Starting phenix.real_space_refine on Fri Aug 22 16:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgn_41242/08_2025/8tgn_41242.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3821 2.51 5 N 894 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2864 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2824 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 21, 'TRANS': 355} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.62, per 1000 atoms: 0.28 Number of scatterers: 5745 At special positions: 0 Unit cell: (75.2, 59.22, 113.74, 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 57 16.00 O 973 8.00 N 894 7.00 C 3821 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: 0.57 Conformation dependent library (CDL) restraints added in 356.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.507A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.754A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 165 removed outlier: 3.647A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 3.984A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.964A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 3.712A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.010A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.597A pdb=" N LEU A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.609A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 341 removed outlier: 4.240A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 3.634A pdb=" N SER A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 4.262A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.602A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.095A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'B' and resid 20 through 41 removed outlier: 3.577A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.662A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 4.689A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.588A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 186 Processing helix chain 'B' and resid 189 through 219 Processing helix chain 'B' and resid 223 through 253 removed outlier: 4.185A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 4.566A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.855A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 330 removed outlier: 3.925A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 363 removed outlier: 3.564A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 Proline residue: B 412 - end of helix removed outlier: 3.600A pdb=" N ARG B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.648A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.550A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 473 through 479 455 hydrogen bonds defined for protein. 1335 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: 0.92 Time building geometry restraints manager: 0.70 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: 858 1.31 - 1.44: 1564 1.44 - 1.57: 3367 1.57 - 1.69: 1 1.69 - 1.82: 100 Bond restraints: 5890 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.403 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CG SRO A 601 " pdb=" CD2 SRO A 601 " ideal model delta sigma weight residual 1.438 1.364 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.492 1.430 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" C37 YHR B 601 " pdb=" O39 YHR B 601 " ideal model delta sigma weight residual 1.342 1.403 -0.061 2.00e-02 2.50e+03 9.16e+00 ... (remaining 5885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 7953 4.14 - 8.28: 61 8.28 - 12.42: 9 12.42 - 16.56: 0 16.56 - 20.70: 1 Bond angle restraints: 8024 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 132.59 -20.70 3.00e+00 1.11e-01 4.76e+01 angle pdb=" C PHE B 356 " pdb=" N GLY B 357 " pdb=" CA GLY B 357 " ideal model delta sigma weight residual 119.94 112.58 7.36 1.11e+00 8.12e-01 4.40e+01 angle pdb=" N LEU A 359 " pdb=" CA LEU A 359 " pdb=" C LEU A 359 " ideal model delta sigma weight residual 113.16 120.84 -7.68 1.24e+00 6.50e-01 3.83e+01 angle pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" C PRO B 482 " ideal model delta sigma weight residual 112.47 122.48 -10.01 2.06e+00 2.36e-01 2.36e+01 angle pdb=" C PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 111.56 103.59 7.97 1.65e+00 3.67e-01 2.33e+01 ... (remaining 8019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 3045 23.20 - 46.39: 346 46.39 - 69.59: 59 69.59 - 92.78: 4 92.78 - 115.98: 3 Dihedral angle restraints: 3457 sinusoidal: 1315 harmonic: 2142 Sorted by residual: dihedral pdb=" CA PHE B 294 " pdb=" C PHE B 294 " pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" C PHE B 131 " pdb=" N PHE B 131 " pdb=" CA PHE B 131 " pdb=" CB PHE B 131 " ideal model delta harmonic sigma weight residual -122.60 -111.48 -11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA PHE A 294 " pdb=" C PHE A 294 " pdb=" N MET A 295 " pdb=" CA MET A 295 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 3454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 842 0.069 - 0.138: 107 0.138 - 0.207: 7 0.207 - 0.276: 2 0.276 - 0.345: 3 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA PHE B 131 " pdb=" N PHE B 131 " pdb=" C PHE B 131 " pdb=" CB PHE B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU A 359 " pdb=" N LEU A 359 " pdb=" C LEU A 359 " pdb=" CB LEU A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.59 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 958 not shown) Planarity restraints: 977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 355 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C LEU B 355 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU B 355 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE B 356 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 320 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO B 321 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 328 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C MET B 328 " -0.051 2.00e-02 2.50e+03 pdb=" O MET B 328 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN B 329 " 0.017 2.00e-02 2.50e+03 ... (remaining 974 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 452 2.74 - 3.28: 6157 3.28 - 3.82: 9855 3.82 - 4.36: 10833 4.36 - 4.90: 19484 Nonbonded interactions: 46781 Sorted by model distance: nonbonded pdb=" O VAL B 304 " pdb=" OH TYR B 471 " model vdw 2.195 3.040 nonbonded pdb=" O ALA B 442 " pdb=" OG SER B 446 " model vdw 2.207 3.040 nonbonded pdb=" O GLY B 158 " pdb=" OG1 THR B 161 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP A 299 " pdb=" NE2 HIS A 422 " model vdw 2.243 3.120 nonbonded pdb=" O LEU A 142 " pdb=" OG SER A 145 " model vdw 2.247 3.040 ... (remaining 46776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 276 or resid 289 through 483)) selection = (chain 'B' and (resid 19 through 51 or resid 134 through 483)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.590 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.005 0.077 5890 Z= 0.275 Angle : 0.970 20.701 8024 Z= 0.509 Chirality : 0.050 0.345 961 Planarity : 0.008 0.075 977 Dihedral : 18.680 115.979 2095 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 28.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.33 % Favored : 98.54 % Rotamer: Outliers : 0.49 % Allowed : 34.64 % Favored : 64.87 % 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: 0.16 (0.29), residues: 751 helix: 0.44 (0.20), residues: 601 sheet: None (None), residues: 0 loop : -0.84 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR A 426 PHE 0.051 0.002 PHE A 294 TRP 0.012 0.001 TRP B 326 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 5890) covalent geometry : angle 0.96988 ( 8024) hydrogen bonds : bond 0.16696 ( 455) hydrogen bonds : angle 6.19796 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 26 VAL cc_start: 0.8043 (m) cc_final: 0.7843 (t) REVERT: B 355 LEU cc_start: 0.8242 (mp) cc_final: 0.7881 (tt) outliers start: 3 outliers final: 2 residues processed: 160 average time/residue: 0.0594 time to fit residues: 13.5547 Evaluate side-chains 155 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain B residue 208 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 388 ASN B 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.152783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137907 restraints weight = 8992.066| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.40 r_work: 0.3749 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5890 Z= 0.236 Angle : 0.766 8.654 8024 Z= 0.380 Chirality : 0.047 0.210 961 Planarity : 0.007 0.057 977 Dihedral : 8.814 86.558 869 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.41 % Allowed : 29.58 % 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 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: 0.78 (0.31), residues: 751 helix: 0.89 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.76 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.012 0.002 TYR B 190 PHE 0.026 0.002 PHE B 174 TRP 0.009 0.001 TRP B 326 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 5890) covalent geometry : angle 0.76635 ( 8024) hydrogen bonds : bond 0.05643 ( 455) hydrogen bonds : angle 4.87548 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.209 Fit side-chains REVERT: A 48 PHE cc_start: 0.7707 (t80) cc_final: 0.7274 (t80) REVERT: A 170 MET cc_start: 0.6712 (tpp) cc_final: 0.6278 (tpp) REVERT: A 365 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7325 (mtt180) REVERT: A 414 MET cc_start: 0.7734 (mtt) cc_final: 0.7225 (mmm) REVERT: A 471 TYR cc_start: 0.8491 (t80) cc_final: 0.7853 (t80) REVERT: B 26 VAL cc_start: 0.7942 (m) cc_final: 0.7714 (t) REVERT: B 296 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6654 (mp) REVERT: B 410 MET cc_start: 0.7976 (mmp) cc_final: 0.7770 (mmp) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.0592 time to fit residues: 14.4435 Evaluate side-chains 168 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.154453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139304 restraints weight = 8807.869| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.34 r_work: 0.3774 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5890 Z= 0.214 Angle : 0.730 9.450 8024 Z= 0.359 Chirality : 0.046 0.252 961 Planarity : 0.007 0.056 977 Dihedral : 8.481 89.725 868 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.25 % Allowed : 31.05 % Favored : 64.71 % 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: 0.95 (0.32), residues: 751 helix: 1.01 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.73 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.010 0.001 TYR A 477 PHE 0.019 0.001 PHE B 174 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 5890) covalent geometry : angle 0.72969 ( 8024) hydrogen bonds : bond 0.05344 ( 455) hydrogen bonds : angle 4.73744 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.239 Fit side-chains REVERT: A 170 MET cc_start: 0.6668 (tpp) cc_final: 0.6292 (tpp) REVERT: A 365 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7527 (mtt180) REVERT: A 414 MET cc_start: 0.7653 (mtt) cc_final: 0.7184 (mmm) REVERT: A 471 TYR cc_start: 0.8498 (t80) cc_final: 0.7861 (t80) REVERT: B 28 PHE cc_start: 0.6672 (t80) cc_final: 0.6328 (t80) REVERT: B 303 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7650 (tp) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 0.0588 time to fit residues: 14.5640 Evaluate side-chains 168 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.152337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137639 restraints weight = 8962.648| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.35 r_work: 0.3761 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5890 Z= 0.205 Angle : 0.726 9.974 8024 Z= 0.355 Chirality : 0.045 0.154 961 Planarity : 0.006 0.055 977 Dihedral : 8.295 88.647 868 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.58 % Allowed : 31.86 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.32), residues: 751 helix: 1.12 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.010 0.001 TYR A 477 PHE 0.017 0.001 PHE B 174 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 5890) covalent geometry : angle 0.72553 ( 8024) hydrogen bonds : bond 0.05122 ( 455) hydrogen bonds : angle 4.69231 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.249 Fit side-chains REVERT: A 34 ASP cc_start: 0.8155 (t0) cc_final: 0.7943 (t0) REVERT: A 299 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: A 328 MET cc_start: 0.6831 (mpp) cc_final: 0.6501 (mpp) REVERT: A 365 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7520 (mtt180) REVERT: B 28 PHE cc_start: 0.6714 (t80) cc_final: 0.6321 (t80) REVERT: B 296 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6641 (mp) REVERT: B 303 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7711 (tp) REVERT: B 328 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7563 (mtp) REVERT: B 338 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8377 (mt) REVERT: B 461 MET cc_start: 0.7860 (mmm) cc_final: 0.7553 (mmm) outliers start: 28 outliers final: 18 residues processed: 173 average time/residue: 0.0617 time to fit residues: 15.1190 Evaluate side-chains 177 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.0170 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 35 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140848 restraints weight = 9053.442| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.36 r_work: 0.3799 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5890 Z= 0.156 Angle : 0.697 10.865 8024 Z= 0.335 Chirality : 0.043 0.245 961 Planarity : 0.006 0.053 977 Dihedral : 8.226 87.342 868 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.41 % Allowed : 32.84 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.32), residues: 751 helix: 1.30 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -0.98 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.007 0.001 TYR A 477 PHE 0.018 0.001 PHE B 174 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5890) covalent geometry : angle 0.69657 ( 8024) hydrogen bonds : bond 0.04714 ( 455) hydrogen bonds : angle 4.56942 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.176 Fit side-chains REVERT: A 34 ASP cc_start: 0.8099 (t0) cc_final: 0.7884 (t0) REVERT: A 36 MET cc_start: 0.8229 (ttm) cc_final: 0.7986 (mtp) REVERT: A 170 MET cc_start: 0.6568 (tpp) cc_final: 0.6339 (tpp) REVERT: A 299 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: A 365 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7529 (mtt180) REVERT: A 414 MET cc_start: 0.7604 (mtt) cc_final: 0.7192 (mmm) REVERT: B 28 PHE cc_start: 0.6647 (t80) cc_final: 0.6293 (t80) REVERT: B 296 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6680 (mp) REVERT: B 303 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7663 (tp) REVERT: B 328 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7349 (mtp) REVERT: B 438 CYS cc_start: 0.8142 (m) cc_final: 0.7905 (m) REVERT: B 461 MET cc_start: 0.7844 (mmm) cc_final: 0.7533 (mmm) outliers start: 27 outliers final: 20 residues processed: 174 average time/residue: 0.0560 time to fit residues: 14.0165 Evaluate side-chains 180 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.154937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140052 restraints weight = 9017.916| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.36 r_work: 0.3786 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5890 Z= 0.182 Angle : 0.730 11.516 8024 Z= 0.349 Chirality : 0.045 0.251 961 Planarity : 0.006 0.052 977 Dihedral : 7.812 84.921 868 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.07 % Allowed : 33.66 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.32), residues: 751 helix: 1.31 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.008 0.001 TYR A 477 PHE 0.020 0.001 PHE B 174 TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5890) covalent geometry : angle 0.72997 ( 8024) hydrogen bonds : bond 0.04805 ( 455) hydrogen bonds : angle 4.61666 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8131 (t0) cc_final: 0.7908 (t0) REVERT: A 36 MET cc_start: 0.8277 (ttm) cc_final: 0.8026 (mtp) REVERT: A 299 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: A 365 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7603 (mtt180) REVERT: A 414 MET cc_start: 0.7589 (mtt) cc_final: 0.7123 (mmm) REVERT: B 26 VAL cc_start: 0.8009 (m) cc_final: 0.7773 (t) REVERT: B 28 PHE cc_start: 0.6655 (t80) cc_final: 0.6289 (t80) REVERT: B 214 MET cc_start: 0.6452 (ttp) cc_final: 0.6138 (ttp) REVERT: B 296 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6696 (mp) REVERT: B 303 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7680 (tp) REVERT: B 328 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: B 438 CYS cc_start: 0.8128 (m) cc_final: 0.7891 (m) REVERT: B 461 MET cc_start: 0.7864 (mmm) cc_final: 0.7453 (mmm) outliers start: 31 outliers final: 25 residues processed: 176 average time/residue: 0.0589 time to fit residues: 14.8471 Evaluate side-chains 186 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141638 restraints weight = 8975.446| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.35 r_work: 0.3805 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5890 Z= 0.150 Angle : 0.703 11.894 8024 Z= 0.335 Chirality : 0.043 0.236 961 Planarity : 0.006 0.050 977 Dihedral : 7.336 82.853 868 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.05 % Allowed : 32.84 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.32), residues: 751 helix: 1.38 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -0.98 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.006 0.001 TYR A 477 PHE 0.020 0.001 PHE B 174 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5890) covalent geometry : angle 0.70255 ( 8024) hydrogen bonds : bond 0.04538 ( 455) hydrogen bonds : angle 4.54793 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8112 (t0) cc_final: 0.7880 (t0) REVERT: A 36 MET cc_start: 0.8198 (ttm) cc_final: 0.7976 (mtp) REVERT: A 299 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: A 365 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7612 (mtt180) REVERT: A 414 MET cc_start: 0.7536 (mtt) cc_final: 0.7141 (mmm) REVERT: B 28 PHE cc_start: 0.6616 (t80) cc_final: 0.6253 (t80) REVERT: B 214 MET cc_start: 0.6584 (ttp) cc_final: 0.6298 (ttp) REVERT: B 296 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6620 (mp) REVERT: B 303 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 328 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: B 376 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 438 CYS cc_start: 0.8147 (m) cc_final: 0.7874 (m) REVERT: B 461 MET cc_start: 0.7850 (mmm) cc_final: 0.7437 (mmm) outliers start: 37 outliers final: 25 residues processed: 183 average time/residue: 0.0599 time to fit residues: 15.4367 Evaluate side-chains 191 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 22 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.155864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140978 restraints weight = 8888.653| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.32 r_work: 0.3795 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5890 Z= 0.171 Angle : 0.736 11.942 8024 Z= 0.349 Chirality : 0.045 0.244 961 Planarity : 0.006 0.050 977 Dihedral : 7.042 81.145 868 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.23 % Allowed : 33.99 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.32), residues: 751 helix: 1.39 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.03 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.008 0.001 TYR A 477 PHE 0.018 0.001 PHE B 174 TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5890) covalent geometry : angle 0.73562 ( 8024) hydrogen bonds : bond 0.04634 ( 455) hydrogen bonds : angle 4.58559 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8118 (t0) cc_final: 0.7870 (t0) REVERT: A 36 MET cc_start: 0.8214 (ttm) cc_final: 0.7912 (mtm) REVERT: A 299 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: A 365 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7583 (mtt180) REVERT: A 414 MET cc_start: 0.7603 (mtt) cc_final: 0.7141 (mmm) REVERT: B 28 PHE cc_start: 0.6689 (t80) cc_final: 0.6310 (t80) REVERT: B 214 MET cc_start: 0.6458 (ttp) cc_final: 0.6134 (ttp) REVERT: B 303 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7636 (tp) REVERT: B 328 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7367 (mtp) REVERT: B 376 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 410 MET cc_start: 0.7892 (mmp) cc_final: 0.7598 (mmm) REVERT: B 438 CYS cc_start: 0.8140 (m) cc_final: 0.7860 (m) REVERT: B 461 MET cc_start: 0.7843 (mmm) cc_final: 0.7515 (mmm) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.0574 time to fit residues: 15.0538 Evaluate side-chains 190 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.155551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140497 restraints weight = 8917.767| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.33 r_work: 0.3788 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5890 Z= 0.183 Angle : 0.756 12.061 8024 Z= 0.361 Chirality : 0.046 0.327 961 Planarity : 0.006 0.052 977 Dihedral : 6.801 79.339 868 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.07 % Allowed : 34.15 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.32), residues: 751 helix: 1.35 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.07 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.009 0.001 TYR A 477 PHE 0.019 0.001 PHE B 174 TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5890) covalent geometry : angle 0.75564 ( 8024) hydrogen bonds : bond 0.04773 ( 455) hydrogen bonds : angle 4.61760 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8111 (t0) cc_final: 0.7867 (t0) REVERT: A 36 MET cc_start: 0.8191 (ttm) cc_final: 0.7891 (mtm) REVERT: A 299 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: A 365 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7614 (mtt180) REVERT: A 414 MET cc_start: 0.7595 (mtt) cc_final: 0.7127 (mmm) REVERT: B 28 PHE cc_start: 0.6662 (t80) cc_final: 0.6280 (t80) REVERT: B 214 MET cc_start: 0.6563 (ttp) cc_final: 0.6266 (ttp) REVERT: B 303 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7664 (tp) REVERT: B 328 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7387 (mtp) REVERT: B 376 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7934 (t) REVERT: B 410 MET cc_start: 0.7901 (mmp) cc_final: 0.7579 (mmm) REVERT: B 438 CYS cc_start: 0.8165 (m) cc_final: 0.7876 (m) REVERT: B 461 MET cc_start: 0.7853 (mmm) cc_final: 0.7516 (mmm) outliers start: 31 outliers final: 23 residues processed: 178 average time/residue: 0.0598 time to fit residues: 15.2332 Evaluate side-chains 186 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 66 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.142240 restraints weight = 8974.948| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.37 r_work: 0.3812 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5890 Z= 0.149 Angle : 0.734 11.268 8024 Z= 0.348 Chirality : 0.043 0.321 961 Planarity : 0.006 0.051 977 Dihedral : 6.532 77.177 868 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.25 % Allowed : 35.13 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.32), residues: 751 helix: 1.42 (0.22), residues: 611 sheet: None (None), residues: 0 loop : -0.96 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.005 0.001 TYR A 477 PHE 0.023 0.001 PHE B 174 TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5890) covalent geometry : angle 0.73391 ( 8024) hydrogen bonds : bond 0.04403 ( 455) hydrogen bonds : angle 4.54521 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8082 (t0) cc_final: 0.7866 (t0) REVERT: A 36 MET cc_start: 0.8143 (ttm) cc_final: 0.7846 (mtm) REVERT: A 214 MET cc_start: 0.7901 (ptm) cc_final: 0.7576 (ptp) REVERT: A 250 MET cc_start: 0.6693 (mmp) cc_final: 0.6427 (mmm) REVERT: A 299 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: A 365 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7649 (mtt180) REVERT: A 414 MET cc_start: 0.7467 (mtt) cc_final: 0.7067 (mmm) REVERT: B 28 PHE cc_start: 0.6639 (t80) cc_final: 0.6256 (t80) REVERT: B 214 MET cc_start: 0.6466 (ttp) cc_final: 0.6159 (ttp) REVERT: B 303 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7587 (tp) REVERT: B 328 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7371 (mtp) REVERT: B 376 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 438 CYS cc_start: 0.8179 (m) cc_final: 0.7895 (m) outliers start: 26 outliers final: 21 residues processed: 182 average time/residue: 0.0580 time to fit residues: 15.1295 Evaluate side-chains 191 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.156481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141585 restraints weight = 8872.154| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.33 r_work: 0.3807 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5890 Z= 0.166 Angle : 0.736 10.991 8024 Z= 0.352 Chirality : 0.044 0.319 961 Planarity : 0.006 0.051 977 Dihedral : 7.045 76.767 868 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.74 % Allowed : 34.31 % Favored : 60.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.32), residues: 751 helix: 1.39 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.02 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.007 0.001 TYR A 477 PHE 0.024 0.001 PHE B 174 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5890) covalent geometry : angle 0.73632 ( 8024) hydrogen bonds : bond 0.04554 ( 455) hydrogen bonds : angle 4.54217 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1232.15 seconds wall clock time: 21 minutes 58.36 seconds (1318.36 seconds total)