Starting phenix.real_space_refine on Thu Mar 6 00:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbn_34638/03_2025/8hbn_34638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbn_34638/03_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_34638/03_2025/8hbn_34638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbn_34638/03_2025/8hbn_34638.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbn_34638/03_2025/8hbn_34638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbn_34638/03_2025/8hbn_34638.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 5} 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, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 3.92, per 1000 atoms: 0.94 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: 0.88 Conformation dependent library (CDL) restraints added in 465.5 milliseconds 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: 0.42 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: 0.98 Time building geometry restraints manager: 1.08 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: 4.360 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- 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= 0.455 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (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 TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS B 86 PHE 0.023 0.002 PHE A 270 TYR 0.021 0.002 TYR A 382 ARG 0.006 0.001 ARG B 109 *********************** 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 : 0.454 Fit side-chains revert: symmetry clash 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: 0.8332 (mmt) REVERT: A 379 PRO cc_start: 0.9471 (OUTLIER) cc_final: 0.8857 (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: 0.1642 time to fit residues: 24.8414 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 : 0.456 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.075381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059368 restraints weight = 17692.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061072 restraints weight = 10322.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062236 restraints weight = 7166.411| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4275 Z= 0.224 Angle : 0.747 7.272 5801 Z= 0.386 Chirality : 0.049 0.186 665 Planarity : 0.005 0.063 748 Dihedral : 8.710 81.570 596 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.68 % Favored : 93.56 % Rotamer: Outliers : 7.41 % Allowed : 26.58 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.37), residues: 528 helix: -0.84 (0.45), residues: 137 sheet: -0.38 (0.51), residues: 111 loop : -0.62 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.002 0.001 HIS B 86 PHE 0.011 0.001 PHE B 104 TYR 0.014 0.002 TYR B 85 ARG 0.005 0.001 ARG A 114 *********************** 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 107 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8804 (tt) REVERT: A 302 LEU cc_start: 0.9378 (mt) cc_final: 0.9167 (mp) REVERT: A 335 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8818 (mmt) REVERT: A 343 LYS cc_start: 0.9312 (tppt) cc_final: 0.9093 (tptt) REVERT: A 398 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8862 (p) REVERT: A 454 MET cc_start: 0.7554 (tpt) cc_final: 0.7213 (tpt) REVERT: B 32 ASP cc_start: 0.8967 (t0) cc_final: 0.8565 (t0) REVERT: B 38 LEU cc_start: 0.9198 (mt) cc_final: 0.8983 (pp) REVERT: B 134 MET cc_start: 0.7393 (ptt) cc_final: 0.6879 (tpt) REVERT: B 183 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8461 (mmmt) outliers start: 34 outliers final: 16 residues processed: 99 average time/residue: 0.1600 time to fit residues: 20.8201 Evaluate side-chains 85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 398 THR 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 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 136 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.054022 restraints weight = 18134.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055553 restraints weight = 10629.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056623 restraints weight = 7476.257| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4275 Z= 0.301 Angle : 0.696 8.174 5801 Z= 0.359 Chirality : 0.047 0.172 665 Planarity : 0.005 0.054 748 Dihedral : 7.111 81.635 576 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.25 % Favored : 93.18 % Rotamer: Outliers : 7.41 % Allowed : 23.75 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.37), residues: 528 helix: -0.45 (0.45), residues: 138 sheet: -0.07 (0.52), residues: 105 loop : -0.52 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 292 HIS 0.004 0.001 HIS A 373 PHE 0.017 0.002 PHE A 240 TYR 0.012 0.002 TYR A 382 ARG 0.002 0.000 ARG B 109 *********************** 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 86 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8960 (tt) REVERT: A 335 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.8807 (mmt) REVERT: A 384 MET cc_start: 0.8409 (tmm) cc_final: 0.8111 (tmm) REVERT: A 398 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 32 ASP cc_start: 0.9024 (t0) cc_final: 0.8630 (t0) REVERT: B 85 TYR cc_start: 0.8458 (p90) cc_final: 0.8153 (p90) REVERT: B 106 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8660 (mp0) REVERT: B 134 MET cc_start: 0.7439 (ptt) cc_final: 0.6846 (tpt) REVERT: B 182 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9355 (mm) REVERT: B 183 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8866 (mmmt) outliers start: 34 outliers final: 20 residues processed: 80 average time/residue: 0.1186 time to fit residues: 12.7790 Evaluate side-chains 74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 A residue 460 ILE 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 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054471 restraints weight = 18189.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056040 restraints weight = 10654.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057118 restraints weight = 7480.557| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4275 Z= 0.191 Angle : 0.657 9.015 5801 Z= 0.329 Chirality : 0.046 0.159 665 Planarity : 0.004 0.048 748 Dihedral : 6.953 80.378 576 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 6.10 % Allowed : 25.71 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.37), residues: 528 helix: -0.25 (0.45), residues: 138 sheet: -0.12 (0.53), residues: 96 loop : -0.65 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 373 PHE 0.009 0.001 PHE A 403 TYR 0.015 0.001 TYR A 428 ARG 0.002 0.000 ARG B 109 *********************** 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 82 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 335 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8810 (mmt) REVERT: A 384 MET cc_start: 0.8469 (tmm) cc_final: 0.8106 (tmm) REVERT: A 398 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8936 (p) REVERT: B 32 ASP cc_start: 0.8990 (t0) cc_final: 0.8631 (t0) REVERT: B 68 MET cc_start: 0.9151 (ptm) cc_final: 0.8644 (ppp) REVERT: B 101 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8428 (mtpp) REVERT: B 134 MET cc_start: 0.7127 (ptt) cc_final: 0.6490 (tpt) REVERT: B 167 SER cc_start: 0.9260 (t) cc_final: 0.9048 (p) REVERT: B 182 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9178 (mm) REVERT: B 183 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8910 (mmmt) outliers start: 28 outliers final: 22 residues processed: 75 average time/residue: 0.1222 time to fit residues: 12.4886 Evaluate side-chains 78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 328 THR 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 153 ILE Chi-restraints excluded: chain B residue 173 MET 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 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 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 = 0.3359 r_free = 0.3359 target = 0.070089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054314 restraints weight = 18550.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055913 restraints weight = 10796.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056994 restraints weight = 7573.354| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4275 Z= 0.190 Angle : 0.658 9.880 5801 Z= 0.324 Chirality : 0.045 0.142 665 Planarity : 0.004 0.044 748 Dihedral : 6.809 79.576 576 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 6.97 % Allowed : 25.93 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.37), residues: 528 helix: -0.21 (0.46), residues: 132 sheet: -0.19 (0.52), residues: 97 loop : -0.56 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE A 284 TYR 0.017 0.001 TYR B 85 ARG 0.003 0.000 ARG A 339 *********************** 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 90 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8919 (mmm) REVERT: A 384 MET cc_start: 0.8523 (tmm) cc_final: 0.8109 (tmm) REVERT: A 398 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 32 ASP cc_start: 0.8938 (t0) cc_final: 0.8222 (p0) REVERT: B 68 MET cc_start: 0.9098 (ptm) cc_final: 0.8672 (ppp) REVERT: B 101 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8448 (mtpp) REVERT: B 134 MET cc_start: 0.7140 (ptt) cc_final: 0.6515 (tpt) REVERT: B 167 SER cc_start: 0.9220 (t) cc_final: 0.8999 (p) REVERT: B 182 LEU cc_start: 0.9510 (mm) cc_final: 0.9177 (mm) REVERT: B 183 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9006 (mmmt) outliers start: 32 outliers final: 23 residues processed: 80 average time/residue: 0.1292 time to fit residues: 13.9066 Evaluate side-chains 77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 328 THR 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 52 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054527 restraints weight = 18298.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056136 restraints weight = 10674.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057219 restraints weight = 7479.528| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4320 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= 0.182 Angle : 0.659 10.330 5801 Z= 0.321 Chirality : 0.045 0.141 665 Planarity : 0.003 0.041 748 Dihedral : 6.758 79.420 576 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.63 % Favored : 92.99 % Rotamer: Outliers : 5.66 % Allowed : 27.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 528 helix: -0.24 (0.46), residues: 132 sheet: -0.20 (0.52), residues: 96 loop : -0.58 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.003 0.001 HIS A 373 PHE 0.007 0.001 PHE A 403 TYR 0.014 0.001 TYR A 428 ARG 0.002 0.000 ARG A 339 *********************** 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 86 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.539 Fit side-chains REVERT: A 124 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9004 (tt) REVERT: A 335 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8943 (mmm) REVERT: A 384 MET cc_start: 0.8584 (tmm) cc_final: 0.8145 (tmm) REVERT: A 398 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 32 ASP cc_start: 0.8903 (t0) cc_final: 0.8559 (t0) REVERT: B 68 MET cc_start: 0.9099 (ptm) cc_final: 0.8623 (ppp) REVERT: B 101 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8358 (mtmt) REVERT: B 106 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8552 (mp0) REVERT: B 134 MET cc_start: 0.7150 (ptt) cc_final: 0.6518 (tpt) REVERT: B 167 SER cc_start: 0.9173 (t) cc_final: 0.8931 (p) REVERT: B 182 LEU cc_start: 0.9532 (mm) cc_final: 0.9225 (mm) REVERT: B 183 LYS cc_start: 0.9275 (mmmt) cc_final: 0.8953 (mmmt) outliers start: 26 outliers final: 22 residues processed: 77 average time/residue: 0.1296 time to fit residues: 13.5203 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 : 0.452 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 328 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** 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 = 0.3366 r_free = 0.3366 target = 0.070333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.055126 restraints weight = 18286.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056695 restraints weight = 10662.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057763 restraints weight = 7489.809| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4555 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= 0.178 Angle : 0.670 12.005 5801 Z= 0.323 Chirality : 0.045 0.141 665 Planarity : 0.003 0.039 748 Dihedral : 6.813 84.741 576 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 5.88 % Allowed : 27.45 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.36), residues: 528 helix: -0.28 (0.45), residues: 132 sheet: -0.28 (0.52), residues: 96 loop : -0.50 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 373 PHE 0.007 0.001 PHE A 403 TYR 0.024 0.001 TYR B 85 ARG 0.002 0.000 ARG A 252 *********************** 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 89 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 326 ASP cc_start: 0.8848 (t0) cc_final: 0.8585 (t0) REVERT: A 335 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9013 (mmm) REVERT: A 384 MET cc_start: 0.8583 (tmm) cc_final: 0.8140 (tmm) REVERT: A 398 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9000 (p) REVERT: B 32 ASP cc_start: 0.8916 (t0) cc_final: 0.8600 (t0) REVERT: B 68 MET cc_start: 0.9034 (ptm) cc_final: 0.8626 (ppp) REVERT: B 101 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8376 (mtmt) REVERT: B 106 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8454 (mp0) REVERT: B 134 MET cc_start: 0.7176 (ptt) cc_final: 0.6530 (tpt) REVERT: B 167 SER cc_start: 0.9091 (t) cc_final: 0.8873 (p) REVERT: B 182 LEU cc_start: 0.9517 (mm) cc_final: 0.9213 (mm) REVERT: B 183 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8965 (mmmt) outliers start: 27 outliers final: 23 residues processed: 79 average time/residue: 0.1671 time to fit residues: 17.9229 Evaluate side-chains 85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 328 THR 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 101 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052835 restraints weight = 18530.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054341 restraints weight = 10972.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055368 restraints weight = 7806.496| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4817 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= 0.227 Angle : 0.697 12.167 5801 Z= 0.334 Chirality : 0.045 0.142 665 Planarity : 0.004 0.039 748 Dihedral : 6.833 82.844 576 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 5.66 % Allowed : 28.10 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.37), residues: 528 helix: -0.07 (0.46), residues: 132 sheet: -0.42 (0.51), residues: 97 loop : -0.46 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 449 HIS 0.003 0.001 HIS A 373 PHE 0.013 0.001 PHE A 284 TYR 0.012 0.001 TYR A 428 ARG 0.002 0.000 ARG A 426 *********************** 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 80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 326 ASP cc_start: 0.8888 (t0) cc_final: 0.8586 (t0) REVERT: A 335 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9030 (mmm) REVERT: A 384 MET cc_start: 0.8633 (tmm) cc_final: 0.8189 (tmm) REVERT: A 398 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.8998 (p) REVERT: B 23 THR cc_start: 0.9617 (m) cc_final: 0.9298 (t) REVERT: B 32 ASP cc_start: 0.8959 (t0) cc_final: 0.8270 (p0) REVERT: B 68 MET cc_start: 0.9095 (ptm) cc_final: 0.8767 (ppp) REVERT: B 101 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8425 (mtmt) REVERT: B 134 MET cc_start: 0.7222 (ptt) cc_final: 0.6535 (tpt) REVERT: B 167 SER cc_start: 0.9068 (t) cc_final: 0.8845 (p) REVERT: B 183 LYS cc_start: 0.9334 (mmmt) cc_final: 0.8971 (mmmt) outliers start: 26 outliers final: 23 residues processed: 73 average time/residue: 0.1257 time to fit residues: 12.5369 Evaluate side-chains 77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 193 LEU 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 328 THR 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 173 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** 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 = 0.3340 r_free = 0.3340 target = 0.068979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053618 restraints weight = 18721.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055216 restraints weight = 10970.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056283 restraints weight = 7702.674| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4943 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= 0.189 Angle : 0.698 12.212 5801 Z= 0.331 Chirality : 0.045 0.146 665 Planarity : 0.003 0.039 748 Dihedral : 6.804 83.508 576 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.63 % Favored : 92.99 % Rotamer: Outliers : 5.23 % Allowed : 29.41 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.37), residues: 528 helix: -0.03 (0.46), residues: 132 sheet: -0.40 (0.51), residues: 97 loop : -0.47 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 449 HIS 0.002 0.001 HIS A 373 PHE 0.008 0.001 PHE A 284 TYR 0.012 0.001 TYR A 428 ARG 0.002 0.000 ARG B 109 *********************** 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 80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 326 ASP cc_start: 0.8940 (t0) cc_final: 0.8623 (t0) REVERT: A 335 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9082 (mmm) REVERT: A 384 MET cc_start: 0.8664 (tmm) cc_final: 0.8197 (tmm) REVERT: A 398 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8971 (p) REVERT: B 32 ASP cc_start: 0.8964 (t0) cc_final: 0.8236 (p0) REVERT: B 68 MET cc_start: 0.9065 (ptm) cc_final: 0.8712 (ppp) REVERT: B 101 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8393 (mtmt) REVERT: B 134 MET cc_start: 0.7148 (ptt) cc_final: 0.6511 (tpt) REVERT: B 167 SER cc_start: 0.9055 (t) cc_final: 0.8828 (p) REVERT: B 183 LYS cc_start: 0.9322 (mmmt) cc_final: 0.8939 (mmmt) outliers start: 24 outliers final: 22 residues processed: 72 average time/residue: 0.1261 time to fit residues: 12.4288 Evaluate side-chains 77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 193 LEU 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 328 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 49 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.069487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054188 restraints weight = 18693.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.055773 restraints weight = 10964.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.056873 restraints weight = 7730.747| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5083 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= 0.180 Angle : 0.701 11.911 5801 Z= 0.332 Chirality : 0.045 0.151 665 Planarity : 0.003 0.039 748 Dihedral : 6.692 82.566 576 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.06 % Favored : 93.56 % Rotamer: Outliers : 5.01 % Allowed : 29.63 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.37), residues: 528 helix: 0.02 (0.46), residues: 132 sheet: -0.55 (0.50), residues: 99 loop : -0.38 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 209 HIS 0.002 0.001 HIS A 373 PHE 0.007 0.001 PHE A 403 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG B 109 ********************** 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 83 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.6523 (mtt) cc_final: 0.6148 (mtt) REVERT: A 326 ASP cc_start: 0.8949 (t0) cc_final: 0.8658 (t0) REVERT: A 335 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9106 (mmm) REVERT: A 384 MET cc_start: 0.8673 (tmm) cc_final: 0.8179 (tmm) REVERT: A 398 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9021 (p) REVERT: B 32 ASP cc_start: 0.8948 (t0) cc_final: 0.8245 (p0) REVERT: B 68 MET cc_start: 0.9030 (ptm) cc_final: 0.8669 (ppp) REVERT: B 101 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8377 (mtmt) REVERT: B 106 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8447 (mp0) REVERT: B 134 MET cc_start: 0.7152 (ptt) cc_final: 0.6522 (tpt) REVERT: B 167 SER cc_start: 0.9012 (t) cc_final: 0.8794 (p) REVERT: B 182 LEU cc_start: 0.9499 (mm) cc_final: 0.9059 (mm) REVERT: B 183 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8938 (mmmt) outliers start: 23 outliers final: 18 residues processed: 75 average time/residue: 0.1216 time to fit residues: 12.4926 Evaluate side-chains 81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 3 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.069499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054156 restraints weight = 18715.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055711 restraints weight = 11006.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056793 restraints weight = 7769.132| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4275 Z= 0.180 Angle : 0.715 11.620 5801 Z= 0.335 Chirality : 0.045 0.151 665 Planarity : 0.003 0.038 748 Dihedral : 6.673 82.057 576 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.49 % Favored : 94.13 % Rotamer: Outliers : 4.36 % Allowed : 30.72 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.37), residues: 528 helix: -0.07 (0.46), residues: 132 sheet: -0.42 (0.51), residues: 98 loop : -0.35 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 449 HIS 0.002 0.001 HIS A 373 PHE 0.007 0.001 PHE A 403 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.02 seconds wall clock time: 42 minutes 8.26 seconds (2528.26 seconds total)