Starting phenix.real_space_refine on Fri Aug 22 14:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbn_34638/08_2025/8hbn_34638.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2668 2.51 5 N 722 2.21 5 O 781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2909 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1280 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.27, per 1000 atoms: 0.30 Number of scatterers: 4189 At special positions: 0 Unit cell: (70.808, 97.528, 85.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 781 8.00 N 722 7.00 C 2668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 168.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 32.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.972A pdb=" N PHE A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.586A pdb=" N ILE A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.806A pdb=" N MET A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 5.087A pdb=" N THR A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 184 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.667A pdb=" N TRP A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 removed outlier: 5.903A pdb=" N LYS A 230 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.819A pdb=" N GLU A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.657A pdb=" N VAL A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.537A pdb=" N ASN A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.715A pdb=" N LEU A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.682A pdb=" N MET A 335 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.711A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.861A pdb=" N THR A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.797A pdb=" N ILE B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 4.085A pdb=" N PHE B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 45' Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.656A pdb=" N PHE B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 6.578A pdb=" N LEU A 122 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 167 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 193 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.704A pdb=" N PHE A 271 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N SER A 388 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER A 444 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL A 467 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 446 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU A 465 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 448 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP A 463 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 450 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 459 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ILE A 459 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN A 306 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 461 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 465 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 355 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.629A pdb=" N ARG B 51 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR B 171 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 53 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET B 173 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE B 166 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 172 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 93 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS B 101 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 80 " --> pdb=" O LYS B 101 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 312 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: 0.57 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 704 1.31 - 1.44: 1113 1.44 - 1.57: 2426 1.57 - 1.70: 0 1.70 - 1.83: 32 Bond restraints: 4275 Sorted by residual: bond pdb=" CA SER A 441 " pdb=" CB SER A 441 " ideal model delta sigma weight residual 1.531 1.443 0.089 1.67e-02 3.59e+03 2.81e+01 bond pdb=" N CYS B 50 " pdb=" CA CYS B 50 " ideal model delta sigma weight residual 1.455 1.512 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" C PRO A 379 " pdb=" O PRO A 379 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.77e+01 bond pdb=" CA ALA B 79 " pdb=" CB ALA B 79 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.69e-02 3.50e+03 1.68e+01 bond pdb=" N PRO A 379 " pdb=" CA PRO A 379 " ideal model delta sigma weight residual 1.469 1.417 0.052 1.28e-02 6.10e+03 1.62e+01 ... (remaining 4270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 5512 2.72 - 5.44: 246 5.44 - 8.16: 31 8.16 - 10.88: 9 10.88 - 13.60: 3 Bond angle restraints: 5801 Sorted by residual: angle pdb=" N PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta sigma weight residual 103.25 93.14 10.11 1.05e+00 9.07e-01 9.27e+01 angle pdb=" C ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta sigma weight residual 110.35 96.75 13.60 1.78e+00 3.16e-01 5.83e+01 angle pdb=" C ILE B 52 " pdb=" N ILE B 53 " pdb=" CA ILE B 53 " ideal model delta sigma weight residual 121.97 135.08 -13.11 1.80e+00 3.09e-01 5.30e+01 angle pdb=" C ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 110.42 98.43 11.99 1.99e+00 2.53e-01 3.63e+01 angle pdb=" CA PHE A 270 " pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.56e+01 ... (remaining 5796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2154 16.50 - 33.00: 287 33.00 - 49.49: 113 49.49 - 65.99: 27 65.99 - 82.49: 8 Dihedral angle restraints: 2589 sinusoidal: 1012 harmonic: 1577 Sorted by residual: dihedral pdb=" C ARG A 217 " pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta harmonic sigma weight residual -122.60 -103.86 -18.74 0 2.50e+00 1.60e-01 5.62e+01 dihedral pdb=" N PRO A 379 " pdb=" C PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta harmonic sigma weight residual 115.10 98.73 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" C PRO A 379 " pdb=" N PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta harmonic sigma weight residual -120.70 -104.40 -16.30 0 2.50e+00 1.60e-01 4.25e+01 ... (remaining 2586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 573 0.081 - 0.162: 70 0.162 - 0.243: 17 0.243 - 0.325: 4 0.325 - 0.406: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ARG A 217 " pdb=" N ARG A 217 " pdb=" C ARG A 217 " pdb=" CB ARG A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ASP B 34 " pdb=" N ASP B 34 " pdb=" C ASP B 34 " pdb=" CB ASP B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASN A 189 " pdb=" N ASN A 189 " pdb=" C ASN A 189 " pdb=" CB ASN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 662 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 79 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ALA B 79 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA B 79 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 80 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 252 " 0.020 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ARG A 252 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG A 252 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 253 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 265 " 0.017 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C MET A 265 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A 265 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS A 266 " 0.021 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1073 2.78 - 3.31: 3966 3.31 - 3.84: 6284 3.84 - 4.37: 7294 4.37 - 4.90: 12513 Nonbonded interactions: 31130 Sorted by model distance: nonbonded pdb=" O GLY A 278 " pdb=" OG SER A 281 " model vdw 2.254 3.040 nonbonded pdb=" O ASP A 102 " pdb=" OG SER A 105 " model vdw 2.315 3.040 nonbonded pdb=" CB ASN A 437 " pdb=" N ASN A 438 " model vdw 2.325 2.816 nonbonded pdb=" O GLN A 255 " pdb=" C LYS A 256 " model vdw 2.328 3.270 nonbonded pdb=" O LEU A 257 " pdb=" N THR A 259 " model vdw 2.331 3.120 ... (remaining 31125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.150 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.007 0.089 4275 Z= 0.456 Angle : 1.240 13.597 5801 Z= 0.781 Chirality : 0.063 0.406 665 Planarity : 0.007 0.090 748 Dihedral : 18.565 82.489 1559 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 2.65 % Allowed : 7.39 % Favored : 89.96 % Rotamer: Outliers : 6.10 % Allowed : 28.10 % Favored : 65.80 % Cbeta Deviations : 0.97 % 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: -1.66 (0.36), residues: 528 helix: -1.59 (0.46), residues: 118 sheet: -0.36 (0.59), residues: 98 loop : -1.12 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.021 0.002 TYR A 382 PHE 0.023 0.002 PHE A 270 TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 4275) covalent geometry : angle 1.24028 ( 5801) hydrogen bonds : bond 0.33328 ( 120) hydrogen bonds : angle 10.55688 ( 312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8331 (mmt) REVERT: A 379 PRO cc_start: 0.9471 (OUTLIER) cc_final: 0.8855 (Cg_exo) REVERT: B 32 ASP cc_start: 0.8854 (t0) cc_final: 0.8620 (t0) REVERT: B 134 MET cc_start: 0.7455 (ptt) cc_final: 0.6901 (tpt) REVERT: B 167 SER cc_start: 0.8630 (p) cc_final: 0.8350 (p) outliers start: 28 outliers final: 9 residues processed: 122 average time/residue: 0.0775 time to fit residues: 11.8650 Evaluate side-chains 80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 379 PRO Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 380 ASN B 49 ASN B 61 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059032 restraints weight = 17748.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060747 restraints weight = 10279.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.061864 restraints weight = 7101.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.062683 restraints weight = 5534.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063179 restraints weight = 4635.917| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4275 Z= 0.146 Angle : 0.746 7.492 5801 Z= 0.383 Chirality : 0.049 0.189 665 Planarity : 0.005 0.063 748 Dihedral : 8.717 82.419 596 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.68 % Favored : 93.56 % Rotamer: Outliers : 7.41 % Allowed : 26.80 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.06 (0.37), residues: 528 helix: -0.88 (0.45), residues: 137 sheet: -0.42 (0.51), residues: 111 loop : -0.61 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 114 TYR 0.016 0.002 TYR B 85 PHE 0.012 0.001 PHE A 395 TRP 0.008 0.001 TRP A 292 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4275) covalent geometry : angle 0.74593 ( 5801) hydrogen bonds : bond 0.04928 ( 120) hydrogen bonds : angle 6.91342 ( 312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8827 (tt) REVERT: A 255 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9252 (pp30) REVERT: A 302 LEU cc_start: 0.9379 (mt) cc_final: 0.9155 (mp) REVERT: A 314 ASP cc_start: 0.8972 (t0) cc_final: 0.8765 (t0) REVERT: A 335 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8777 (mmt) REVERT: A 343 LYS cc_start: 0.9299 (tppt) cc_final: 0.9066 (tptt) REVERT: A 454 MET cc_start: 0.7543 (tpt) cc_final: 0.7207 (tpt) REVERT: B 32 ASP cc_start: 0.8937 (t0) cc_final: 0.8552 (t0) REVERT: B 38 LEU cc_start: 0.9217 (mt) cc_final: 0.9012 (pp) REVERT: B 101 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8553 (mtpp) REVERT: B 134 MET cc_start: 0.7385 (ptt) cc_final: 0.6877 (tpt) REVERT: B 183 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8553 (mmmt) outliers start: 34 outliers final: 18 residues processed: 101 average time/residue: 0.0575 time to fit residues: 7.7001 Evaluate side-chains 89 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.0670 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056147 restraints weight = 17950.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057771 restraints weight = 10389.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058879 restraints weight = 7246.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059574 restraints weight = 5655.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060131 restraints weight = 4785.449| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4275 Z= 0.140 Angle : 0.665 8.440 5801 Z= 0.338 Chirality : 0.046 0.177 665 Planarity : 0.004 0.053 748 Dihedral : 7.304 79.929 579 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 6.32 % Allowed : 26.36 % Favored : 67.32 % 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: -0.63 (0.37), residues: 528 helix: -0.45 (0.44), residues: 138 sheet: 0.05 (0.53), residues: 105 loop : -0.49 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 109 TYR 0.012 0.001 TYR A 382 PHE 0.012 0.001 PHE B 65 TRP 0.009 0.001 TRP A 292 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4275) covalent geometry : angle 0.66476 ( 5801) hydrogen bonds : bond 0.04218 ( 120) hydrogen bonds : angle 6.23348 ( 312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.163 Fit side-chains REVERT: A 116 ASP cc_start: 0.8907 (t0) cc_final: 0.8602 (t0) REVERT: A 124 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9000 (tt) REVERT: A 335 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8874 (mmm) REVERT: A 374 HIS cc_start: 0.8172 (m-70) cc_final: 0.7949 (m-70) REVERT: A 384 MET cc_start: 0.8374 (tmm) cc_final: 0.8070 (tmm) REVERT: A 398 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8926 (p) REVERT: A 429 ASN cc_start: 0.9245 (p0) cc_final: 0.9037 (p0) REVERT: B 32 ASP cc_start: 0.8937 (t0) cc_final: 0.8559 (t0) REVERT: B 134 MET cc_start: 0.7384 (ptt) cc_final: 0.6874 (tpt) REVERT: B 182 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9260 (mm) REVERT: B 183 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8859 (mmmt) outliers start: 29 outliers final: 17 residues processed: 85 average time/residue: 0.0512 time to fit residues: 6.0186 Evaluate side-chains 73 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN B 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.071157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055481 restraints weight = 17864.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057058 restraints weight = 10470.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.058116 restraints weight = 7382.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058858 restraints weight = 5809.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059374 restraints weight = 4925.257| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4275 Z= 0.125 Angle : 0.653 8.941 5801 Z= 0.328 Chirality : 0.046 0.148 665 Planarity : 0.004 0.048 748 Dihedral : 7.117 88.189 576 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 6.54 % Allowed : 26.58 % Favored : 66.88 % 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: -0.66 (0.37), residues: 528 helix: -0.35 (0.45), residues: 132 sheet: 0.03 (0.54), residues: 96 loop : -0.57 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.017 0.002 TYR B 85 PHE 0.013 0.001 PHE A 284 TRP 0.009 0.001 TRP A 292 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4275) covalent geometry : angle 0.65336 ( 5801) hydrogen bonds : bond 0.03699 ( 120) hydrogen bonds : angle 5.87313 ( 312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.134 Fit side-chains REVERT: A 335 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8945 (mmm) REVERT: A 384 MET cc_start: 0.8423 (tmm) cc_final: 0.8069 (tmm) REVERT: A 398 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 32 ASP cc_start: 0.8904 (t0) cc_final: 0.8539 (t0) REVERT: B 68 MET cc_start: 0.9089 (ptm) cc_final: 0.8620 (ppp) REVERT: B 134 MET cc_start: 0.7202 (ptt) cc_final: 0.6545 (tpt) REVERT: B 167 SER cc_start: 0.9203 (t) cc_final: 0.9001 (p) REVERT: B 182 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 183 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8890 (mmmt) outliers start: 30 outliers final: 21 residues processed: 78 average time/residue: 0.0504 time to fit residues: 5.3363 Evaluate side-chains 75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.0170 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055216 restraints weight = 17956.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056776 restraints weight = 10544.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057845 restraints weight = 7421.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058590 restraints weight = 5844.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059052 restraints weight = 4953.243| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4275 Z= 0.119 Angle : 0.662 11.898 5801 Z= 0.322 Chirality : 0.045 0.143 665 Planarity : 0.004 0.044 748 Dihedral : 6.770 78.396 576 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.63 % Favored : 92.99 % Rotamer: Outliers : 6.75 % Allowed : 25.27 % Favored : 67.97 % 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: -0.52 (0.37), residues: 528 helix: -0.10 (0.47), residues: 126 sheet: 0.02 (0.54), residues: 97 loop : -0.51 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 109 TYR 0.013 0.001 TYR A 428 PHE 0.008 0.001 PHE A 240 TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4275) covalent geometry : angle 0.66189 ( 5801) hydrogen bonds : bond 0.03387 ( 120) hydrogen bonds : angle 5.54912 ( 312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.170 Fit side-chains REVERT: A 124 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9026 (tt) REVERT: A 335 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8982 (mmm) REVERT: A 384 MET cc_start: 0.8501 (tmm) cc_final: 0.8097 (tmm) REVERT: A 398 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8930 (p) REVERT: B 32 ASP cc_start: 0.8824 (t0) cc_final: 0.8476 (t0) REVERT: B 68 MET cc_start: 0.9067 (ptm) cc_final: 0.8622 (ppp) REVERT: B 106 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8476 (mp0) REVERT: B 134 MET cc_start: 0.7212 (ptt) cc_final: 0.6550 (tpt) REVERT: B 167 SER cc_start: 0.9165 (t) cc_final: 0.8940 (p) REVERT: B 182 LEU cc_start: 0.9541 (mm) cc_final: 0.9241 (mm) REVERT: B 183 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9031 (mmmt) outliers start: 31 outliers final: 23 residues processed: 79 average time/residue: 0.0540 time to fit residues: 5.7179 Evaluate side-chains 82 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055677 restraints weight = 18769.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057331 restraints weight = 10873.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058444 restraints weight = 7582.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059221 restraints weight = 5906.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059780 restraints weight = 4965.481| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4275 Z= 0.108 Angle : 0.654 10.880 5801 Z= 0.316 Chirality : 0.045 0.142 665 Planarity : 0.004 0.041 748 Dihedral : 6.711 78.681 576 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 5.23 % Allowed : 27.89 % Favored : 66.88 % 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: -0.46 (0.36), residues: 528 helix: -0.08 (0.47), residues: 126 sheet: 0.05 (0.53), residues: 97 loop : -0.45 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 109 TYR 0.029 0.002 TYR B 85 PHE 0.007 0.001 PHE A 284 TRP 0.008 0.001 TRP A 292 HIS 0.005 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4275) covalent geometry : angle 0.65405 ( 5801) hydrogen bonds : bond 0.03108 ( 120) hydrogen bonds : angle 5.38182 ( 312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 335 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9028 (mmm) REVERT: A 384 MET cc_start: 0.8573 (tmm) cc_final: 0.8154 (tmm) REVERT: A 398 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8968 (p) REVERT: B 32 ASP cc_start: 0.8897 (t0) cc_final: 0.8511 (t0) REVERT: B 68 MET cc_start: 0.9014 (ptm) cc_final: 0.8606 (ppp) REVERT: B 106 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8465 (mp0) REVERT: B 134 MET cc_start: 0.7221 (ptt) cc_final: 0.6555 (tpt) REVERT: B 167 SER cc_start: 0.9088 (t) cc_final: 0.8871 (p) REVERT: B 182 LEU cc_start: 0.9527 (mm) cc_final: 0.9225 (mm) REVERT: B 183 LYS cc_start: 0.9331 (mmmt) cc_final: 0.8999 (mmmt) outliers start: 24 outliers final: 21 residues processed: 80 average time/residue: 0.0519 time to fit residues: 5.6689 Evaluate side-chains 85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 173 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054247 restraints weight = 18754.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055845 restraints weight = 10960.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056932 restraints weight = 7682.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057681 restraints weight = 5995.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058159 restraints weight = 5055.285| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4275 Z= 0.124 Angle : 0.671 11.077 5801 Z= 0.319 Chirality : 0.044 0.141 665 Planarity : 0.003 0.040 748 Dihedral : 6.672 77.848 576 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 5.45 % Allowed : 28.98 % Favored : 65.58 % 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: -0.50 (0.37), residues: 528 helix: -0.03 (0.45), residues: 132 sheet: -0.10 (0.52), residues: 97 loop : -0.48 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.012 0.001 TYR A 428 PHE 0.010 0.001 PHE A 284 TRP 0.008 0.001 TRP A 449 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4275) covalent geometry : angle 0.67128 ( 5801) hydrogen bonds : bond 0.03111 ( 120) hydrogen bonds : angle 5.35529 ( 312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: A 116 ASP cc_start: 0.8860 (t0) cc_final: 0.8526 (t0) REVERT: A 326 ASP cc_start: 0.8808 (t0) cc_final: 0.8539 (t0) REVERT: A 335 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9030 (mmm) REVERT: A 384 MET cc_start: 0.8592 (tmm) cc_final: 0.8159 (tmm) REVERT: A 398 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 32 ASP cc_start: 0.8927 (t0) cc_final: 0.8159 (p0) REVERT: B 68 MET cc_start: 0.8989 (ptm) cc_final: 0.8635 (ppp) REVERT: B 85 TYR cc_start: 0.8704 (p90) cc_final: 0.7917 (p90) REVERT: B 106 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8306 (mp0) REVERT: B 134 MET cc_start: 0.7254 (ptt) cc_final: 0.6560 (tpt) REVERT: B 167 SER cc_start: 0.9050 (t) cc_final: 0.8836 (p) REVERT: B 182 LEU cc_start: 0.9530 (mm) cc_final: 0.9219 (mm) REVERT: B 183 LYS cc_start: 0.9308 (mmmt) cc_final: 0.8980 (mmmt) outliers start: 25 outliers final: 22 residues processed: 79 average time/residue: 0.0509 time to fit residues: 5.5352 Evaluate side-chains 78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 173 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.054365 restraints weight = 18521.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055948 restraints weight = 10902.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057032 restraints weight = 7680.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057774 restraints weight = 6035.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058255 restraints weight = 5098.841| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4275 Z= 0.116 Angle : 0.677 11.143 5801 Z= 0.324 Chirality : 0.044 0.140 665 Planarity : 0.003 0.039 748 Dihedral : 6.505 71.050 576 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 5.45 % Allowed : 29.41 % Favored : 65.14 % 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: -0.44 (0.37), residues: 528 helix: 0.18 (0.46), residues: 132 sheet: -0.09 (0.51), residues: 97 loop : -0.51 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.011 0.001 TYR A 428 PHE 0.008 0.001 PHE A 284 TRP 0.007 0.001 TRP A 292 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4275) covalent geometry : angle 0.67682 ( 5801) hydrogen bonds : bond 0.03087 ( 120) hydrogen bonds : angle 5.26964 ( 312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.229 Fit side-chains REVERT: A 116 ASP cc_start: 0.8869 (t0) cc_final: 0.8536 (t0) REVERT: A 326 ASP cc_start: 0.8834 (t0) cc_final: 0.8544 (t0) REVERT: A 335 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9046 (mmm) REVERT: A 384 MET cc_start: 0.8611 (tmm) cc_final: 0.8154 (tmm) REVERT: A 398 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 32 ASP cc_start: 0.8941 (t0) cc_final: 0.8184 (p0) REVERT: B 68 MET cc_start: 0.9007 (ptm) cc_final: 0.8679 (ppp) REVERT: B 85 TYR cc_start: 0.8744 (p90) cc_final: 0.8098 (p90) REVERT: B 106 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8408 (mp0) REVERT: B 134 MET cc_start: 0.7244 (ptt) cc_final: 0.6550 (tpt) REVERT: B 182 LEU cc_start: 0.9520 (mm) cc_final: 0.9072 (mm) REVERT: B 183 LYS cc_start: 0.9313 (mmmt) cc_final: 0.8966 (mmmt) outliers start: 25 outliers final: 22 residues processed: 75 average time/residue: 0.0580 time to fit residues: 5.9566 Evaluate side-chains 82 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 173 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054485 restraints weight = 18866.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056070 restraints weight = 11048.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057189 restraints weight = 7768.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057919 restraints weight = 6079.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058453 restraints weight = 5140.396| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4275 Z= 0.110 Angle : 0.684 11.567 5801 Z= 0.325 Chirality : 0.044 0.134 665 Planarity : 0.003 0.038 748 Dihedral : 6.485 71.621 576 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.63 % Favored : 92.99 % Rotamer: Outliers : 5.45 % Allowed : 29.41 % Favored : 65.14 % 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: -0.41 (0.37), residues: 528 helix: 0.20 (0.46), residues: 132 sheet: -0.01 (0.51), residues: 96 loop : -0.51 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.011 0.001 TYR A 428 PHE 0.007 0.001 PHE A 403 TRP 0.007 0.001 TRP A 292 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4275) covalent geometry : angle 0.68362 ( 5801) hydrogen bonds : bond 0.03011 ( 120) hydrogen bonds : angle 5.16863 ( 312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.171 Fit side-chains REVERT: A 116 ASP cc_start: 0.8872 (t0) cc_final: 0.8539 (t0) REVERT: A 326 ASP cc_start: 0.8807 (t0) cc_final: 0.8503 (t0) REVERT: A 335 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (mmm) REVERT: A 384 MET cc_start: 0.8604 (tmm) cc_final: 0.8138 (tmm) REVERT: A 398 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 32 ASP cc_start: 0.8904 (t0) cc_final: 0.8546 (t0) REVERT: B 68 MET cc_start: 0.8964 (ptm) cc_final: 0.8648 (ppp) REVERT: B 85 TYR cc_start: 0.8703 (p90) cc_final: 0.8349 (p90) REVERT: B 106 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8475 (mp0) REVERT: B 134 MET cc_start: 0.7257 (ptt) cc_final: 0.6556 (tpt) REVERT: B 182 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9041 (mm) REVERT: B 183 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8956 (mmmt) outliers start: 25 outliers final: 22 residues processed: 76 average time/residue: 0.0542 time to fit residues: 5.6529 Evaluate side-chains 84 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 16 optimal weight: 0.0030 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054935 restraints weight = 18367.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056530 restraints weight = 10837.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057635 restraints weight = 7631.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058397 restraints weight = 5975.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058923 restraints weight = 5039.239| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4275 Z= 0.107 Angle : 0.686 11.585 5801 Z= 0.325 Chirality : 0.044 0.139 665 Planarity : 0.003 0.038 748 Dihedral : 6.601 80.636 576 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 5.23 % Allowed : 30.28 % Favored : 64.49 % 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: -0.38 (0.37), residues: 528 helix: 0.22 (0.47), residues: 132 sheet: -0.15 (0.51), residues: 98 loop : -0.43 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.011 0.001 TYR A 428 PHE 0.007 0.001 PHE A 403 TRP 0.006 0.001 TRP A 292 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4275) covalent geometry : angle 0.68597 ( 5801) hydrogen bonds : bond 0.02831 ( 120) hydrogen bonds : angle 5.04443 ( 312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.183 Fit side-chains REVERT: A 116 ASP cc_start: 0.8754 (t0) cc_final: 0.8493 (t0) REVERT: A 326 ASP cc_start: 0.8857 (t0) cc_final: 0.8562 (t0) REVERT: A 335 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9057 (mmm) REVERT: A 384 MET cc_start: 0.8622 (tmm) cc_final: 0.8221 (tmm) REVERT: A 398 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 32 ASP cc_start: 0.8866 (t0) cc_final: 0.8206 (p0) REVERT: B 68 MET cc_start: 0.8951 (ptm) cc_final: 0.8625 (ppp) REVERT: B 85 TYR cc_start: 0.8641 (p90) cc_final: 0.8340 (p90) REVERT: B 106 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8459 (mp0) REVERT: B 134 MET cc_start: 0.7272 (ptt) cc_final: 0.6560 (tpt) REVERT: B 182 LEU cc_start: 0.9489 (mm) cc_final: 0.9029 (mm) REVERT: B 183 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8945 (mmmt) outliers start: 24 outliers final: 20 residues processed: 76 average time/residue: 0.0549 time to fit residues: 5.6729 Evaluate side-chains 81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 173 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055030 restraints weight = 18672.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.056642 restraints weight = 10970.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057754 restraints weight = 7696.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058515 restraints weight = 6023.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059000 restraints weight = 5078.586| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4275 Z= 0.111 Angle : 0.704 11.814 5801 Z= 0.333 Chirality : 0.044 0.143 665 Planarity : 0.003 0.037 748 Dihedral : 5.309 51.788 573 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.25 % Favored : 93.56 % Rotamer: Outliers : 5.01 % Allowed : 30.94 % Favored : 64.05 % 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: -0.28 (0.37), residues: 528 helix: 0.17 (0.47), residues: 126 sheet: -0.08 (0.52), residues: 98 loop : -0.29 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.010 0.001 TYR A 428 PHE 0.007 0.001 PHE A 403 TRP 0.006 0.001 TRP A 449 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4275) covalent geometry : angle 0.70353 ( 5801) hydrogen bonds : bond 0.02891 ( 120) hydrogen bonds : angle 4.98806 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1006.11 seconds wall clock time: 18 minutes 0.79 seconds (1080.79 seconds total)