Starting phenix.real_space_refine on Fri Jul 19 02:14:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_41242_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_41242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_41242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_41242_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgn_41242/07_2024/8tgn_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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.10, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 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: 2.54 Conformation dependent library (CDL) restraints added in 991.7 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: 0.56 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: 1.65 Time building geometry restraints manager: 2.75 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: 97.73 - 105.42: 158 105.42 - 113.11: 3219 113.11 - 120.80: 3014 120.80 - 128.49: 1589 128.49 - 136.18: 44 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 2.440 nonbonded pdb=" O ALA B 442 " pdb=" OG SER B 446 " model vdw 2.207 2.440 nonbonded pdb=" O GLY B 158 " pdb=" OG1 THR B 161 " model vdw 2.214 2.440 nonbonded pdb=" OD2 ASP A 299 " pdb=" NE2 HIS A 422 " model vdw 2.243 2.520 nonbonded pdb=" O LEU A 142 " pdb=" OG SER A 145 " model vdw 2.247 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.220 Find NCS groups from input model: 0.290 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 0.613 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: 0.1324 time to fit residues: 29.4331 Evaluate side-chains 155 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 0.1980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5890 Z= 0.248 Angle : 0.732 8.641 8024 Z= 0.354 Chirality : 0.044 0.170 961 Planarity : 0.007 0.054 977 Dihedral : 8.676 84.793 869 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.43 % Allowed : 31.21 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.31), residues: 751 helix: 1.15 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.96 (0.52), residues: 150 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 0.027 0.002 PHE B 174 TYR 0.010 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 186 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7244 (mtt180) REVERT: A 414 MET cc_start: 0.7994 (mtt) cc_final: 0.7530 (mmm) REVERT: A 471 TYR cc_start: 0.8560 (t80) cc_final: 0.8115 (t80) REVERT: B 26 VAL cc_start: 0.7983 (m) cc_final: 0.7774 (t) REVERT: B 36 MET cc_start: 0.7942 (tpp) cc_final: 0.7622 (tpp) REVERT: B 296 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6604 (mm) REVERT: B 303 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7665 (tp) REVERT: B 327 MET cc_start: 0.8078 (mtt) cc_final: 0.7805 (mtm) REVERT: B 410 MET cc_start: 0.7822 (mmp) cc_final: 0.7519 (mmm) REVERT: B 438 CYS cc_start: 0.8428 (m) cc_final: 0.8199 (m) outliers start: 21 outliers final: 6 residues processed: 175 average time/residue: 0.1343 time to fit residues: 32.6126 Evaluate side-chains 164 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE 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 154 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 54 optimal weight: 0.8980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1414 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= 0.250 Angle : 0.698 9.506 8024 Z= 0.335 Chirality : 0.043 0.191 961 Planarity : 0.006 0.053 977 Dihedral : 8.224 85.783 868 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.92 % Allowed : 31.21 % 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: 1.25 (0.32), residues: 751 helix: 1.27 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -0.89 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 PHE 0.018 0.001 PHE B 174 TYR 0.007 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 184 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 0.540 Fit side-chains REVERT: A 365 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7433 (mtt180) REVERT: A 414 MET cc_start: 0.7945 (mtt) cc_final: 0.7446 (mmm) REVERT: A 471 TYR cc_start: 0.8580 (t80) cc_final: 0.8107 (t80) REVERT: B 36 MET cc_start: 0.7980 (tpp) cc_final: 0.7670 (tpp) REVERT: B 303 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7664 (tp) REVERT: B 327 MET cc_start: 0.8112 (mtt) cc_final: 0.7867 (mtm) REVERT: B 410 MET cc_start: 0.7814 (mmp) cc_final: 0.7536 (mmm) REVERT: B 438 CYS cc_start: 0.8458 (m) cc_final: 0.8186 (m) outliers start: 24 outliers final: 18 residues processed: 170 average time/residue: 0.1481 time to fit residues: 35.3387 Evaluate side-chains 172 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 299 ASP 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 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 303 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5890 Z= 0.233 Angle : 0.691 10.133 8024 Z= 0.330 Chirality : 0.043 0.231 961 Planarity : 0.006 0.051 977 Dihedral : 8.107 89.598 868 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.58 % Allowed : 33.01 % 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: 1.32 (0.32), residues: 751 helix: 1.36 (0.22), residues: 615 sheet: None (None), residues: 0 loop : -1.22 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 PHE 0.016 0.001 PHE A 246 TYR 0.008 0.001 TYR A 430 ARG 0.006 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 185 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 0.622 Fit side-chains REVERT: A 34 ASP cc_start: 0.8154 (t0) cc_final: 0.7926 (t0) REVERT: A 36 MET cc_start: 0.8092 (ttm) cc_final: 0.7734 (mtm) REVERT: A 325 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6558 (mp) REVERT: A 365 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7447 (mtt180) REVERT: A 414 MET cc_start: 0.7935 (mtt) cc_final: 0.7457 (mmm) REVERT: A 471 TYR cc_start: 0.8575 (t80) cc_final: 0.8079 (t80) REVERT: B 26 VAL cc_start: 0.8084 (m) cc_final: 0.7858 (t) REVERT: B 36 MET cc_start: 0.7980 (tpp) cc_final: 0.7639 (tpp) REVERT: B 214 MET cc_start: 0.6669 (ttp) cc_final: 0.6294 (ttp) REVERT: B 296 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6401 (mp) REVERT: B 303 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7650 (tp) REVERT: B 327 MET cc_start: 0.8092 (mtt) cc_final: 0.7868 (mtm) REVERT: B 328 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: B 410 MET cc_start: 0.7822 (mmp) cc_final: 0.7532 (mmm) REVERT: B 438 CYS cc_start: 0.8468 (m) cc_final: 0.8182 (m) outliers start: 28 outliers final: 19 residues processed: 168 average time/residue: 0.1304 time to fit residues: 30.3534 Evaluate side-chains 176 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 325 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 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 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5890 Z= 0.283 Angle : 0.710 11.279 8024 Z= 0.342 Chirality : 0.045 0.286 961 Planarity : 0.006 0.051 977 Dihedral : 8.009 87.468 868 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.90 % Allowed : 33.99 % 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 (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: 1.37 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -1.26 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 PHE 0.017 0.001 PHE B 174 TYR 0.009 0.001 TYR A 477 ARG 0.007 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 187 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 0.547 Fit side-chains REVERT: A 34 ASP cc_start: 0.8163 (t0) cc_final: 0.7947 (t0) REVERT: A 36 MET cc_start: 0.8114 (ttm) cc_final: 0.7783 (mtm) REVERT: A 365 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7468 (mtt180) REVERT: A 414 MET cc_start: 0.7997 (mtt) cc_final: 0.7442 (mmm) REVERT: B 28 PHE cc_start: 0.6658 (t80) cc_final: 0.6252 (t80) REVERT: B 36 MET cc_start: 0.7978 (tpp) cc_final: 0.7567 (tpp) REVERT: B 214 MET cc_start: 0.6751 (ttp) cc_final: 0.6362 (ttp) REVERT: B 303 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7721 (tp) REVERT: B 327 MET cc_start: 0.8112 (mtt) cc_final: 0.7882 (mtm) REVERT: B 328 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: B 410 MET cc_start: 0.7816 (mmp) cc_final: 0.7503 (mmm) REVERT: B 411 MET cc_start: 0.7890 (mmm) cc_final: 0.7654 (mmm) outliers start: 30 outliers final: 24 residues processed: 169 average time/residue: 0.1211 time to fit residues: 28.7777 Evaluate side-chains 183 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 330 THR 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 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 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 THR 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 378 THR Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5890 Z= 0.229 Angle : 0.704 11.820 8024 Z= 0.335 Chirality : 0.043 0.282 961 Planarity : 0.006 0.050 977 Dihedral : 7.496 85.318 868 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.39 % Allowed : 34.48 % Favored : 60.13 % 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: 1.52 (0.32), residues: 751 helix: 1.49 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.01 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.000 HIS B 387 PHE 0.018 0.001 PHE B 174 TYR 0.007 0.001 TYR A 430 ARG 0.006 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 192 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8185 (t0) cc_final: 0.7955 (t0) REVERT: A 36 MET cc_start: 0.8040 (ttm) cc_final: 0.7713 (mtm) REVERT: A 365 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7477 (mtt180) REVERT: A 414 MET cc_start: 0.7949 (mtt) cc_final: 0.7460 (mmm) REVERT: B 28 PHE cc_start: 0.6588 (t80) cc_final: 0.6200 (t80) REVERT: B 36 MET cc_start: 0.7964 (tpp) cc_final: 0.7538 (tpp) REVERT: B 214 MET cc_start: 0.6695 (ttp) cc_final: 0.6300 (ttp) REVERT: B 303 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7700 (tp) REVERT: B 327 MET cc_start: 0.8067 (mtt) cc_final: 0.7859 (mtm) REVERT: B 328 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7927 (mtp) REVERT: B 376 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 410 MET cc_start: 0.7786 (mmp) cc_final: 0.7460 (mmm) REVERT: B 411 MET cc_start: 0.7829 (mmm) cc_final: 0.7595 (mmm) outliers start: 33 outliers final: 24 residues processed: 175 average time/residue: 0.1333 time to fit residues: 32.4026 Evaluate side-chains 183 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 330 THR 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 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 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 THR 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 378 THR Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5890 Z= 0.295 Angle : 0.717 12.159 8024 Z= 0.345 Chirality : 0.044 0.262 961 Planarity : 0.006 0.050 977 Dihedral : 7.115 81.693 868 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.39 % Allowed : 33.82 % 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: 1.40 (0.32), residues: 751 helix: 1.45 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.17 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 PHE 0.019 0.001 PHE B 174 TYR 0.009 0.001 TYR A 477 ARG 0.005 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 190 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8177 (t0) cc_final: 0.7954 (t0) REVERT: A 36 MET cc_start: 0.8075 (ttm) cc_final: 0.7836 (mtp) REVERT: A 365 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7515 (mtt180) REVERT: B 28 PHE cc_start: 0.6713 (t80) cc_final: 0.6286 (t80) REVERT: B 36 MET cc_start: 0.7999 (tpp) cc_final: 0.7569 (tpp) REVERT: B 214 MET cc_start: 0.6728 (ttp) cc_final: 0.6357 (ttp) REVERT: B 303 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 327 MET cc_start: 0.8087 (mtt) cc_final: 0.7868 (mtm) REVERT: B 328 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: B 338 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 376 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (t) REVERT: B 410 MET cc_start: 0.7788 (mmp) cc_final: 0.7470 (mmm) REVERT: B 411 MET cc_start: 0.7933 (mmm) cc_final: 0.7708 (mmm) outliers start: 33 outliers final: 26 residues processed: 172 average time/residue: 0.1282 time to fit residues: 30.7516 Evaluate side-chains 188 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 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 330 THR 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 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 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 THR 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 378 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5890 Z= 0.238 Angle : 0.709 11.687 8024 Z= 0.341 Chirality : 0.043 0.246 961 Planarity : 0.006 0.050 977 Dihedral : 6.802 79.809 866 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.56 % Allowed : 33.99 % Favored : 60.46 % 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: 1.47 (0.32), residues: 751 helix: 1.49 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.13 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.000 HIS B 387 PHE 0.018 0.001 PHE B 174 TYR 0.007 0.001 TYR A 477 ARG 0.004 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 195 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 0.590 Fit side-chains REVERT: A 34 ASP cc_start: 0.8188 (t0) cc_final: 0.7948 (t0) REVERT: A 36 MET cc_start: 0.8041 (ttm) cc_final: 0.7822 (mtp) REVERT: A 365 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7555 (mtt180) REVERT: A 414 MET cc_start: 0.7951 (mtt) cc_final: 0.7431 (mmm) REVERT: B 26 VAL cc_start: 0.8140 (m) cc_final: 0.7904 (t) REVERT: B 28 PHE cc_start: 0.6644 (t80) cc_final: 0.6221 (t80) REVERT: B 36 MET cc_start: 0.7966 (tpp) cc_final: 0.7545 (tpp) REVERT: B 214 MET cc_start: 0.6686 (ttp) cc_final: 0.6297 (ttp) REVERT: B 296 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6348 (mp) REVERT: B 303 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 327 MET cc_start: 0.8027 (mtt) cc_final: 0.7824 (mtm) REVERT: B 328 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7926 (mtp) REVERT: B 338 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 376 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7902 (t) REVERT: B 410 MET cc_start: 0.7736 (mmp) cc_final: 0.7429 (mmm) REVERT: B 411 MET cc_start: 0.7908 (mmm) cc_final: 0.7684 (mmm) outliers start: 34 outliers final: 27 residues processed: 178 average time/residue: 0.1234 time to fit residues: 31.0329 Evaluate side-chains 193 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 330 THR 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 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 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 THR 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 378 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 44 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 5890 Z= 0.260 Angle : 0.732 11.197 8024 Z= 0.349 Chirality : 0.045 0.244 961 Planarity : 0.006 0.049 977 Dihedral : 6.661 78.008 866 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.39 % Allowed : 35.13 % Favored : 59.48 % 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: 1.40 (0.32), residues: 751 helix: 1.45 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.16 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.000 HIS B 387 PHE 0.022 0.001 PHE B 174 TYR 0.008 0.001 TYR A 477 ARG 0.004 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 195 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 0.604 Fit side-chains REVERT: A 34 ASP cc_start: 0.8204 (t0) cc_final: 0.7949 (t0) REVERT: A 36 MET cc_start: 0.8032 (ttm) cc_final: 0.7809 (mtp) REVERT: A 316 VAL cc_start: 0.8427 (t) cc_final: 0.8200 (p) REVERT: A 365 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7557 (mtt180) REVERT: A 414 MET cc_start: 0.7956 (mtt) cc_final: 0.7403 (mmm) REVERT: B 26 VAL cc_start: 0.8158 (m) cc_final: 0.7920 (t) REVERT: B 28 PHE cc_start: 0.6646 (t80) cc_final: 0.6219 (t80) REVERT: B 36 MET cc_start: 0.7984 (tpp) cc_final: 0.7550 (tpp) REVERT: B 214 MET cc_start: 0.6677 (ttp) cc_final: 0.6293 (ttp) REVERT: B 303 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 328 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: B 338 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 376 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7905 (t) REVERT: B 410 MET cc_start: 0.7737 (mmp) cc_final: 0.7457 (mmm) REVERT: B 411 MET cc_start: 0.7908 (mmm) cc_final: 0.7683 (mmm) outliers start: 33 outliers final: 25 residues processed: 178 average time/residue: 0.1285 time to fit residues: 31.8322 Evaluate side-chains 188 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 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 330 THR 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 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 303 LEU Chi-restraints excluded: chain B residue 322 THR 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 378 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5890 Z= 0.218 Angle : 0.749 11.821 8024 Z= 0.351 Chirality : 0.045 0.357 961 Planarity : 0.006 0.049 977 Dihedral : 6.539 76.130 866 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.90 % Allowed : 34.48 % 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: 1.43 (0.32), residues: 751 helix: 1.46 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.13 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS B 387 PHE 0.021 0.001 PHE B 174 TYR 0.008 0.001 TYR A 349 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 192 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.611 Fit side-chains REVERT: A 34 ASP cc_start: 0.8193 (t0) cc_final: 0.7940 (t0) REVERT: A 36 MET cc_start: 0.8001 (ttm) cc_final: 0.7700 (mtm) REVERT: A 365 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7552 (mtt180) REVERT: A 414 MET cc_start: 0.7917 (mtt) cc_final: 0.7407 (mmm) REVERT: B 26 VAL cc_start: 0.8118 (m) cc_final: 0.7892 (t) REVERT: B 28 PHE cc_start: 0.6616 (t80) cc_final: 0.6190 (t80) REVERT: B 36 MET cc_start: 0.7996 (tpp) cc_final: 0.7531 (tpp) REVERT: B 214 MET cc_start: 0.6689 (ttp) cc_final: 0.6296 (ttp) REVERT: B 296 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6365 (mp) REVERT: B 303 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7688 (tp) REVERT: B 328 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7920 (mtp) REVERT: B 376 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 410 MET cc_start: 0.7712 (mmp) cc_final: 0.7436 (mmm) REVERT: B 411 MET cc_start: 0.7889 (mmm) cc_final: 0.7669 (mmm) outliers start: 30 outliers final: 21 residues processed: 175 average time/residue: 0.1262 time to fit residues: 30.8024 Evaluate side-chains 184 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 330 THR 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 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 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 THR 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 378 THR 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 54 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 59 optimal weight: 0.0970 chunk 24 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 overall best weight: 0.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142631 restraints weight = 8859.707| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.36 r_work: 0.3820 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5890 Z= 0.189 Angle : 0.732 11.144 8024 Z= 0.344 Chirality : 0.043 0.331 961 Planarity : 0.006 0.048 977 Dihedral : 6.949 76.623 866 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.27 % Allowed : 36.60 % Favored : 60.13 % 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: 1.51 (0.32), residues: 751 helix: 1.53 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.15 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.019 0.002 PHE B 174 TYR 0.005 0.001 TYR B 166 ARG 0.005 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.70 seconds wall clock time: 28 minutes 47.46 seconds (1727.46 seconds total)