Starting phenix.real_space_refine on Sat Dec 28 04:48:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.map" model { file = "/net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baa_44402/12_2024/9baa_44402.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.042 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 43 5.16 5 C 5072 2.51 5 N 1264 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7771 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3372 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 8, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4399 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain breaks: 5 Time building chain proxies: 5.48, per 1000 atoms: 0.71 Number of scatterers: 7771 At special positions: 0 Unit cell: (91.227, 97.05, 116.46, 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 43 16.00 O 1392 8.00 N 1264 7.00 C 5072 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: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 75.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.547A pdb=" N VAL A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.643A pdb=" N PHE A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 251 Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.674A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 289 removed outlier: 3.630A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.662A pdb=" N GLY A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 4.621A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.520A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 removed outlier: 4.014A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.578A pdb=" N ILE A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.561A pdb=" N LEU A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.076A pdb=" N ILE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.536A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.248A pdb=" N GLY B 134 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.684A pdb=" N ASP B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 253 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.952A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 305 removed outlier: 4.092A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 353 removed outlier: 3.739A pdb=" N PHE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 364 through 417 Processing helix chain 'B' and resid 421 through 444 removed outlier: 3.736A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 444 through 464 removed outlier: 4.781A pdb=" N LEU B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.888A pdb=" N MET B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.541A pdb=" N ASN B 552 " --> pdb=" O SER B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.582A pdb=" N ILE B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 590 through 596 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 629 through 639 Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.866A pdb=" N ALA B 87 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 562 through 564 removed outlier: 6.268A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 532 hydrogen bonds defined for protein. 1572 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: 2.01 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2415 1.34 - 1.46: 1571 1.46 - 1.58: 3825 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 7889 Sorted by residual: bond pdb=" N PHE A 188 " pdb=" CA PHE A 188 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.42e-02 4.96e+03 1.97e+00 bond pdb=" CA PHE A 188 " pdb=" C PHE A 188 " ideal model delta sigma weight residual 1.522 1.542 -0.021 1.72e-02 3.38e+03 1.44e+00 bond pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CB MET B 387 " pdb=" CG MET B 387 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CG1 ILE A 337 " pdb=" CD1 ILE A 337 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.11e-01 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 10388 1.83 - 3.65: 182 3.65 - 5.48: 35 5.48 - 7.31: 8 7.31 - 9.14: 2 Bond angle restraints: 10615 Sorted by residual: angle pdb=" CA ARG A 630 " pdb=" CB ARG A 630 " pdb=" CG ARG A 630 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB MET B 387 " pdb=" CG MET B 387 " pdb=" SD MET B 387 " ideal model delta sigma weight residual 112.70 103.65 9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C ASN B 153 " pdb=" N MET B 154 " pdb=" CA MET B 154 " ideal model delta sigma weight residual 120.63 124.99 -4.36 1.61e+00 3.86e-01 7.34e+00 angle pdb=" N VAL A 415 " pdb=" CA VAL A 415 " pdb=" C VAL A 415 " ideal model delta sigma weight residual 110.42 107.91 2.51 9.60e-01 1.09e+00 6.84e+00 angle pdb=" CA LEU B 165 " pdb=" CB LEU B 165 " pdb=" CG LEU B 165 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.81e+00 ... (remaining 10610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4201 16.54 - 33.08: 435 33.08 - 49.62: 111 49.62 - 66.15: 19 66.15 - 82.69: 11 Dihedral angle restraints: 4777 sinusoidal: 1907 harmonic: 2870 Sorted by residual: dihedral pdb=" CA VAL B 93 " pdb=" C VAL B 93 " pdb=" N ASP B 94 " pdb=" CA ASP B 94 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" N MET B 154 " pdb=" CA MET B 154 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE B 200 " pdb=" C PHE B 200 " pdb=" N GLU B 201 " pdb=" CA GLU B 201 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 794 0.032 - 0.064: 349 0.064 - 0.097: 94 0.097 - 0.129: 25 0.129 - 0.161: 3 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ASP A 590 " pdb=" N ASP A 590 " pdb=" C ASP A 590 " pdb=" CB ASP A 590 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL A 587 " pdb=" CA VAL A 587 " pdb=" CG1 VAL A 587 " pdb=" CG2 VAL A 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA LYS B 328 " pdb=" N LYS B 328 " pdb=" C LYS B 328 " pdb=" CB LYS B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1262 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 589 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C MET A 589 " 0.037 2.00e-02 2.50e+03 pdb=" O MET A 589 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 590 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 253 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 254 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 498 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ARG B 498 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG B 498 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 499 " 0.009 2.00e-02 2.50e+03 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1389 2.76 - 3.30: 8121 3.30 - 3.83: 12522 3.83 - 4.37: 13340 4.37 - 4.90: 23918 Nonbonded interactions: 59290 Sorted by model distance: nonbonded pdb=" O SER A 281 " pdb=" OG1 THR A 284 " model vdw 2.231 3.040 nonbonded pdb=" O LYS B 252 " pdb=" OG1 THR B 467 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 421 " pdb=" OE1 GLN A 424 " model vdw 2.243 3.040 nonbonded pdb=" O LYS A 561 " pdb=" N ASP A 642 " model vdw 2.317 3.120 nonbonded pdb=" OD1 ASN B 259 " pdb=" OH TYR B 536 " model vdw 2.323 3.040 ... (remaining 59285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.800 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.640 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.004 0.034 7889 Z= 0.244 Angle : 0.631 9.137 10615 Z= 0.330 Chirality : 0.039 0.161 1265 Planarity : 0.004 0.041 1304 Dihedral : 14.975 82.693 2925 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.09 % Favored : 91.70 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % 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: 1.06 (0.28), residues: 976 helix: 1.85 (0.20), residues: 704 sheet: 0.27 (1.61), residues: 12 loop : -2.65 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.010 0.001 PHE B 194 TYR 0.020 0.002 TYR B 389 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.925 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1932 time to fit residues: 35.8177 Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 499 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.190 Angle : 0.570 8.296 10615 Z= 0.293 Chirality : 0.038 0.158 1265 Planarity : 0.003 0.039 1304 Dihedral : 4.501 52.303 1051 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 1.65 % Allowed : 9.89 % Favored : 88.46 % 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: 1.52 (0.29), residues: 976 helix: 2.26 (0.20), residues: 695 sheet: 0.89 (1.62), residues: 12 loop : -2.59 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.003 0.001 HIS A 249 PHE 0.009 0.001 PHE B 128 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.947 Fit side-chains REVERT: A 155 MET cc_start: 0.6216 (mpp) cc_final: 0.5600 (mmt) REVERT: A 304 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: A 458 ARG cc_start: 0.7287 (ptp-170) cc_final: 0.7052 (ptm160) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.2005 time to fit residues: 35.4964 Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.179 Angle : 0.547 7.745 10615 Z= 0.280 Chirality : 0.038 0.160 1265 Planarity : 0.003 0.038 1304 Dihedral : 3.885 22.297 1047 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.21 % Rotamer: Outliers : 1.88 % Allowed : 13.31 % Favored : 84.81 % 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: 1.59 (0.29), residues: 976 helix: 2.32 (0.20), residues: 695 sheet: 0.93 (1.60), residues: 12 loop : -2.59 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.008 0.001 PHE A 217 TYR 0.013 0.001 TYR B 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.962 Fit side-chains REVERT: A 155 MET cc_start: 0.6055 (mpp) cc_final: 0.5739 (mmt) REVERT: A 244 MET cc_start: 0.7713 (tpp) cc_final: 0.7413 (tpp) REVERT: A 304 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6414 (mp10) REVERT: B 387 MET cc_start: 0.8657 (tpp) cc_final: 0.8373 (tpp) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.2078 time to fit residues: 35.2327 Evaluate side-chains 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 60 optimal weight: 0.0170 chunk 90 optimal weight: 30.0000 chunk 95 optimal weight: 0.0370 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.179 Angle : 0.548 9.715 10615 Z= 0.279 Chirality : 0.037 0.156 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.861 21.433 1047 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 976 helix: 2.33 (0.20), residues: 695 sheet: 0.75 (1.59), residues: 12 loop : -2.58 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE B 128 TYR 0.013 0.001 TYR A 225 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.821 Fit side-chains REVERT: A 155 MET cc_start: 0.6009 (mpp) cc_final: 0.5684 (mmt) REVERT: A 304 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.6362 (mp10) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.1854 time to fit residues: 31.8943 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 0.0470 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 81 optimal weight: 0.2980 chunk 66 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7889 Z= 0.141 Angle : 0.535 10.566 10615 Z= 0.269 Chirality : 0.037 0.203 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.775 21.598 1047 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.83 % Allowed : 16.14 % Favored : 81.04 % 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: 1.76 (0.29), residues: 976 helix: 2.45 (0.20), residues: 695 sheet: 1.02 (1.63), residues: 12 loop : -2.52 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.005 0.001 HIS B 249 PHE 0.009 0.001 PHE A 257 TYR 0.011 0.001 TYR B 179 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.007 Fit side-chains REVERT: A 155 MET cc_start: 0.6024 (mpp) cc_final: 0.5769 (mmt) REVERT: A 239 ASP cc_start: 0.8206 (t0) cc_final: 0.7880 (t0) REVERT: A 244 MET cc_start: 0.7685 (tpp) cc_final: 0.7259 (tpp) REVERT: A 304 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.6262 (mp10) REVERT: A 543 ILE cc_start: -0.2634 (OUTLIER) cc_final: -0.3178 (mp) REVERT: B 604 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5441 (p90) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 0.1718 time to fit residues: 32.6090 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.175 Angle : 0.565 10.922 10615 Z= 0.282 Chirality : 0.037 0.184 1265 Planarity : 0.003 0.033 1304 Dihedral : 3.782 22.823 1047 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.58 % Favored : 92.32 % Rotamer: Outliers : 2.59 % Allowed : 17.08 % Favored : 80.33 % 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: 1.76 (0.29), residues: 976 helix: 2.45 (0.20), residues: 695 sheet: 0.92 (1.59), residues: 12 loop : -2.52 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.011 0.001 PHE A 428 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.821 Fit side-chains REVERT: A 244 MET cc_start: 0.7695 (tpp) cc_final: 0.7439 (tpp) REVERT: A 304 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6366 (mp10) REVERT: A 543 ILE cc_start: -0.2589 (OUTLIER) cc_final: -0.3138 (mp) REVERT: B 548 HIS cc_start: 0.6847 (p-80) cc_final: 0.6600 (p90) REVERT: B 604 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5414 (p90) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.1759 time to fit residues: 30.6692 Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.168 Angle : 0.556 11.728 10615 Z= 0.278 Chirality : 0.037 0.190 1265 Planarity : 0.003 0.033 1304 Dihedral : 3.760 22.350 1047 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.99 % Favored : 91.91 % Rotamer: Outliers : 2.71 % Allowed : 17.79 % Favored : 79.51 % 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: 1.80 (0.29), residues: 976 helix: 2.49 (0.20), residues: 695 sheet: 1.01 (1.59), residues: 12 loop : -2.56 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.008 0.001 PHE B 604 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.927 Fit side-chains REVERT: A 244 MET cc_start: 0.7737 (tpp) cc_final: 0.7535 (tpp) REVERT: A 304 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6278 (mp10) REVERT: A 543 ILE cc_start: -0.2569 (OUTLIER) cc_final: -0.3118 (mp) REVERT: B 301 LEU cc_start: 0.7617 (mt) cc_final: 0.7220 (mt) REVERT: B 604 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5428 (p90) outliers start: 23 outliers final: 17 residues processed: 123 average time/residue: 0.2106 time to fit residues: 37.9410 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.167 Angle : 0.563 11.691 10615 Z= 0.284 Chirality : 0.037 0.198 1265 Planarity : 0.003 0.032 1304 Dihedral : 3.733 22.359 1047 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.79 % Favored : 92.11 % Rotamer: Outliers : 2.94 % Allowed : 17.79 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.29), residues: 976 helix: 2.53 (0.20), residues: 695 sheet: 0.82 (1.53), residues: 12 loop : -2.52 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.008 0.001 PHE B 604 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.886 Fit side-chains REVERT: A 304 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.6244 (mp10) REVERT: A 434 TYR cc_start: 0.8663 (m-80) cc_final: 0.8393 (m-80) REVERT: A 543 ILE cc_start: -0.2577 (OUTLIER) cc_final: -0.3132 (mp) REVERT: B 125 MET cc_start: 0.7230 (tpt) cc_final: 0.6728 (mpp) REVERT: B 301 LEU cc_start: 0.7601 (mt) cc_final: 0.7182 (mt) REVERT: B 604 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5399 (p90) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 0.1968 time to fit residues: 33.9889 Evaluate side-chains 121 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.183 Angle : 0.594 12.046 10615 Z= 0.294 Chirality : 0.037 0.191 1265 Planarity : 0.003 0.032 1304 Dihedral : 3.769 22.625 1047 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.99 % Favored : 91.91 % Rotamer: Outliers : 2.71 % Allowed : 18.61 % Favored : 78.68 % 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: 1.83 (0.29), residues: 976 helix: 2.50 (0.20), residues: 696 sheet: 0.65 (1.49), residues: 12 loop : -2.50 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE B 383 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.909 Fit side-chains REVERT: A 244 MET cc_start: 0.7735 (tpp) cc_final: 0.7445 (tpp) REVERT: A 304 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: A 434 TYR cc_start: 0.8713 (m-80) cc_final: 0.8436 (m-80) REVERT: A 543 ILE cc_start: -0.2691 (OUTLIER) cc_final: -0.3241 (mp) REVERT: B 604 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5410 (p90) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.1921 time to fit residues: 32.4314 Evaluate side-chains 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7889 Z= 0.168 Angle : 0.588 12.348 10615 Z= 0.292 Chirality : 0.037 0.200 1265 Planarity : 0.003 0.032 1304 Dihedral : 3.743 21.997 1047 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.79 % Favored : 92.01 % Rotamer: Outliers : 2.59 % Allowed : 18.96 % Favored : 78.45 % 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: 1.86 (0.29), residues: 976 helix: 2.55 (0.20), residues: 695 sheet: 0.71 (1.48), residues: 12 loop : -2.54 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.010 0.001 PHE A 564 TYR 0.012 0.001 TYR B 225 ARG 0.004 0.000 ARG A 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.970 Fit side-chains REVERT: A 244 MET cc_start: 0.7759 (tpp) cc_final: 0.7416 (tpp) REVERT: A 304 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.6171 (mp10) REVERT: A 434 TYR cc_start: 0.8703 (m-80) cc_final: 0.8431 (m-80) REVERT: A 543 ILE cc_start: -0.2681 (OUTLIER) cc_final: -0.3225 (mp) REVERT: B 123 TYR cc_start: 0.6196 (m-80) cc_final: 0.5917 (m-10) REVERT: B 604 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5389 (p90) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.1834 time to fit residues: 32.6963 Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133848 restraints weight = 9277.485| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.13 r_work: 0.3472 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7889 Z= 0.220 Angle : 0.612 11.570 10615 Z= 0.305 Chirality : 0.038 0.204 1265 Planarity : 0.003 0.031 1304 Dihedral : 3.869 23.342 1047 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.20 % Favored : 91.60 % Rotamer: Outliers : 2.59 % Allowed : 19.20 % Favored : 78.21 % 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: 1.66 (0.29), residues: 976 helix: 2.41 (0.20), residues: 694 sheet: 0.41 (1.46), residues: 12 loop : -2.62 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.033 0.001 PHE A 173 TYR 0.016 0.001 TYR A 225 ARG 0.004 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.59 seconds wall clock time: 36 minutes 10.91 seconds (2170.91 seconds total)