Starting phenix.real_space_refine on Wed Sep 17 22:59:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hnp_52311/09_2025/9hnp_52311.map" } resolution = 2.53 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= 0.001 sd= 0.018 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 S 28 5.16 5 C 3954 2.51 5 N 932 2.21 5 O 1010 1.98 5 H 5940 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11864 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5862 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "A" Number of atoms: 5862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5862 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.05, per 1000 atoms: 0.17 Number of scatterers: 11864 At special positions: 0 Unit cell: (67.7215, 120.282, 75.8077, 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 28 16.00 O 1010 8.00 N 932 7.00 C 3954 6.00 H 5940 1.00 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: 1.03 Conformation dependent library (CDL) restraints added in 352.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 85.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 4 through 35 removed outlier: 3.798A pdb=" N ASN B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.959A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.741A pdb=" N ALA B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 116 through 136 removed outlier: 3.659A pdb=" N GLY B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 5.791A pdb=" N PHE B 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY B 149 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS B 150 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 189 removed outlier: 4.554A pdb=" N ILE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 190 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.685A pdb=" N TRP B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.626A pdb=" N SER B 251 " --> pdb=" O GLY B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 259 removed outlier: 4.010A pdb=" N PHE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.456A pdb=" N ALA B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.993A pdb=" N SER B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 330 removed outlier: 3.711A pdb=" N TYR B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 355 through 379 removed outlier: 4.027A pdb=" N ILE B 359 " --> pdb=" O TRP B 355 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.573A pdb=" N LYS A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Proline residue: A 19 - end of helix removed outlier: 3.959A pdb=" N VAL A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 75 through 102 removed outlier: 3.741A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 116 through 136 removed outlier: 3.659A pdb=" N GLY A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 5.791A pdb=" N PHE A 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A 149 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 189 removed outlier: 4.554A pdb=" N ILE A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.685A pdb=" N TRP A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.626A pdb=" N SER A 251 " --> pdb=" O GLY A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.010A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.456A pdb=" N ALA A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.994A pdb=" N SER A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.712A pdb=" N TYR A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 355 through 379 removed outlier: 4.027A pdb=" N ILE A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 410 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 1336 1.02 - 1.22: 4623 1.22 - 1.42: 2504 1.42 - 1.62: 3521 1.62 - 1.82: 52 Bond restraints: 12036 Sorted by residual: bond pdb=" C TRP B 172 " pdb=" O TRP B 172 " ideal model delta sigma weight residual 1.244 1.105 0.138 1.00e-02 1.00e+04 1.92e+02 bond pdb=" C TRP A 172 " pdb=" O TRP A 172 " ideal model delta sigma weight residual 1.244 1.105 0.138 1.00e-02 1.00e+04 1.91e+02 bond pdb=" N ASN A 36 " pdb=" H ASN A 36 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CD2 PHE A 71 " pdb=" HD2 PHE A 71 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N PHE A 337 " pdb=" H PHE A 337 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 12031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 17777 2.35 - 4.71: 3160 4.71 - 7.06: 685 7.06 - 9.42: 135 9.42 - 11.77: 11 Bond angle restraints: 21768 Sorted by residual: angle pdb=" CA TRP B 172 " pdb=" C TRP B 172 " pdb=" O TRP B 172 " ideal model delta sigma weight residual 118.73 111.86 6.87 9.80e-01 1.04e+00 4.92e+01 angle pdb=" CA TRP A 172 " pdb=" C TRP A 172 " pdb=" O TRP A 172 " ideal model delta sigma weight residual 118.73 111.87 6.86 9.80e-01 1.04e+00 4.91e+01 angle pdb=" CA TRP B 172 " pdb=" C TRP B 172 " pdb=" N PRO B 173 " ideal model delta sigma weight residual 120.77 126.84 -6.07 9.70e-01 1.06e+00 3.92e+01 angle pdb=" CA TRP A 172 " pdb=" C TRP A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 120.77 126.82 -6.05 9.70e-01 1.06e+00 3.89e+01 angle pdb=" CA ALA A 287 " pdb=" C ALA A 287 " pdb=" O ALA A 287 " ideal model delta sigma weight residual 119.97 113.03 6.94 1.15e+00 7.56e-01 3.65e+01 ... (remaining 21763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5227 17.86 - 35.71: 318 35.71 - 53.57: 169 53.57 - 71.42: 146 71.42 - 89.28: 10 Dihedral angle restraints: 5870 sinusoidal: 3192 harmonic: 2678 Sorted by residual: dihedral pdb=" CD ARG B 332 " pdb=" NE ARG B 332 " pdb=" CZ ARG B 332 " pdb=" NH1 ARG B 332 " ideal model delta sinusoidal sigma weight residual 0.00 -83.86 83.86 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CD ARG B 203 " pdb=" NE ARG B 203 " pdb=" CZ ARG B 203 " pdb=" NH1 ARG B 203 " ideal model delta sinusoidal sigma weight residual 0.00 -82.01 82.01 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CD ARG A 332 " pdb=" NE ARG A 332 " pdb=" CZ ARG A 332 " pdb=" NH1 ARG A 332 " ideal model delta sinusoidal sigma weight residual 0.00 -79.99 79.99 1 1.00e+01 1.00e-02 7.93e+01 ... (remaining 5867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 811 0.138 - 0.276: 139 0.276 - 0.414: 14 0.414 - 0.552: 0 0.552 - 0.690: 4 Chirality restraints: 968 Sorted by residual: chirality pdb=" C2B LMT A 502 " pdb=" C1B LMT A 502 " pdb=" C3B LMT A 502 " pdb=" O2B LMT A 502 " both_signs ideal model delta sigma weight residual False -2.44 -1.75 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C2B LMT B 502 " pdb=" C1B LMT B 502 " pdb=" C3B LMT B 502 " pdb=" O2B LMT B 502 " both_signs ideal model delta sigma weight residual False -2.44 -1.75 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C3' LMT A 501 " pdb=" C2' LMT A 501 " pdb=" C4' LMT A 501 " pdb=" O3' LMT A 501 " both_signs ideal model delta sigma weight residual False 2.43 1.75 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 965 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 386 " -0.241 9.50e-02 1.11e+02 4.40e-01 4.22e+03 pdb=" NE ARG A 386 " -0.258 2.00e-02 2.50e+03 pdb=" CZ ARG A 386 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 386 " 0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG A 386 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 386 " -0.660 2.00e-02 2.50e+03 pdb="HH12 ARG A 386 " 0.867 2.00e-02 2.50e+03 pdb="HH21 ARG A 386 " 0.480 2.00e-02 2.50e+03 pdb="HH22 ARG A 386 " -0.442 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 386 " -0.437 9.50e-02 1.11e+02 4.13e-01 3.37e+03 pdb=" NE ARG B 386 " -0.304 2.00e-02 2.50e+03 pdb=" CZ ARG B 386 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG B 386 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG B 386 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG B 386 " -0.631 2.00e-02 2.50e+03 pdb="HH12 ARG B 386 " 0.807 2.00e-02 2.50e+03 pdb="HH21 ARG B 386 " 0.362 2.00e-02 2.50e+03 pdb="HH22 ARG B 386 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 373 " 0.379 9.50e-02 1.11e+02 4.04e-01 3.33e+03 pdb=" NE ARG A 373 " -0.500 2.00e-02 2.50e+03 pdb=" CZ ARG A 373 " -0.135 2.00e-02 2.50e+03 pdb=" NH1 ARG A 373 " 0.060 2.00e-02 2.50e+03 pdb=" NH2 ARG A 373 " 0.059 2.00e-02 2.50e+03 pdb="HH11 ARG A 373 " -0.393 2.00e-02 2.50e+03 pdb="HH12 ARG A 373 " 0.643 2.00e-02 2.50e+03 pdb="HH21 ARG A 373 " 0.600 2.00e-02 2.50e+03 pdb="HH22 ARG A 373 " -0.350 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 822 2.24 - 2.83: 23274 2.83 - 3.42: 34732 3.42 - 4.01: 45430 4.01 - 4.60: 65534 Nonbonded interactions: 169792 Sorted by model distance: nonbonded pdb=" O GLY B 295 " pdb=" HG SER B 338 " model vdw 1.645 2.450 nonbonded pdb=" O GLY A 295 " pdb=" HG SER A 338 " model vdw 1.645 2.450 nonbonded pdb=" HG1 THR A 335 " pdb=" OD2 ASP A 343 " model vdw 1.659 2.450 nonbonded pdb=" HG1 THR B 335 " pdb=" OD2 ASP B 343 " model vdw 1.660 2.450 nonbonded pdb=" HG1 THR B 297 " pdb=" OE1 GLU B 301 " model vdw 1.663 2.450 ... (remaining 169787 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.060 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.014 0.138 6096 Z= 0.862 Angle : 1.859 10.633 8296 Z= 1.266 Chirality : 0.106 0.690 968 Planarity : 0.039 0.490 1010 Dihedral : 13.610 83.862 2282 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.34 % Allowed : 0.85 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.45 (0.29), residues: 762 helix: -0.35 (0.20), residues: 538 sheet: -0.09 (1.01), residues: 24 loop : 0.37 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 386 TYR 0.102 0.022 TYR A 364 PHE 0.055 0.011 PHE A 306 TRP 0.076 0.023 TRP A 355 HIS 0.012 0.003 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.01426 ( 6096) covalent geometry : angle 1.85929 ( 8296) hydrogen bonds : bond 0.18220 ( 410) hydrogen bonds : angle 7.72273 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ASN cc_start: 0.7781 (m-40) cc_final: 0.7544 (m-40) REVERT: B 59 MET cc_start: 0.8318 (mmt) cc_final: 0.7504 (mmt) REVERT: B 74 ASN cc_start: 0.7835 (t0) cc_final: 0.7564 (t0) REVERT: B 131 MET cc_start: 0.8874 (mmt) cc_final: 0.8050 (mmt) REVERT: B 152 PHE cc_start: 0.8188 (t80) cc_final: 0.7928 (t80) REVERT: B 241 MET cc_start: 0.8592 (mtm) cc_final: 0.8378 (mtp) REVERT: B 302 PHE cc_start: 0.8555 (m-80) cc_final: 0.8105 (m-80) REVERT: A 59 MET cc_start: 0.8278 (mmt) cc_final: 0.7451 (mmt) REVERT: A 86 TYR cc_start: 0.8601 (t80) cc_final: 0.8295 (t80) REVERT: A 131 MET cc_start: 0.8805 (mmt) cc_final: 0.7755 (mmt) REVERT: A 231 GLN cc_start: 0.7762 (mt0) cc_final: 0.7544 (mt0) REVERT: A 241 MET cc_start: 0.8523 (mtm) cc_final: 0.8264 (mtp) REVERT: A 259 TYR cc_start: 0.8551 (m-80) cc_final: 0.8251 (m-80) REVERT: A 302 PHE cc_start: 0.8602 (m-80) cc_final: 0.8309 (m-80) outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.7025 time to fit residues: 112.3778 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 219 GLN B 350 ASN A 190 ASN A 219 GLN A 350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104751 restraints weight = 22331.879| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.53 r_work: 0.3299 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6096 Z= 0.207 Angle : 0.644 8.382 8296 Z= 0.347 Chirality : 0.046 0.132 968 Planarity : 0.013 0.234 1010 Dihedral : 9.465 86.337 1056 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.37 % Allowed : 7.12 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.32 (0.30), residues: 762 helix: 1.16 (0.21), residues: 550 sheet: -0.57 (0.84), residues: 24 loop : 0.53 (0.52), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 332 TYR 0.010 0.002 TYR B 198 PHE 0.018 0.002 PHE A 256 TRP 0.011 0.002 TRP A 214 HIS 0.004 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6096) covalent geometry : angle 0.64401 ( 8296) hydrogen bonds : bond 0.05736 ( 410) hydrogen bonds : angle 5.30626 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.304 Fit side-chains REVERT: B 8 ASN cc_start: 0.8219 (m-40) cc_final: 0.7989 (m-40) REVERT: B 59 MET cc_start: 0.8400 (mmt) cc_final: 0.7674 (mmt) REVERT: B 115 ASP cc_start: 0.8371 (t70) cc_final: 0.8119 (t0) REVERT: B 152 PHE cc_start: 0.8066 (t80) cc_final: 0.7758 (t80) REVERT: B 302 PHE cc_start: 0.8536 (m-80) cc_final: 0.8226 (m-80) REVERT: A 134 ARG cc_start: 0.6598 (mmm160) cc_final: 0.6293 (ttt-90) REVERT: A 259 TYR cc_start: 0.8502 (m-80) cc_final: 0.8272 (m-80) REVERT: A 302 PHE cc_start: 0.8587 (m-80) cc_final: 0.8099 (m-80) REVERT: A 306 PHE cc_start: 0.7900 (m-80) cc_final: 0.7656 (m-80) outliers start: 14 outliers final: 5 residues processed: 126 average time/residue: 0.7341 time to fit residues: 99.5540 Evaluate side-chains 124 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104462 restraints weight = 22372.530| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.64 r_work: 0.3271 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6096 Z= 0.196 Angle : 0.577 5.701 8296 Z= 0.309 Chirality : 0.043 0.129 968 Planarity : 0.006 0.048 1010 Dihedral : 8.149 59.607 1052 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.53 % Allowed : 11.19 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.79 (0.30), residues: 762 helix: 1.52 (0.22), residues: 548 sheet: -0.35 (0.85), residues: 20 loop : 0.66 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 239 TYR 0.011 0.002 TYR A 312 PHE 0.017 0.002 PHE A 195 TRP 0.009 0.002 TRP B 214 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6096) covalent geometry : angle 0.57671 ( 8296) hydrogen bonds : bond 0.05180 ( 410) hydrogen bonds : angle 4.97569 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.331 Fit side-chains REVERT: B 8 ASN cc_start: 0.8167 (m-40) cc_final: 0.7893 (m-40) REVERT: B 59 MET cc_start: 0.8414 (mmp) cc_final: 0.7682 (mmt) REVERT: B 131 MET cc_start: 0.8822 (mmt) cc_final: 0.7536 (mmt) REVERT: B 152 PHE cc_start: 0.8044 (t80) cc_final: 0.7646 (t80) REVERT: B 302 PHE cc_start: 0.8539 (m-80) cc_final: 0.8218 (m-80) REVERT: A 259 TYR cc_start: 0.8490 (m-80) cc_final: 0.8287 (m-80) REVERT: A 302 PHE cc_start: 0.8605 (m-80) cc_final: 0.8289 (m-80) REVERT: A 343 ASP cc_start: 0.7968 (m-30) cc_final: 0.7746 (m-30) outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.7344 time to fit residues: 102.2091 Evaluate side-chains 126 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 9 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN B 231 GLN A 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105300 restraints weight = 22309.654| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.60 r_work: 0.3289 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6096 Z= 0.167 Angle : 0.535 5.321 8296 Z= 0.285 Chirality : 0.041 0.119 968 Planarity : 0.006 0.050 1010 Dihedral : 7.715 58.294 1052 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.86 % Allowed : 12.20 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.89 (0.31), residues: 762 helix: 1.68 (0.22), residues: 548 sheet: -0.44 (0.80), residues: 20 loop : 0.37 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.010 0.001 TYR B 86 PHE 0.015 0.001 PHE A 195 TRP 0.007 0.001 TRP B 185 HIS 0.003 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6096) covalent geometry : angle 0.53536 ( 8296) hydrogen bonds : bond 0.04739 ( 410) hydrogen bonds : angle 4.86020 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.314 Fit side-chains REVERT: B 8 ASN cc_start: 0.8252 (m-40) cc_final: 0.7983 (m-40) REVERT: B 59 MET cc_start: 0.8424 (mmp) cc_final: 0.7716 (mmt) REVERT: B 152 PHE cc_start: 0.8036 (t80) cc_final: 0.7575 (t80) REVERT: B 302 PHE cc_start: 0.8527 (m-80) cc_final: 0.8182 (m-80) REVERT: A 134 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.6304 (ttt-90) REVERT: A 302 PHE cc_start: 0.8582 (m-80) cc_final: 0.8262 (m-80) outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 0.7241 time to fit residues: 102.3607 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 47 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106189 restraints weight = 22339.667| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.59 r_work: 0.3306 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6096 Z= 0.123 Angle : 0.509 5.260 8296 Z= 0.269 Chirality : 0.040 0.119 968 Planarity : 0.005 0.039 1010 Dihedral : 7.247 58.393 1052 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.86 % Allowed : 11.86 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.12 (0.31), residues: 762 helix: 1.91 (0.22), residues: 540 sheet: -0.52 (0.79), residues: 20 loop : 0.37 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.009 0.001 TYR B 86 PHE 0.013 0.001 PHE A 195 TRP 0.007 0.001 TRP A 185 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6096) covalent geometry : angle 0.50926 ( 8296) hydrogen bonds : bond 0.04317 ( 410) hydrogen bonds : angle 4.73523 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.307 Fit side-chains REVERT: B 8 ASN cc_start: 0.8254 (m-40) cc_final: 0.7989 (m-40) REVERT: B 59 MET cc_start: 0.8429 (mmp) cc_final: 0.7750 (mmt) REVERT: B 131 MET cc_start: 0.8802 (mmt) cc_final: 0.7496 (mmt) REVERT: B 152 PHE cc_start: 0.8016 (t80) cc_final: 0.7568 (t80) REVERT: B 302 PHE cc_start: 0.8517 (m-80) cc_final: 0.8211 (m-80) REVERT: A 134 ARG cc_start: 0.6553 (mmm-85) cc_final: 0.6256 (ttt-90) REVERT: A 302 PHE cc_start: 0.8568 (m-80) cc_final: 0.8271 (m-80) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.7018 time to fit residues: 99.1417 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 102 HIS A 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106310 restraints weight = 22327.672| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.58 r_work: 0.3306 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6096 Z= 0.148 Angle : 0.520 5.287 8296 Z= 0.274 Chirality : 0.040 0.119 968 Planarity : 0.005 0.040 1010 Dihedral : 7.005 57.931 1052 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.69 % Allowed : 12.37 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.11 (0.31), residues: 762 helix: 1.95 (0.23), residues: 540 sheet: -0.59 (0.78), residues: 20 loop : 0.23 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.010 0.001 TYR B 86 PHE 0.014 0.001 PHE A 195 TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6096) covalent geometry : angle 0.51956 ( 8296) hydrogen bonds : bond 0.04381 ( 410) hydrogen bonds : angle 4.72261 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.297 Fit side-chains REVERT: B 8 ASN cc_start: 0.8281 (m-40) cc_final: 0.8024 (m-40) REVERT: B 59 MET cc_start: 0.8457 (mmp) cc_final: 0.7750 (mmt) REVERT: B 131 MET cc_start: 0.8806 (mmt) cc_final: 0.7436 (mmt) REVERT: B 302 PHE cc_start: 0.8540 (m-80) cc_final: 0.8193 (m-80) REVERT: A 134 ARG cc_start: 0.6564 (mmm-85) cc_final: 0.6269 (ttt-90) REVERT: A 302 PHE cc_start: 0.8595 (m-80) cc_final: 0.8327 (m-80) outliers start: 10 outliers final: 4 residues processed: 127 average time/residue: 0.7563 time to fit residues: 103.3554 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 335 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103437 restraints weight = 22464.710| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.65 r_work: 0.3272 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6096 Z= 0.219 Angle : 0.566 5.990 8296 Z= 0.299 Chirality : 0.043 0.127 968 Planarity : 0.006 0.042 1010 Dihedral : 7.067 56.598 1052 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.86 % Allowed : 12.54 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.88 (0.31), residues: 762 helix: 1.81 (0.22), residues: 538 sheet: -0.53 (0.82), residues: 20 loop : 0.04 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 203 TYR 0.012 0.002 TYR B 86 PHE 0.017 0.002 PHE A 195 TRP 0.008 0.002 TRP A 185 HIS 0.005 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6096) covalent geometry : angle 0.56612 ( 8296) hydrogen bonds : bond 0.04810 ( 410) hydrogen bonds : angle 4.81936 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.254 Fit side-chains REVERT: B 8 ASN cc_start: 0.8259 (m-40) cc_final: 0.7990 (m-40) REVERT: B 59 MET cc_start: 0.8458 (mmp) cc_final: 0.7693 (mmt) REVERT: B 131 MET cc_start: 0.8788 (mmt) cc_final: 0.7436 (mmt) REVERT: B 302 PHE cc_start: 0.8541 (m-80) cc_final: 0.8007 (m-80) REVERT: A 134 ARG cc_start: 0.6636 (mmm-85) cc_final: 0.6335 (ttt-90) REVERT: A 302 PHE cc_start: 0.8596 (m-80) cc_final: 0.8282 (m-80) outliers start: 11 outliers final: 8 residues processed: 130 average time/residue: 0.6909 time to fit residues: 96.9432 Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105907 restraints weight = 22336.621| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.59 r_work: 0.3304 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6096 Z= 0.125 Angle : 0.513 5.289 8296 Z= 0.270 Chirality : 0.040 0.135 968 Planarity : 0.005 0.040 1010 Dihedral : 6.708 58.487 1052 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.69 % Allowed : 13.90 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.09 (0.31), residues: 762 helix: 1.98 (0.23), residues: 540 sheet: -0.61 (0.79), residues: 20 loop : 0.06 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 239 TYR 0.010 0.001 TYR B 86 PHE 0.013 0.001 PHE A 152 TRP 0.008 0.001 TRP A 185 HIS 0.002 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6096) covalent geometry : angle 0.51262 ( 8296) hydrogen bonds : bond 0.04198 ( 410) hydrogen bonds : angle 4.69268 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: B 8 ASN cc_start: 0.8273 (m-40) cc_final: 0.8013 (m-40) REVERT: B 59 MET cc_start: 0.8463 (mmp) cc_final: 0.7713 (mmt) REVERT: B 131 MET cc_start: 0.8784 (mmt) cc_final: 0.7388 (mmt) REVERT: B 302 PHE cc_start: 0.8500 (m-80) cc_final: 0.8164 (m-80) REVERT: A 131 MET cc_start: 0.8646 (mmt) cc_final: 0.7056 (mmt) REVERT: A 134 ARG cc_start: 0.6579 (mmm-85) cc_final: 0.6277 (ttt-90) REVERT: A 302 PHE cc_start: 0.8560 (m-80) cc_final: 0.8243 (m-80) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.7402 time to fit residues: 104.5328 Evaluate side-chains 132 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 364 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105336 restraints weight = 22187.469| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.64 r_work: 0.3287 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6096 Z= 0.169 Angle : 0.548 7.730 8296 Z= 0.287 Chirality : 0.041 0.129 968 Planarity : 0.005 0.041 1010 Dihedral : 6.683 57.878 1052 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.69 % Allowed : 13.90 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.97 (0.31), residues: 762 helix: 1.90 (0.23), residues: 538 sheet: -0.60 (0.78), residues: 20 loop : 0.01 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.009 0.001 TYR B 86 PHE 0.015 0.001 PHE A 152 TRP 0.008 0.001 TRP A 185 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6096) covalent geometry : angle 0.54813 ( 8296) hydrogen bonds : bond 0.04428 ( 410) hydrogen bonds : angle 4.72624 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.315 Fit side-chains REVERT: B 8 ASN cc_start: 0.8255 (m-40) cc_final: 0.7997 (m-40) REVERT: B 131 MET cc_start: 0.8769 (mmt) cc_final: 0.7402 (mmt) REVERT: B 279 LYS cc_start: 0.6596 (mppt) cc_final: 0.6310 (mppt) REVERT: B 302 PHE cc_start: 0.8511 (m-80) cc_final: 0.8186 (m-80) REVERT: B 364 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: A 131 MET cc_start: 0.8604 (mmt) cc_final: 0.7030 (mmt) REVERT: A 134 ARG cc_start: 0.6605 (mmm-85) cc_final: 0.6302 (ttt-90) REVERT: A 302 PHE cc_start: 0.8574 (m-80) cc_final: 0.8259 (m-80) REVERT: A 364 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.6574 (m-80) outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.7417 time to fit residues: 108.0518 Evaluate side-chains 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 364 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104514 restraints weight = 22480.440| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.63 r_work: 0.3290 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6096 Z= 0.157 Angle : 0.543 9.387 8296 Z= 0.285 Chirality : 0.041 0.157 968 Planarity : 0.005 0.041 1010 Dihedral : 6.580 58.149 1052 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.53 % Allowed : 14.24 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.96 (0.31), residues: 762 helix: 1.90 (0.23), residues: 538 sheet: -0.68 (0.77), residues: 20 loop : -0.01 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.010 0.001 TYR B 86 PHE 0.014 0.001 PHE A 195 TRP 0.008 0.001 TRP A 185 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6096) covalent geometry : angle 0.54332 ( 8296) hydrogen bonds : bond 0.04358 ( 410) hydrogen bonds : angle 4.71854 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 8 ASN cc_start: 0.8255 (m-40) cc_final: 0.8006 (m-40) REVERT: B 131 MET cc_start: 0.8763 (mmt) cc_final: 0.7395 (mmt) REVERT: B 302 PHE cc_start: 0.8503 (m-80) cc_final: 0.8172 (m-80) REVERT: B 364 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: A 131 MET cc_start: 0.8600 (mmt) cc_final: 0.6992 (mmt) REVERT: A 134 ARG cc_start: 0.6597 (mmm-85) cc_final: 0.6289 (ttt-90) REVERT: A 302 PHE cc_start: 0.8568 (m-80) cc_final: 0.8253 (m-80) outliers start: 9 outliers final: 6 residues processed: 136 average time/residue: 0.7440 time to fit residues: 109.2116 Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 364 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105686 restraints weight = 22233.943| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.60 r_work: 0.3301 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6096 Z= 0.139 Angle : 0.520 5.267 8296 Z= 0.274 Chirality : 0.040 0.138 968 Planarity : 0.005 0.040 1010 Dihedral : 6.487 58.677 1052 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.53 % Allowed : 14.92 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.03 (0.31), residues: 762 helix: 1.96 (0.23), residues: 538 sheet: -0.68 (0.77), residues: 20 loop : -0.00 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.010 0.001 TYR B 86 PHE 0.014 0.001 PHE A 152 TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6096) covalent geometry : angle 0.52026 ( 8296) hydrogen bonds : bond 0.04217 ( 410) hydrogen bonds : angle 4.67310 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.08 seconds wall clock time: 71 minutes 30.97 seconds (4290.97 seconds total)