Starting phenix.real_space_refine on Tue Feb 11 13:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgn_41242/02_2025/8tgn_41242_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgn_41242/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgn_41242/02_2025/8tgn_41242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgn_41242/02_2025/8tgn_41242.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgn_41242/02_2025/8tgn_41242_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgn_41242/02_2025/8tgn_41242_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.48, per 1000 atoms: 0.78 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: 1.59 Conformation dependent library (CDL) restraints added in 859.3 milliseconds 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: 0.48 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: 1.57 Time building geometry restraints manager: 1.66 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: 2.600 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.240 Find NCS groups from input model: 0.240 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- 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= 0.339 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 (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: 0.16 (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 TRP 0.012 0.001 TRP B 326 HIS 0.007 0.001 HIS B 387 PHE 0.051 0.002 PHE A 294 TYR 0.018 0.001 TYR A 426 ARG 0.005 0.000 ARG A 20 *********************** 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 : 0.610 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: 0.1403 time to fit residues: 30.9907 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 : 0.627 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.141146 restraints weight = 8760.895| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.36 r_work: 0.3791 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5890 Z= 0.290 Angle : 0.743 8.889 8024 Z= 0.365 Chirality : 0.045 0.159 961 Planarity : 0.007 0.055 977 Dihedral : 8.810 85.857 869 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.76 % Allowed : 30.07 % Favored : 66.18 % 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: 0.93 (0.31), residues: 751 helix: 1.00 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.70 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 PHE 0.025 0.002 PHE B 174 TYR 0.009 0.001 TYR B 190 ARG 0.005 0.000 ARG A 20 *********************** 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: 23 poor density : 164 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7668 (t80) cc_final: 0.7227 (t80) REVERT: A 365 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7318 (mtt180) REVERT: A 414 MET cc_start: 0.7643 (mtt) cc_final: 0.7224 (mmm) REVERT: A 471 TYR cc_start: 0.8456 (t80) cc_final: 0.7915 (t80) REVERT: B 26 VAL cc_start: 0.7896 (m) cc_final: 0.7673 (t) REVERT: B 296 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6806 (mm) REVERT: B 303 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7618 (tp) REVERT: B 410 MET cc_start: 0.7933 (mmp) cc_final: 0.7697 (mmm) outliers start: 23 outliers final: 11 residues processed: 175 average time/residue: 0.1448 time to fit residues: 34.8384 Evaluate side-chains 167 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 0.2980 chunk 69 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140836 restraints weight = 8905.034| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.34 r_work: 0.3796 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5890 Z= 0.265 Angle : 0.713 9.264 8024 Z= 0.346 Chirality : 0.044 0.205 961 Planarity : 0.006 0.054 977 Dihedral : 8.346 87.173 868 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.58 % Allowed : 30.72 % 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 (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: 1.12 (0.32), residues: 751 helix: 1.14 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -0.75 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 PHE 0.017 0.001 PHE B 174 TYR 0.008 0.001 TYR A 477 ARG 0.002 0.000 ARG A 20 *********************** 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 190 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7547 (mtt180) REVERT: A 414 MET cc_start: 0.7594 (mtt) cc_final: 0.7202 (mmm) REVERT: A 471 TYR cc_start: 0.8454 (t80) cc_final: 0.7847 (t80) REVERT: B 183 MET cc_start: 0.6603 (ttt) cc_final: 0.6330 (ttt) REVERT: B 303 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7625 (tp) REVERT: B 327 MET cc_start: 0.8014 (mtt) cc_final: 0.7806 (mtm) outliers start: 28 outliers final: 16 residues processed: 176 average time/residue: 0.1310 time to fit residues: 32.1893 Evaluate side-chains 171 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 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 3 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.154737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139676 restraints weight = 9007.320| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.37 r_work: 0.3779 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1677 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= 0.294 Angle : 0.720 10.025 8024 Z= 0.349 Chirality : 0.045 0.258 961 Planarity : 0.006 0.054 977 Dihedral : 8.204 88.761 868 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.41 % Allowed : 31.37 % Favored : 64.22 % 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: 1.20 (0.32), residues: 751 helix: 1.23 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -0.85 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.003 0.001 HIS B 387 PHE 0.016 0.001 PHE B 174 TYR 0.009 0.001 TYR A 477 ARG 0.005 0.000 ARG A 20 *********************** 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 183 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8103 (t0) cc_final: 0.7877 (t0) REVERT: A 36 MET cc_start: 0.8248 (ttm) cc_final: 0.8004 (mtp) REVERT: A 146 LYS cc_start: 0.7722 (tttt) cc_final: 0.7416 (ttmt) REVERT: A 365 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7536 (mtt180) REVERT: A 414 MET cc_start: 0.7607 (mtt) cc_final: 0.7155 (mmm) REVERT: B 26 VAL cc_start: 0.8007 (m) cc_final: 0.7752 (t) REVERT: B 28 PHE cc_start: 0.6698 (t80) cc_final: 0.6336 (t80) REVERT: B 214 MET cc_start: 0.6400 (ttp) cc_final: 0.6112 (ttp) REVERT: B 296 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6746 (mp) REVERT: B 303 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7664 (tp) REVERT: B 328 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7389 (mtp) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 0.1338 time to fit residues: 31.7826 Evaluate side-chains 172 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.0010 chunk 18 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3764 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.156007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140972 restraints weight = 8953.200| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.33 r_work: 0.3800 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1842 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= 0.238 Angle : 0.701 11.008 8024 Z= 0.336 Chirality : 0.043 0.276 961 Planarity : 0.006 0.052 977 Dihedral : 8.046 87.115 868 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.90 % Allowed : 32.68 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.32), residues: 751 helix: 1.36 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -0.94 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 PHE 0.017 0.001 PHE B 174 TYR 0.007 0.001 TYR A 477 ARG 0.005 0.000 ARG A 20 *********************** 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: 30 poor density : 159 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8084 (t0) cc_final: 0.7869 (t0) REVERT: A 36 MET cc_start: 0.8205 (ttm) cc_final: 0.7926 (mtp) REVERT: A 299 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: A 414 MET cc_start: 0.7526 (mtt) cc_final: 0.7157 (mmm) REVERT: B 28 PHE cc_start: 0.6612 (t80) cc_final: 0.6264 (t80) REVERT: B 183 MET cc_start: 0.6565 (ttt) cc_final: 0.6284 (ttt) REVERT: B 296 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6658 (mp) REVERT: B 303 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7623 (tp) REVERT: B 328 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7172 (mpp) outliers start: 30 outliers final: 21 residues processed: 171 average time/residue: 0.1290 time to fit residues: 31.0023 Evaluate side-chains 178 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 388 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.0060 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140867 restraints weight = 8916.325| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.33 r_work: 0.3797 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1962 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= 0.246 Angle : 0.705 11.755 8024 Z= 0.336 Chirality : 0.044 0.267 961 Planarity : 0.006 0.051 977 Dihedral : 7.722 84.980 868 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.74 % Allowed : 33.01 % Favored : 62.25 % 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: 1.42 (0.32), residues: 751 helix: 1.42 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -0.97 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 PHE 0.017 0.001 PHE B 174 TYR 0.008 0.001 TYR A 477 ARG 0.004 0.000 ARG A 20 *********************** 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 183 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8099 (t0) cc_final: 0.7855 (t0) REVERT: A 36 MET cc_start: 0.8197 (ttm) cc_final: 0.7985 (mtp) REVERT: A 299 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: A 414 MET cc_start: 0.7549 (mtt) cc_final: 0.7121 (mmm) REVERT: B 28 PHE cc_start: 0.6624 (t80) cc_final: 0.6261 (t80) REVERT: B 214 MET cc_start: 0.6436 (ttp) cc_final: 0.6124 (ttp) REVERT: B 296 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6603 (mp) REVERT: B 303 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7600 (tp) REVERT: B 328 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7369 (mtp) REVERT: B 376 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (t) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 0.1284 time to fit residues: 30.6854 Evaluate side-chains 179 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4098 r_free = 0.4098 target = 0.155963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141016 restraints weight = 8971.558| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.34 r_work: 0.3794 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5890 Z= 0.245 Angle : 0.700 12.006 8024 Z= 0.334 Chirality : 0.043 0.259 961 Planarity : 0.006 0.050 977 Dihedral : 7.249 82.403 868 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.72 % Allowed : 33.66 % 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 (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: 1.45 (0.32), residues: 751 helix: 1.44 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -0.98 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 PHE 0.014 0.001 PHE B 174 TYR 0.007 0.001 TYR A 477 ARG 0.004 0.000 ARG A 20 *********************** 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 192 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8082 (t0) cc_final: 0.7846 (t0) REVERT: A 36 MET cc_start: 0.8174 (ttm) cc_final: 0.7960 (mtp) REVERT: A 299 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: A 414 MET cc_start: 0.7555 (mtt) cc_final: 0.7122 (mmm) REVERT: B 28 PHE cc_start: 0.6718 (t80) cc_final: 0.6338 (t80) REVERT: B 183 MET cc_start: 0.6643 (ttt) cc_final: 0.6373 (ttt) REVERT: B 214 MET cc_start: 0.6526 (ttp) cc_final: 0.6228 (ttp) REVERT: B 296 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6567 (mp) REVERT: B 303 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 328 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7416 (mtp) REVERT: B 376 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7875 (t) outliers start: 35 outliers final: 24 residues processed: 176 average time/residue: 0.1318 time to fit residues: 32.2118 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 : 0.612 ------------------------------------------------------------------------------- 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 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 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 359 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 409 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.154611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139736 restraints weight = 8848.753| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.32 r_work: 0.3779 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5890 Z= 0.313 Angle : 0.749 12.345 8024 Z= 0.358 Chirality : 0.045 0.235 961 Planarity : 0.006 0.052 977 Dihedral : 7.162 80.852 868 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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 (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: 1.25 (0.32), residues: 751 helix: 1.30 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.02 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 PHE 0.022 0.001 PHE B 174 TYR 0.009 0.001 TYR A 477 ARG 0.003 0.000 ARG A 20 *********************** 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 188 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8102 (t0) cc_final: 0.7858 (t0) REVERT: A 36 MET cc_start: 0.8214 (ttm) cc_final: 0.8005 (mtp) REVERT: A 299 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: A 414 MET cc_start: 0.7592 (mtt) cc_final: 0.7124 (mmm) REVERT: B 26 VAL cc_start: 0.8013 (m) cc_final: 0.7777 (t) REVERT: B 28 PHE cc_start: 0.6709 (t80) cc_final: 0.6316 (t80) REVERT: B 214 MET cc_start: 0.6490 (ttp) cc_final: 0.6188 (ttp) REVERT: B 296 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6582 (mp) REVERT: B 303 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7623 (tp) REVERT: B 328 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7411 (mtp) REVERT: B 376 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7904 (t) outliers start: 31 outliers final: 23 residues processed: 173 average time/residue: 0.1346 time to fit residues: 32.5144 Evaluate side-chains 180 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 328 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.155386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140318 restraints weight = 8871.328| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.34 r_work: 0.3791 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 5890 Z= 0.272 Angle : 0.753 12.041 8024 Z= 0.357 Chirality : 0.044 0.221 961 Planarity : 0.006 0.052 977 Dihedral : 7.043 80.153 868 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.07 % Allowed : 34.64 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.32), residues: 751 helix: 1.31 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -1.07 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 PHE 0.022 0.001 PHE B 174 TYR 0.008 0.001 TYR A 477 ARG 0.003 0.000 ARG A 20 *********************** 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 187 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8103 (t0) cc_final: 0.7863 (t0) REVERT: A 36 MET cc_start: 0.8181 (ttm) cc_final: 0.7885 (mtm) REVERT: A 299 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: A 414 MET cc_start: 0.7559 (mtt) cc_final: 0.7105 (mmm) REVERT: B 26 VAL cc_start: 0.8022 (m) cc_final: 0.7801 (t) REVERT: B 28 PHE cc_start: 0.6666 (t80) cc_final: 0.6277 (t80) REVERT: B 214 MET cc_start: 0.6492 (ttp) cc_final: 0.6168 (ttp) REVERT: B 296 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6570 (mp) REVERT: B 303 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7599 (tp) REVERT: B 328 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7395 (mtp) REVERT: B 376 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 461 MET cc_start: 0.7787 (mmm) cc_final: 0.7351 (mmm) outliers start: 31 outliers final: 23 residues processed: 171 average time/residue: 0.1256 time to fit residues: 30.4720 Evaluate side-chains 183 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 328 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142213 restraints weight = 8881.588| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.35 r_work: 0.3812 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5890 Z= 0.223 Angle : 0.731 11.906 8024 Z= 0.346 Chirality : 0.043 0.186 961 Planarity : 0.006 0.050 977 Dihedral : 6.891 78.789 868 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.58 % Allowed : 34.64 % 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 (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: 1.32 (0.32), residues: 751 helix: 1.36 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.05 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS B 422 PHE 0.021 0.001 PHE B 174 TYR 0.006 0.001 TYR A 477 ARG 0.004 0.000 ARG A 20 ********************** 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 191 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8071 (t0) cc_final: 0.7854 (t0) REVERT: A 36 MET cc_start: 0.8159 (ttm) cc_final: 0.7866 (mtm) REVERT: A 250 MET cc_start: 0.6782 (mmp) cc_final: 0.6513 (mmm) REVERT: A 299 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: A 414 MET cc_start: 0.7471 (mtt) cc_final: 0.7083 (mmm) REVERT: B 26 VAL cc_start: 0.7997 (m) cc_final: 0.7764 (t) REVERT: B 28 PHE cc_start: 0.6654 (t80) cc_final: 0.6280 (t80) REVERT: B 214 MET cc_start: 0.6477 (ttp) cc_final: 0.6171 (ttp) REVERT: B 296 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6438 (mp) REVERT: B 303 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7559 (tp) REVERT: B 328 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7434 (mtp) REVERT: B 376 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7897 (t) outliers start: 28 outliers final: 21 residues processed: 178 average time/residue: 0.1243 time to fit residues: 31.2099 Evaluate side-chains 188 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 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 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 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 60 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142182 restraints weight = 8928.013| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.34 r_work: 0.3814 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5890 Z= 0.217 Angle : 0.718 11.845 8024 Z= 0.340 Chirality : 0.043 0.188 961 Planarity : 0.006 0.050 977 Dihedral : 7.290 80.241 868 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.58 % Allowed : 34.48 % 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 (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: 1.38 (0.32), residues: 751 helix: 1.40 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.05 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS B 422 PHE 0.017 0.001 PHE B 174 TYR 0.005 0.001 TYR A 477 ARG 0.003 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.57 seconds wall clock time: 45 minutes 52.94 seconds (2752.94 seconds total)