Starting phenix.real_space_refine on Thu Mar 6 06:27:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.map" model { file = "/net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csw_26973/03_2025/8csw_26973.cif" } resolution = 2.5 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= 0.272 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 23 5.16 5 C 3278 2.51 5 N 915 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5332 Number of models: 1 Model: "" Number of chains: 2 Chain: "X" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5167 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Time building chain proxies: 5.41, per 1000 atoms: 1.01 Number of scatterers: 5332 At special positions: 0 Unit cell: (95.45, 102.92, 71.795, 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 23 16.00 O 1116 8.00 N 915 7.00 C 3278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.2% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.658A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 3.998A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.118A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.363A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.745A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.869A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 3.509A pdb=" N GLU X 96 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.693A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL X 288 " --> pdb=" O LYS X 421 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS X 421 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE X 292 " --> pdb=" O ASN X 417 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN X 417 " --> pdb=" O PHE X 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS X 505 " --> pdb=" O LEU X 533 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU X 533 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL X 507 " --> pdb=" O LEU X 531 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU X 531 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU X 509 " --> pdb=" O LYS X 529 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS X 529 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE X 511 " --> pdb=" O TRP X 527 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP X 527 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL X 513 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS X 525 " --> pdb=" O VAL X 513 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA X 515 " --> pdb=" O ALA X 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.536A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 600 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: 2.51 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 899 1.32 - 1.44: 1339 1.44 - 1.57: 3004 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5273 Sorted by residual: bond pdb=" N TRP X 89 " pdb=" CA TRP X 89 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.17e-02 7.31e+03 1.14e+01 bond pdb=" N GLU X 405 " pdb=" CA GLU X 405 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" N ILE X 104 " pdb=" CA ILE X 104 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER X 105 " pdb=" CB SER X 105 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.43e-02 4.89e+03 9.52e+00 bond pdb=" N VAL X 211 " pdb=" CA VAL X 211 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.17e+00 ... (remaining 5268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 6768 1.78 - 3.56: 322 3.56 - 5.33: 50 5.33 - 7.11: 11 7.11 - 8.89: 2 Bond angle restraints: 7153 Sorted by residual: angle pdb=" N ASP X 408 " pdb=" CA ASP X 408 " pdb=" C ASP X 408 " ideal model delta sigma weight residual 109.96 101.96 8.00 1.50e+00 4.44e-01 2.85e+01 angle pdb=" C THR X 403 " pdb=" N LEU X 404 " pdb=" CA LEU X 404 " ideal model delta sigma weight residual 123.11 117.38 5.73 1.42e+00 4.96e-01 1.63e+01 angle pdb=" C GLY X 85 " pdb=" N ASP X 86 " pdb=" CA ASP X 86 " ideal model delta sigma weight residual 121.99 116.05 5.94 1.49e+00 4.50e-01 1.59e+01 angle pdb=" CA LEU X 404 " pdb=" C LEU X 404 " pdb=" O LEU X 404 " ideal model delta sigma weight residual 120.46 116.22 4.24 1.07e+00 8.73e-01 1.57e+01 angle pdb=" CB ARG X 287 " pdb=" CG ARG X 287 " pdb=" CD ARG X 287 " ideal model delta sigma weight residual 111.30 102.41 8.89 2.30e+00 1.89e-01 1.49e+01 ... (remaining 7148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2890 17.21 - 34.42: 199 34.42 - 51.63: 59 51.63 - 68.84: 21 68.84 - 86.04: 7 Dihedral angle restraints: 3176 sinusoidal: 1276 harmonic: 1900 Sorted by residual: dihedral pdb=" CA GLU X 185 " pdb=" C GLU X 185 " pdb=" N GLY X 186 " pdb=" CA GLY X 186 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" C ILE X 431 " pdb=" N ILE X 431 " pdb=" CA ILE X 431 " pdb=" CB ILE X 431 " ideal model delta harmonic sigma weight residual -122.00 -129.86 7.86 0 2.50e+00 1.60e-01 9.88e+00 ... (remaining 3173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 577 0.050 - 0.100: 168 0.100 - 0.150: 39 0.150 - 0.199: 17 0.199 - 0.249: 8 Chirality restraints: 809 Sorted by residual: chirality pdb=" CB VAL X 106 " pdb=" CA VAL X 106 " pdb=" CG1 VAL X 106 " pdb=" CG2 VAL X 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU X 349 " pdb=" N LEU X 349 " pdb=" C LEU X 349 " pdb=" CB LEU X 349 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER X 329 " pdb=" N SER X 329 " pdb=" C SER X 329 " pdb=" CB SER X 329 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 806 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X 364 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ASP X 364 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP X 364 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU X 365 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER X 576 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C SER X 576 " -0.052 2.00e-02 2.50e+03 pdb=" O SER X 576 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS X 577 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP X 89 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C TRP X 89 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP X 89 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP X 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 691 2.76 - 3.29: 4879 3.29 - 3.83: 9713 3.83 - 4.36: 11710 4.36 - 4.90: 19288 Nonbonded interactions: 46281 Sorted by model distance: nonbonded pdb=" O HOH X 738 " pdb=" O HOH X 851 " model vdw 2.219 3.040 nonbonded pdb=" O HOH X 768 " pdb=" O HOH X 798 " model vdw 2.236 3.040 nonbonded pdb=" O HOH X 792 " pdb=" O HOH X 838 " model vdw 2.261 3.040 nonbonded pdb=" O HOH X 755 " pdb=" O HOH X 839 " model vdw 2.271 3.040 nonbonded pdb=" O ASP X 426 " pdb=" O HOH X 701 " model vdw 2.283 3.040 ... (remaining 46276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 71.730 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: 0.470 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.070 Find NCS groups from input model: 0.090 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:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 5273 Z= 0.429 Angle : 0.862 8.892 7153 Z= 0.555 Chirality : 0.057 0.249 809 Planarity : 0.006 0.038 921 Dihedral : 14.462 86.044 1944 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.33 % Allowed : 8.24 % Favored : 89.43 % 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: 0.83 (0.31), residues: 647 helix: 0.80 (0.45), residues: 116 sheet: 0.87 (0.31), residues: 250 loop : 0.30 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 90 HIS 0.005 0.001 HIS X 632 PHE 0.022 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.003 0.001 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.679 Fit side-chains REVERT: X 16 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7217 (tmm-80) REVERT: X 88 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7557 (mmpt) REVERT: X 143 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7961 (ttm-80) REVERT: X 194 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: X 442 LEU cc_start: 0.8074 (mp) cc_final: 0.7733 (mm) REVERT: X 445 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7647 (ttpp) REVERT: X 446 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7537 (tm-30) REVERT: X 452 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6893 (mt-10) REVERT: X 483 SER cc_start: 0.8344 (p) cc_final: 0.8047 (m) REVERT: X 508 GLN cc_start: 0.7339 (tt0) cc_final: 0.6839 (mt0) REVERT: X 593 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8154 (tppt) REVERT: X 638 ARG cc_start: 0.7856 (mpt90) cc_final: 0.6170 (mtm110) REVERT: X 647 THR cc_start: 0.8417 (m) cc_final: 0.8179 (p) REVERT: X 651 LYS cc_start: 0.7522 (mptt) cc_final: 0.7244 (pttp) outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 2.0521 time to fit residues: 278.2894 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 404 LEU Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 576 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 64 GLN X 76 GLN X 133 GLN X 154 GLN X 314 GLN X 433 GLN X 559 ASN X 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.128562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.103904 restraints weight = 4985.190| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.25 r_work: 0.2919 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5273 Z= 0.143 Angle : 0.493 5.409 7153 Z= 0.258 Chirality : 0.041 0.145 809 Planarity : 0.004 0.041 921 Dihedral : 6.191 58.775 719 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.69 % Allowed : 11.47 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.31), residues: 647 helix: 1.80 (0.46), residues: 117 sheet: 0.63 (0.31), residues: 246 loop : 0.57 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.006 0.001 HIS X 570 PHE 0.010 0.001 PHE X 548 TYR 0.011 0.001 TYR X 167 ARG 0.008 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.599 Fit side-chains REVERT: X 16 ARG cc_start: 0.7616 (ttm170) cc_final: 0.7406 (tmm-80) REVERT: X 127 LYS cc_start: 0.6397 (ttpp) cc_final: 0.5940 (ttpt) REVERT: X 133 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7731 (mm110) REVERT: X 143 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7917 (ttm-80) REVERT: X 194 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7735 (ttm110) REVERT: X 442 LEU cc_start: 0.7947 (mp) cc_final: 0.7582 (mm) REVERT: X 445 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7675 (ttpp) REVERT: X 446 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7627 (tm-30) REVERT: X 452 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6777 (mt-10) REVERT: X 483 SER cc_start: 0.8236 (p) cc_final: 0.8020 (m) REVERT: X 508 GLN cc_start: 0.7614 (tt0) cc_final: 0.6897 (mt0) REVERT: X 593 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8247 (tppt) REVERT: X 597 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7645 (mtmt) REVERT: X 599 GLU cc_start: 0.8305 (tt0) cc_final: 0.7858 (tm-30) REVERT: X 638 ARG cc_start: 0.7811 (mpt90) cc_final: 0.5916 (mtm110) REVERT: X 647 THR cc_start: 0.8352 (m) cc_final: 0.8111 (p) REVERT: X 651 LYS cc_start: 0.7421 (mptt) cc_final: 0.7010 (pttp) outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 1.5478 time to fit residues: 176.9393 Evaluate side-chains 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 570 HIS Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain X residue 597 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 154 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.128834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.104267 restraints weight = 5023.239| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.25 r_work: 0.2900 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5273 Z= 0.151 Angle : 0.490 5.479 7153 Z= 0.253 Chirality : 0.041 0.138 809 Planarity : 0.004 0.033 921 Dihedral : 4.812 46.111 713 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.79 % Allowed : 12.19 % Favored : 86.02 % 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: 1.18 (0.32), residues: 647 helix: 2.00 (0.47), residues: 117 sheet: 0.57 (0.31), residues: 245 loop : 0.64 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 90 HIS 0.003 0.001 HIS X 570 PHE 0.010 0.001 PHE X 639 TYR 0.012 0.001 TYR X 167 ARG 0.006 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.568 Fit side-chains REVERT: X 16 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7427 (tmm-80) REVERT: X 127 LYS cc_start: 0.6404 (ttpp) cc_final: 0.6020 (ttpt) REVERT: X 143 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.7897 (ttm-80) REVERT: X 442 LEU cc_start: 0.7946 (mp) cc_final: 0.7562 (mm) REVERT: X 445 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7677 (ttpp) REVERT: X 446 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7567 (tm-30) REVERT: X 452 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6750 (mt-10) REVERT: X 593 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8206 (ttmt) REVERT: X 599 GLU cc_start: 0.8313 (tt0) cc_final: 0.7819 (tm-30) REVERT: X 638 ARG cc_start: 0.7787 (mpt90) cc_final: 0.5870 (mtm110) REVERT: X 651 LYS cc_start: 0.7430 (mptt) cc_final: 0.6883 (mmtp) REVERT: X 672 MET cc_start: 0.8474 (mmp) cc_final: 0.8159 (mmm) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 2.1536 time to fit residues: 241.2478 Evaluate side-chains 102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.128177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.103183 restraints weight = 5127.601| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.28 r_work: 0.2890 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5273 Z= 0.164 Angle : 0.484 5.512 7153 Z= 0.250 Chirality : 0.041 0.138 809 Planarity : 0.004 0.035 921 Dihedral : 4.696 46.836 711 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 13.26 % Favored : 84.77 % 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: 1.13 (0.32), residues: 647 helix: 2.06 (0.47), residues: 117 sheet: 0.49 (0.31), residues: 248 loop : 0.61 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.011 0.001 PHE X 639 TYR 0.013 0.001 TYR X 167 ARG 0.008 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.592 Fit side-chains REVERT: X 127 LYS cc_start: 0.6437 (ttpp) cc_final: 0.6044 (ttpt) REVERT: X 143 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7899 (ttm-80) REVERT: X 405 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6534 (tp30) REVERT: X 442 LEU cc_start: 0.7954 (mp) cc_final: 0.7566 (mm) REVERT: X 445 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7667 (ttpp) REVERT: X 446 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7409 (tm-30) REVERT: X 452 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6760 (mt-10) REVERT: X 593 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8209 (ttmt) REVERT: X 599 GLU cc_start: 0.8297 (tt0) cc_final: 0.7795 (tm-30) REVERT: X 638 ARG cc_start: 0.7792 (mpt90) cc_final: 0.5844 (mtm110) REVERT: X 651 LYS cc_start: 0.7451 (mptt) cc_final: 0.6905 (mmtp) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 1.5159 time to fit residues: 170.9094 Evaluate side-chains 106 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 35 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 416 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.131662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107280 restraints weight = 5001.208| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.26 r_work: 0.2953 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5273 Z= 0.111 Angle : 0.443 5.405 7153 Z= 0.227 Chirality : 0.040 0.130 809 Planarity : 0.003 0.034 921 Dihedral : 4.391 51.275 711 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.61 % Allowed : 14.70 % Favored : 83.69 % 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: 1.29 (0.32), residues: 647 helix: 2.27 (0.48), residues: 117 sheet: 0.53 (0.31), residues: 243 loop : 0.74 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 90 HIS 0.001 0.000 HIS X 22 PHE 0.008 0.001 PHE X 548 TYR 0.009 0.001 TYR X 167 ARG 0.008 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.597 Fit side-chains REVERT: X 127 LYS cc_start: 0.6462 (ttpp) cc_final: 0.6057 (ttpt) REVERT: X 133 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: X 143 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.7883 (ttm-80) REVERT: X 310 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: X 405 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6696 (tp30) REVERT: X 442 LEU cc_start: 0.7923 (mp) cc_final: 0.7535 (mm) REVERT: X 445 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7627 (ttpp) REVERT: X 446 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7420 (tm-30) REVERT: X 452 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6766 (mt-10) REVERT: X 533 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7052 (mt) REVERT: X 593 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8055 (mttp) REVERT: X 597 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7644 (mtmt) REVERT: X 599 GLU cc_start: 0.8236 (tt0) cc_final: 0.7765 (tm-30) REVERT: X 638 ARG cc_start: 0.7705 (mpt90) cc_final: 0.5807 (mtm110) REVERT: X 651 LYS cc_start: 0.7367 (mptt) cc_final: 0.6952 (ptmm) REVERT: X 672 MET cc_start: 0.8439 (mmp) cc_final: 0.8116 (mmm) outliers start: 9 outliers final: 3 residues processed: 112 average time/residue: 1.4408 time to fit residues: 167.3300 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 0.0060 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 122 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.102315 restraints weight = 5019.732| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.23 r_work: 0.2884 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5273 Z= 0.219 Angle : 0.518 5.560 7153 Z= 0.266 Chirality : 0.042 0.143 809 Planarity : 0.004 0.037 921 Dihedral : 4.831 48.604 711 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.69 % Allowed : 13.80 % Favored : 83.51 % 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: 1.15 (0.32), residues: 647 helix: 2.04 (0.47), residues: 116 sheet: 0.49 (0.31), residues: 244 loop : 0.66 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 90 HIS 0.004 0.001 HIS X 22 PHE 0.010 0.002 PHE X 549 TYR 0.014 0.002 TYR X 167 ARG 0.010 0.001 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.593 Fit side-chains REVERT: X 127 LYS cc_start: 0.6447 (ttpp) cc_final: 0.6079 (ttpt) REVERT: X 143 ARG cc_start: 0.8492 (ttp-170) cc_final: 0.7901 (ttm-80) REVERT: X 213 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7957 (mtt180) REVERT: X 405 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6682 (tp30) REVERT: X 442 LEU cc_start: 0.7986 (mp) cc_final: 0.7584 (mm) REVERT: X 445 LYS cc_start: 0.8209 (tmtt) cc_final: 0.7595 (ttpp) REVERT: X 446 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7423 (tm-30) REVERT: X 452 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6740 (mt-10) REVERT: X 593 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8205 (ttmt) REVERT: X 599 GLU cc_start: 0.8274 (tt0) cc_final: 0.7797 (tm-30) REVERT: X 638 ARG cc_start: 0.7782 (mpt90) cc_final: 0.5822 (mtm110) REVERT: X 651 LYS cc_start: 0.7474 (mptt) cc_final: 0.6928 (mmtp) outliers start: 15 outliers final: 7 residues processed: 113 average time/residue: 1.4828 time to fit residues: 173.5653 Evaluate side-chains 110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.101358 restraints weight = 4955.114| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.25 r_work: 0.2881 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5273 Z= 0.248 Angle : 0.543 5.628 7153 Z= 0.279 Chirality : 0.042 0.144 809 Planarity : 0.004 0.039 921 Dihedral : 4.994 47.125 711 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.69 % Allowed : 14.70 % Favored : 82.62 % 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: 0.94 (0.32), residues: 647 helix: 1.83 (0.46), residues: 116 sheet: 0.39 (0.31), residues: 249 loop : 0.51 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.004 0.001 HIS X 22 PHE 0.012 0.002 PHE X 639 TYR 0.015 0.002 TYR X 167 ARG 0.010 0.001 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.591 Fit side-chains REVERT: X 96 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: X 143 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.7896 (ttm-80) REVERT: X 213 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: X 405 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6516 (tp30) REVERT: X 439 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: X 442 LEU cc_start: 0.7996 (mp) cc_final: 0.7620 (mm) REVERT: X 445 LYS cc_start: 0.8209 (tmtt) cc_final: 0.7671 (ttpp) REVERT: X 446 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7390 (tm-30) REVERT: X 452 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6739 (mt-10) REVERT: X 593 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8206 (ttmt) REVERT: X 599 GLU cc_start: 0.8276 (tt0) cc_final: 0.7758 (tm-30) REVERT: X 638 ARG cc_start: 0.7810 (mpt90) cc_final: 0.5884 (mtm110) REVERT: X 651 LYS cc_start: 0.7501 (mptt) cc_final: 0.6954 (mmtp) REVERT: X 672 MET cc_start: 0.8580 (mmp) cc_final: 0.8305 (mmm) outliers start: 15 outliers final: 8 residues processed: 112 average time/residue: 1.4593 time to fit residues: 169.3081 Evaluate side-chains 112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 45 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.101581 restraints weight = 4986.362| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.25 r_work: 0.2868 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5273 Z= 0.237 Angle : 0.540 5.597 7153 Z= 0.279 Chirality : 0.042 0.144 809 Planarity : 0.004 0.042 921 Dihedral : 5.008 47.049 711 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.15 % Allowed : 15.05 % Favored : 82.80 % 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: 0.91 (0.32), residues: 647 helix: 1.82 (0.47), residues: 116 sheet: 0.35 (0.31), residues: 249 loop : 0.50 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.004 0.001 HIS X 22 PHE 0.010 0.002 PHE X 639 TYR 0.015 0.002 TYR X 167 ARG 0.011 0.001 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.621 Fit side-chains REVERT: X 96 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: X 127 LYS cc_start: 0.6441 (ttpp) cc_final: 0.5971 (ttpt) REVERT: X 143 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.7903 (ttm-80) REVERT: X 213 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7952 (mtt180) REVERT: X 405 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6518 (tp30) REVERT: X 439 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: X 442 LEU cc_start: 0.7987 (mp) cc_final: 0.7604 (mm) REVERT: X 445 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7691 (ttpp) REVERT: X 446 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7450 (tm-30) REVERT: X 452 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6732 (mt-10) REVERT: X 593 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8220 (ttmt) REVERT: X 599 GLU cc_start: 0.8285 (tt0) cc_final: 0.7762 (tm-30) REVERT: X 638 ARG cc_start: 0.7839 (mpt90) cc_final: 0.5914 (mtm110) REVERT: X 651 LYS cc_start: 0.7513 (mptt) cc_final: 0.6965 (mmtp) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 1.5291 time to fit residues: 172.7286 Evaluate side-chains 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.104290 restraints weight = 4970.189| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.25 r_work: 0.2905 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5273 Z= 0.154 Angle : 0.491 6.884 7153 Z= 0.252 Chirality : 0.041 0.136 809 Planarity : 0.004 0.045 921 Dihedral : 4.715 49.745 711 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.79 % Allowed : 15.59 % Favored : 82.62 % 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: 1.08 (0.32), residues: 647 helix: 2.01 (0.47), residues: 117 sheet: 0.41 (0.32), residues: 243 loop : 0.62 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 90 HIS 0.004 0.001 HIS X 658 PHE 0.008 0.001 PHE X 326 TYR 0.011 0.001 TYR X 167 ARG 0.011 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.614 Fit side-chains REVERT: X 96 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: X 127 LYS cc_start: 0.6431 (ttpp) cc_final: 0.5991 (ttpt) REVERT: X 143 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.7908 (ttm-80) REVERT: X 405 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6499 (tp30) REVERT: X 439 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: X 442 LEU cc_start: 0.7955 (mp) cc_final: 0.7560 (mm) REVERT: X 445 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7632 (ttpp) REVERT: X 446 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7428 (tm-30) REVERT: X 452 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6719 (mt-10) REVERT: X 533 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7158 (mt) REVERT: X 593 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8219 (ttmt) REVERT: X 599 GLU cc_start: 0.8258 (tt0) cc_final: 0.7775 (tm-30) REVERT: X 638 ARG cc_start: 0.7775 (mpt90) cc_final: 0.5850 (mtm110) REVERT: X 651 LYS cc_start: 0.7450 (mptt) cc_final: 0.6905 (mmtm) REVERT: X 672 MET cc_start: 0.8526 (mmp) cc_final: 0.8296 (mmm) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 1.4561 time to fit residues: 165.9485 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.100054 restraints weight = 5025.606| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.26 r_work: 0.2848 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5273 Z= 0.349 Angle : 0.613 5.896 7153 Z= 0.315 Chirality : 0.045 0.151 809 Planarity : 0.005 0.046 921 Dihedral : 5.228 45.595 711 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.15 % Allowed : 15.41 % Favored : 82.44 % 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: 0.81 (0.31), residues: 647 helix: 1.79 (0.46), residues: 114 sheet: 0.36 (0.31), residues: 246 loop : 0.35 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP X 205 HIS 0.005 0.001 HIS X 22 PHE 0.029 0.003 PHE X 548 TYR 0.018 0.002 TYR X 167 ARG 0.013 0.001 ARG X 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.529 Fit side-chains REVERT: X 96 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: X 127 LYS cc_start: 0.6474 (ttpp) cc_final: 0.5984 (ttpt) REVERT: X 143 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.7943 (ttm-80) REVERT: X 405 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6658 (tp30) REVERT: X 439 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: X 442 LEU cc_start: 0.8004 (mp) cc_final: 0.7604 (mm) REVERT: X 445 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7689 (ttpp) REVERT: X 446 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7443 (tm-30) REVERT: X 452 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6750 (mt-10) REVERT: X 593 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8217 (ttmt) REVERT: X 599 GLU cc_start: 0.8279 (tt0) cc_final: 0.7780 (tm-30) REVERT: X 638 ARG cc_start: 0.7879 (mpt90) cc_final: 0.5911 (mtm110) REVERT: X 651 LYS cc_start: 0.7554 (mptt) cc_final: 0.6993 (mmtp) REVERT: X 672 MET cc_start: 0.8636 (mmp) cc_final: 0.8388 (mmm) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 1.5592 time to fit residues: 177.4068 Evaluate side-chains 110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 58 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 646 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104493 restraints weight = 5061.984| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.26 r_work: 0.2915 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5273 Z= 0.145 Angle : 0.491 6.818 7153 Z= 0.252 Chirality : 0.041 0.136 809 Planarity : 0.004 0.047 921 Dihedral : 4.720 49.327 711 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.43 % Allowed : 16.85 % Favored : 81.72 % 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 (0.32), residues: 647 helix: 1.99 (0.47), residues: 117 sheet: 0.36 (0.31), residues: 252 loop : 0.63 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.002 0.001 HIS X 350 PHE 0.008 0.001 PHE X 326 TYR 0.010 0.001 TYR X 167 ARG 0.011 0.000 ARG X 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6459.31 seconds wall clock time: 112 minutes 8.97 seconds (6728.97 seconds total)