, 6, 51, 67, 87] chunk 13 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 0.0010 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.274256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.236155 restraints weight = 12308.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.236730 restraints weight = 20523.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.235410 restraints weight = 10368.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.236591 restraints weight = 8415.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.237970 restraints weight = 6145.325| |-----------------------------------------------------------------------------| r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11003 Z= 0.121 Angle : 0.668 10.767 15023 Z= 0.315 Chirality : 0.039 0.170 1685 Planarity : 0.004 0.041 1748 Dihedral : 22.299 158.221 2965 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.75 % Allowed : 25.54 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.47 (0.24), residues: 1245 helix: 0.88 (0.21), residues: 621 sheet: -0.27 (0.71), residues: 52 loop : -0.15 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 234 TYR 0.020 0.002 TYR A 170 PHE 0.043 0.002 PHE D 42 TRP 0.071 0.003 TRP D 166 HIS 0.010 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11003) covalent geometry : angle 0.66759 / 0.32 (15023) hydrogen bonds : bond 0.03723 / 2.52 ( 437) hydrogen bonds : angle 4.67120 / 3.40 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1866.03 seconds wall clock time: 33 minutes 2.25 seconds (1982.25 seconds total)