Starting phenix.real_space_refine on Wed May 14 16:52:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hnp_52311/05_2025/9hnp_52311_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hnp_52311/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hnp_52311/05_2025/9hnp_52311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hnp_52311/05_2025/9hnp_52311.map" model { file = "/net/cci-nas-00/data/ceres_data/9hnp_52311/05_2025/9hnp_52311_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hnp_52311/05_2025/9hnp_52311_trim.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.43, per 1000 atoms: 0.54 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: 3.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 4.00 Time building geometry restraints manager: 3.99 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.860 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.076 0.023 TRP A 355 HIS 0.012 0.003 HIS A 315 PHE 0.055 0.011 PHE A 306 TYR 0.102 0.022 TYR A 364 ARG 0.009 0.002 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.18220 ( 410) hydrogen bonds : angle 7.72273 ( 1200) covalent geometry : bond 0.01426 ( 6096) covalent geometry : angle 1.85929 ( 8296) *********************** 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 : 0.864 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: 0.7505 (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: 1.3626 time to fit residues: 219.1634 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 : 0.895 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.118991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104954 restraints weight = 22249.590| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.55 r_work: 0.3301 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2628 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= 0.186 Angle : 0.643 8.321 8296 Z= 0.349 Chirality : 0.045 0.125 968 Planarity : 0.013 0.237 1010 Dihedral : 9.450 85.591 1056 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 762 helix: 1.18 (0.21), residues: 550 sheet: -0.56 (0.84), residues: 24 loop : 0.56 (0.53), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 214 HIS 0.004 0.001 HIS B 339 PHE 0.019 0.002 PHE A 256 TYR 0.009 0.002 TYR B 86 ARG 0.006 0.001 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 410) hydrogen bonds : angle 5.31958 ( 1200) covalent geometry : bond 0.00427 ( 6096) covalent geometry : angle 0.64256 ( 8296) *********************** 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.979 Fit side-chains REVERT: B 8 ASN cc_start: 0.8212 (m-40) cc_final: 0.7986 (m-40) REVERT: B 59 MET cc_start: 0.8394 (mmt) cc_final: 0.7674 (mmt) REVERT: B 115 ASP cc_start: 0.8372 (t70) cc_final: 0.8122 (t0) REVERT: B 152 PHE cc_start: 0.8067 (t80) cc_final: 0.7747 (t80) REVERT: B 302 PHE cc_start: 0.8530 (m-80) cc_final: 0.8222 (m-80) REVERT: B 332 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8191 (mtm110) REVERT: A 134 ARG cc_start: 0.6605 (mmm160) cc_final: 0.6299 (ttt-90) REVERT: A 259 TYR cc_start: 0.8508 (m-80) cc_final: 0.8268 (m-80) REVERT: A 302 PHE cc_start: 0.8584 (m-80) cc_final: 0.8095 (m-80) REVERT: A 306 PHE cc_start: 0.7897 (m-80) cc_final: 0.7649 (m-80) outliers start: 14 outliers final: 5 residues processed: 125 average time/residue: 1.5375 time to fit residues: 208.8058 Evaluate side-chains 124 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 332 ARG 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 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN 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 = 0.3577 r_free = 0.3577 target = 0.118836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104836 restraints weight = 22623.267| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.57 r_work: 0.3300 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6096 Z= 0.157 Angle : 0.547 5.547 8296 Z= 0.292 Chirality : 0.042 0.122 968 Planarity : 0.006 0.083 1010 Dihedral : 8.071 59.688 1056 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.86 % Allowed : 10.51 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.31), residues: 762 helix: 1.63 (0.22), residues: 550 sheet: -0.31 (0.85), residues: 20 loop : 0.65 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS B 339 PHE 0.014 0.001 PHE A 195 TYR 0.010 0.002 TYR A 312 ARG 0.003 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 410) hydrogen bonds : angle 4.91286 ( 1200) covalent geometry : bond 0.00353 ( 6096) covalent geometry : angle 0.54715 ( 8296) *********************** 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.935 Fit side-chains REVERT: B 8 ASN cc_start: 0.8175 (m-40) cc_final: 0.7914 (m-40) REVERT: B 59 MET cc_start: 0.8428 (mmp) cc_final: 0.7721 (mmt) REVERT: B 131 MET cc_start: 0.8821 (mmt) cc_final: 0.7483 (mmt) REVERT: B 152 PHE cc_start: 0.8014 (t80) cc_final: 0.7636 (t80) REVERT: B 302 PHE cc_start: 0.8557 (m-80) cc_final: 0.8228 (m-80) REVERT: A 134 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6364 (ttt-90) REVERT: A 302 PHE cc_start: 0.8605 (m-80) cc_final: 0.8269 (m-80) REVERT: A 343 ASP cc_start: 0.7944 (m-30) cc_final: 0.7723 (m-30) outliers start: 11 outliers final: 4 residues processed: 129 average time/residue: 1.4175 time to fit residues: 198.0471 Evaluate side-chains 125 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 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 = 0.3592 r_free = 0.3592 target = 0.119576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104800 restraints weight = 22242.189| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.64 r_work: 0.3279 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6096 Z= 0.187 Angle : 0.549 5.353 8296 Z= 0.291 Chirality : 0.042 0.122 968 Planarity : 0.006 0.059 1010 Dihedral : 7.620 59.434 1052 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.31), residues: 762 helix: 1.69 (0.22), residues: 548 sheet: -0.45 (0.80), residues: 20 loop : 0.41 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS B 339 PHE 0.016 0.001 PHE A 195 TYR 0.011 0.002 TYR A 312 ARG 0.003 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 410) hydrogen bonds : angle 4.87480 ( 1200) covalent geometry : bond 0.00451 ( 6096) covalent geometry : angle 0.54852 ( 8296) *********************** 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 139 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.965 Fit side-chains REVERT: B 8 ASN cc_start: 0.8250 (m-40) cc_final: 0.8002 (m-40) REVERT: B 59 MET cc_start: 0.8416 (mmp) cc_final: 0.7721 (mmt) REVERT: B 152 PHE cc_start: 0.8042 (t80) cc_final: 0.7586 (t80) REVERT: B 302 PHE cc_start: 0.8541 (m-80) cc_final: 0.8200 (m-80) REVERT: A 134 ARG cc_start: 0.6621 (mmm160) cc_final: 0.6286 (ttt-90) REVERT: A 302 PHE cc_start: 0.8594 (m-80) cc_final: 0.8264 (m-80) outliers start: 11 outliers final: 6 residues processed: 131 average time/residue: 1.4672 time to fit residues: 207.5180 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.120646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106556 restraints weight = 22077.785| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.56 r_work: 0.3311 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6096 Z= 0.138 Angle : 0.517 5.301 8296 Z= 0.273 Chirality : 0.040 0.120 968 Planarity : 0.005 0.040 1010 Dihedral : 7.144 59.773 1052 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.53 % Allowed : 12.03 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.31), residues: 762 helix: 1.90 (0.22), residues: 540 sheet: -0.46 (0.82), residues: 20 loop : 0.30 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.003 0.001 HIS B 211 PHE 0.013 0.001 PHE A 195 TYR 0.010 0.001 TYR B 86 ARG 0.002 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 410) hydrogen bonds : angle 4.74548 ( 1200) covalent geometry : bond 0.00317 ( 6096) covalent geometry : angle 0.51701 ( 8296) *********************** 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 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.935 Fit side-chains REVERT: B 8 ASN cc_start: 0.8230 (m-40) cc_final: 0.7968 (m-40) REVERT: B 59 MET cc_start: 0.8468 (mmp) cc_final: 0.7770 (mmt) REVERT: B 131 MET cc_start: 0.8818 (mmt) cc_final: 0.7530 (mmt) REVERT: B 152 PHE cc_start: 0.8060 (t80) cc_final: 0.7563 (t80) REVERT: B 302 PHE cc_start: 0.8548 (m-80) cc_final: 0.8199 (m-80) REVERT: A 134 ARG cc_start: 0.6618 (mmm160) cc_final: 0.6288 (ttt-90) REVERT: A 302 PHE cc_start: 0.8597 (m-80) cc_final: 0.8264 (m-80) outliers start: 9 outliers final: 5 residues processed: 130 average time/residue: 1.4106 time to fit residues: 198.4798 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.118811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104065 restraints weight = 22487.542| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.64 r_work: 0.3271 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6096 Z= 0.219 Angle : 0.562 5.312 8296 Z= 0.298 Chirality : 0.043 0.126 968 Planarity : 0.006 0.043 1010 Dihedral : 7.197 58.288 1052 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.30), residues: 762 helix: 1.79 (0.22), residues: 540 sheet: -0.41 (0.83), residues: 20 loop : 0.06 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 185 HIS 0.005 0.001 HIS B 211 PHE 0.017 0.002 PHE A 195 TYR 0.011 0.002 TYR B 86 ARG 0.003 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 410) hydrogen bonds : angle 4.83765 ( 1200) covalent geometry : bond 0.00537 ( 6096) covalent geometry : angle 0.56231 ( 8296) *********************** 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: 11 poor density : 124 time to evaluate : 0.894 Fit side-chains REVERT: B 8 ASN cc_start: 0.8269 (m-40) cc_final: 0.8003 (m-40) REVERT: B 59 MET cc_start: 0.8458 (mmp) cc_final: 0.7708 (mmt) REVERT: B 131 MET cc_start: 0.8796 (mmt) cc_final: 0.7442 (mmt) REVERT: B 152 PHE cc_start: 0.8101 (t80) cc_final: 0.7623 (t80) REVERT: B 302 PHE cc_start: 0.8540 (m-80) cc_final: 0.8212 (m-80) REVERT: B 335 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8028 (t) REVERT: A 302 PHE cc_start: 0.8605 (m-80) cc_final: 0.8287 (m-80) outliers start: 11 outliers final: 6 residues processed: 126 average time/residue: 1.4534 time to fit residues: 198.1355 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 : 0.916 ------------------------------------------------------------------------------- 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 335 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain A residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 234 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 = 0.3592 r_free = 0.3592 target = 0.119752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105587 restraints weight = 22547.069| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.55 r_work: 0.3306 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6096 Z= 0.129 Angle : 0.516 5.431 8296 Z= 0.272 Chirality : 0.040 0.120 968 Planarity : 0.005 0.041 1010 Dihedral : 6.851 57.992 1052 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.53 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.31), residues: 762 helix: 1.93 (0.23), residues: 540 sheet: -0.61 (0.80), residues: 20 loop : 0.01 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS B 211 PHE 0.013 0.001 PHE A 195 TYR 0.009 0.001 TYR B 86 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 410) hydrogen bonds : angle 4.71579 ( 1200) covalent geometry : bond 0.00297 ( 6096) covalent geometry : angle 0.51616 ( 8296) *********************** 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 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.912 Fit side-chains REVERT: B 8 ASN cc_start: 0.8220 (m-40) cc_final: 0.7953 (m-40) REVERT: B 59 MET cc_start: 0.8471 (mmp) cc_final: 0.7729 (mmt) REVERT: B 131 MET cc_start: 0.8809 (mmt) cc_final: 0.7411 (mmt) REVERT: B 152 PHE cc_start: 0.8094 (t80) cc_final: 0.7570 (t80) REVERT: B 302 PHE cc_start: 0.8507 (m-80) cc_final: 0.8162 (m-80) REVERT: B 335 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8014 (t) REVERT: A 134 ARG cc_start: 0.6595 (mmm160) cc_final: 0.6265 (ttt-90) REVERT: A 302 PHE cc_start: 0.8570 (m-80) cc_final: 0.8250 (m-80) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 1.4323 time to fit residues: 200.0052 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 B residue 343 ASP Chi-restraints excluded: chain A residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.118991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104345 restraints weight = 22441.548| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.62 r_work: 0.3277 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3593 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= 0.215 Angle : 0.562 7.201 8296 Z= 0.297 Chirality : 0.043 0.126 968 Planarity : 0.006 0.043 1010 Dihedral : 6.917 56.894 1052 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.69 % Allowed : 12.88 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.30), residues: 762 helix: 1.80 (0.22), residues: 538 sheet: -0.60 (0.79), residues: 20 loop : -0.15 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 185 HIS 0.005 0.001 HIS B 211 PHE 0.017 0.001 PHE A 195 TYR 0.010 0.002 TYR B 86 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 410) hydrogen bonds : angle 4.80844 ( 1200) covalent geometry : bond 0.00527 ( 6096) covalent geometry : angle 0.56206 ( 8296) *********************** 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 : 0.872 Fit side-chains REVERT: B 8 ASN cc_start: 0.8238 (m-40) cc_final: 0.7972 (m-40) REVERT: B 59 MET cc_start: 0.8468 (mmp) cc_final: 0.7712 (mmt) REVERT: B 131 MET cc_start: 0.8777 (mmt) cc_final: 0.7409 (mmt) REVERT: B 152 PHE cc_start: 0.8080 (t80) cc_final: 0.7551 (t80) REVERT: B 302 PHE cc_start: 0.8528 (m-80) cc_final: 0.8204 (m-80) REVERT: B 335 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8040 (t) REVERT: A 302 PHE cc_start: 0.8584 (m-80) cc_final: 0.8278 (m-80) REVERT: A 364 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6664 (m-80) outliers start: 10 outliers final: 5 residues processed: 129 average time/residue: 1.4275 time to fit residues: 199.8380 Evaluate side-chains 132 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 343 ASP Chi-restraints excluded: chain A residue 9 LEU 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 48 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN A 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 = 0.3605 r_free = 0.3605 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105871 restraints weight = 22276.335| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.64 r_work: 0.3303 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6096 Z= 0.123 Angle : 0.515 6.756 8296 Z= 0.271 Chirality : 0.040 0.145 968 Planarity : 0.005 0.041 1010 Dihedral : 6.611 59.069 1052 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.69 % Allowed : 13.22 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.31), residues: 762 helix: 1.93 (0.23), residues: 542 sheet: -0.75 (0.77), residues: 20 loop : -0.01 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.002 0.001 HIS A 234 PHE 0.012 0.001 PHE A 152 TYR 0.008 0.001 TYR B 86 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 410) hydrogen bonds : angle 4.67473 ( 1200) covalent geometry : bond 0.00281 ( 6096) covalent geometry : angle 0.51470 ( 8296) *********************** 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 139 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: B 8 ASN cc_start: 0.8202 (m-40) cc_final: 0.7933 (m-40) REVERT: B 131 MET cc_start: 0.8768 (mmt) cc_final: 0.7400 (mmt) REVERT: B 302 PHE cc_start: 0.8485 (m-80) cc_final: 0.8151 (m-80) REVERT: B 335 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8009 (t) REVERT: B 364 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: A 134 ARG cc_start: 0.6627 (mmm160) cc_final: 0.6290 (ttt-90) REVERT: A 302 PHE cc_start: 0.8552 (m-80) cc_final: 0.8004 (m-80) outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 1.4046 time to fit residues: 204.0299 Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 276 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 364 TYR 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 15 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.0020 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 231 GLN A 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107017 restraints weight = 22157.896| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3319 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6096 Z= 0.130 Angle : 0.516 5.632 8296 Z= 0.272 Chirality : 0.040 0.135 968 Planarity : 0.005 0.041 1010 Dihedral : 6.504 59.584 1052 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.36 % Allowed : 14.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.31), residues: 762 helix: 2.01 (0.23), residues: 540 sheet: -0.77 (0.77), residues: 20 loop : -0.03 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.003 0.001 HIS B 211 PHE 0.013 0.001 PHE A 195 TYR 0.008 0.001 TYR B 240 ARG 0.001 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 410) hydrogen bonds : angle 4.64359 ( 1200) covalent geometry : bond 0.00301 ( 6096) covalent geometry : angle 0.51629 ( 8296) ********************** 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 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.976 Fit side-chains REVERT: B 8 ASN cc_start: 0.8299 (m-40) cc_final: 0.8052 (m-40) REVERT: B 131 MET cc_start: 0.8769 (mmt) cc_final: 0.7412 (mmt) REVERT: B 302 PHE cc_start: 0.8519 (m-80) cc_final: 0.8193 (m-80) REVERT: B 335 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8013 (t) REVERT: B 364 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 131 MET cc_start: 0.8593 (mmt) cc_final: 0.7072 (mmt) REVERT: A 134 ARG cc_start: 0.6610 (mmm160) cc_final: 0.6279 (ttt-90) REVERT: A 302 PHE cc_start: 0.8572 (m-80) cc_final: 0.8253 (m-80) outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 1.4140 time to fit residues: 200.5963 Evaluate side-chains 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 343 ASP Chi-restraints excluded: chain B residue 364 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.120497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106195 restraints weight = 22148.434| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.58 r_work: 0.3302 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6096 Z= 0.168 Angle : 0.559 9.284 8296 Z= 0.291 Chirality : 0.041 0.151 968 Planarity : 0.005 0.042 1010 Dihedral : 6.530 58.250 1052 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.53 % Allowed : 14.41 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.31), residues: 762 helix: 1.90 (0.23), residues: 540 sheet: -0.69 (0.76), residues: 20 loop : -0.08 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.004 0.001 HIS B 211 PHE 0.015 0.001 PHE A 195 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 410) hydrogen bonds : angle 4.69119 ( 1200) covalent geometry : bond 0.00406 ( 6096) covalent geometry : angle 0.55857 ( 8296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8056.90 seconds wall clock time: 138 minutes 32.18 seconds (8312.18 seconds total)