Starting phenix.real_space_refine on Tue Mar 11 18:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuu_60914/03_2025/9iuu_60914.cif" } resolution = 3.29 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= 0.050 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4170 2.51 5 N 1072 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 6513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1557 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.12, per 1000 atoms: 0.79 Number of scatterers: 6513 At special positions: 0 Unit cell: (73.528, 87.264, 116.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1232 8.00 N 1072 7.00 C 4170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 913.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 57.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.229A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.564A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.860A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.593A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.460A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.640A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.687A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.561A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.944A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.595A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.159A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.529A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.693A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.774A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.503A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.117A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.803A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.222A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 311 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1078 1.31 - 1.45: 1981 1.45 - 1.58: 3582 1.58 - 1.72: 1 1.72 - 1.85: 58 Bond restraints: 6700 Sorted by residual: bond pdb=" C LEU A 79 " pdb=" O LEU A 79 " ideal model delta sigma weight residual 1.237 1.368 -0.131 1.19e-02 7.06e+03 1.21e+02 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.524 1.628 -0.104 1.26e-02 6.30e+03 6.86e+01 bond pdb=" C GLU A 75 " pdb=" O GLU A 75 " ideal model delta sigma weight residual 1.237 1.323 -0.087 1.17e-02 7.31e+03 5.49e+01 bond pdb=" N TYR A 83 " pdb=" CA TYR A 83 " ideal model delta sigma weight residual 1.457 1.550 -0.093 1.41e-02 5.03e+03 4.33e+01 bond pdb=" C THR A 78 " pdb=" O THR A 78 " ideal model delta sigma weight residual 1.236 1.306 -0.070 1.18e-02 7.18e+03 3.50e+01 ... (remaining 6695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 8877 2.50 - 5.01: 190 5.01 - 7.51: 36 7.51 - 10.02: 2 10.02 - 12.52: 2 Bond angle restraints: 9107 Sorted by residual: angle pdb=" N GLN A 81 " pdb=" CA GLN A 81 " pdb=" C GLN A 81 " ideal model delta sigma weight residual 111.07 101.98 9.09 1.07e+00 8.73e-01 7.21e+01 angle pdb=" N TYR A 83 " pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 109.81 122.20 -12.39 2.21e+00 2.05e-01 3.14e+01 angle pdb=" N GLU A 56 " pdb=" CA GLU A 56 " pdb=" C GLU A 56 " ideal model delta sigma weight residual 113.41 106.67 6.74 1.22e+00 6.72e-01 3.06e+01 angle pdb=" C GLU A 37 " pdb=" N ASP A 38 " pdb=" CA ASP A 38 " ideal model delta sigma weight residual 120.44 113.27 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" N GLU A 35 " pdb=" CA GLU A 35 " pdb=" C GLU A 35 " ideal model delta sigma weight residual 113.23 106.54 6.69 1.24e+00 6.50e-01 2.91e+01 ... (remaining 9102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3482 17.95 - 35.89: 412 35.89 - 53.84: 103 53.84 - 71.78: 18 71.78 - 89.73: 13 Dihedral angle restraints: 4028 sinusoidal: 1704 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PHE B 400 " pdb=" C PHE B 400 " pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 52.42 40.58 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C ASN A 58 " pdb=" N ASN A 58 " pdb=" CA ASN A 58 " pdb=" CB ASN A 58 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 4025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 733 0.051 - 0.102: 194 0.102 - 0.154: 26 0.154 - 0.205: 8 0.205 - 0.256: 2 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA ASN A 58 " pdb=" N ASN A 58 " pdb=" C ASN A 58 " pdb=" CB ASN A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 229 " pdb=" CA THR A 229 " pdb=" OG1 THR A 229 " pdb=" CG2 THR A 229 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TYR B 501 " pdb=" N TYR B 501 " pdb=" C TYR B 501 " pdb=" CB TYR B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 960 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 83 " -0.039 2.00e-02 2.50e+03 7.58e-02 5.74e+01 pdb=" C TYR A 83 " 0.131 2.00e-02 2.50e+03 pdb=" O TYR A 83 " -0.045 2.00e-02 2.50e+03 pdb=" N PRO A 84 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 346 " -0.567 9.50e-02 1.11e+02 2.54e-01 3.94e+01 pdb=" NE ARG B 346 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 346 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 346 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 498 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.64e+01 pdb=" NE ARG B 498 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 498 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 498 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 498 " -0.011 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6157 3.31 - 3.84: 11023 3.84 - 4.37: 12725 4.37 - 4.90: 22336 Nonbonded interactions: 53814 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 129 " pdb=" OG1 THR A 129 " model vdw 2.260 3.040 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.268 3.040 nonbonded pdb=" NE2 GLN B 474 " pdb=" O GLY B 476 " model vdw 2.288 3.120 ... (remaining 53809 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.260 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.006 0.131 6700 Z= 0.414 Angle : 0.852 12.524 9107 Z= 0.546 Chirality : 0.049 0.256 963 Planarity : 0.011 0.254 1172 Dihedral : 16.624 89.727 2515 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.86 % Allowed : 16.98 % Favored : 82.16 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.50 % 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: -0.39 (0.29), residues: 787 helix: 0.62 (0.26), residues: 379 sheet: -1.49 (0.72), residues: 45 loop : -0.99 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.007 0.001 HIS A 34 PHE 0.022 0.002 PHE A 32 TYR 0.014 0.001 TYR A 237 ARG 0.005 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.752 Fit side-chains REVERT: A 35 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: A 313 LYS cc_start: 0.8136 (tttt) cc_final: 0.7892 (ttpt) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.1813 time to fit residues: 19.4796 Evaluate side-chains 73 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 60 GLN ** A 524 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 = 0.3714 r_free = 0.3714 target = 0.145756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125813 restraints weight = 8581.914| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.78 r_work: 0.3392 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6700 Z= 0.190 Angle : 0.519 5.860 9107 Z= 0.280 Chirality : 0.042 0.192 963 Planarity : 0.004 0.051 1172 Dihedral : 5.678 60.505 993 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 14.82 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.06 (0.29), residues: 787 helix: 1.10 (0.26), residues: 381 sheet: -1.29 (0.75), residues: 43 loop : -0.91 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 230 TYR 0.019 0.001 TYR A 41 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.704 Fit side-chains REVERT: A 33 ASN cc_start: 0.8721 (m-40) cc_final: 0.8504 (m-40) REVERT: A 35 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 163 TRP cc_start: 0.6977 (t60) cc_final: 0.6644 (t60) REVERT: A 313 LYS cc_start: 0.8022 (tttt) cc_final: 0.7809 (ttpt) REVERT: B 400 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: B 428 ASP cc_start: 0.8910 (p0) cc_final: 0.8694 (p0) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.1623 time to fit residues: 22.4257 Evaluate side-chains 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 60 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 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 = 0.3729 r_free = 0.3729 target = 0.147176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127368 restraints weight = 8639.757| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.78 r_work: 0.3410 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6700 Z= 0.159 Angle : 0.483 7.009 9107 Z= 0.258 Chirality : 0.041 0.189 963 Planarity : 0.004 0.051 1172 Dihedral : 4.949 52.415 989 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.88 % Allowed : 15.54 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.25 (0.29), residues: 787 helix: 1.30 (0.26), residues: 382 sheet: -1.40 (0.74), residues: 43 loop : -0.85 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.012 0.001 PHE A 230 TYR 0.012 0.001 TYR A 41 ARG 0.002 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.736 Fit side-chains REVERT: A 35 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 73 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 129 THR cc_start: 0.8118 (t) cc_final: 0.7902 (t) REVERT: A 163 TRP cc_start: 0.6999 (t60) cc_final: 0.6639 (t60) REVERT: A 435 GLU cc_start: 0.7392 (pt0) cc_final: 0.6955 (mt-10) REVERT: B 400 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8514 (m-10) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 0.1316 time to fit residues: 19.0736 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 41 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 4 optimal weight: 5.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129636 restraints weight = 8506.440| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.81 r_work: 0.3441 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6700 Z= 0.130 Angle : 0.458 5.676 9107 Z= 0.245 Chirality : 0.040 0.183 963 Planarity : 0.004 0.050 1172 Dihedral : 4.598 45.455 989 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 16.12 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.50 (0.30), residues: 787 helix: 1.54 (0.26), residues: 382 sheet: -1.42 (0.72), residues: 43 loop : -0.73 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE A 230 TYR 0.011 0.001 TYR A 41 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.780 Fit side-chains REVERT: A 35 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 73 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 163 TRP cc_start: 0.6990 (t60) cc_final: 0.6633 (t60) REVERT: A 435 GLU cc_start: 0.7350 (pt0) cc_final: 0.6897 (mt-10) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.1451 time to fit residues: 20.4940 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 51 ASN A 60 GLN A 194 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120607 restraints weight = 8498.686| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.78 r_work: 0.3294 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6700 Z= 0.339 Angle : 0.581 7.769 9107 Z= 0.308 Chirality : 0.045 0.187 963 Planarity : 0.005 0.050 1172 Dihedral : 5.050 46.283 989 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.03 % Allowed : 14.96 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 787 helix: 1.20 (0.25), residues: 381 sheet: -1.37 (0.73), residues: 43 loop : -0.87 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 606 HIS 0.005 0.001 HIS A 241 PHE 0.019 0.002 PHE A 230 TYR 0.019 0.002 TYR A 237 ARG 0.003 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.807 Fit side-chains REVERT: A 35 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: A 73 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8593 (mt) REVERT: A 474 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8045 (mmp) REVERT: B 400 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8714 (m-10) outliers start: 28 outliers final: 17 residues processed: 96 average time/residue: 0.1472 time to fit residues: 21.2307 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 524 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 = 0.3610 r_free = 0.3610 target = 0.136848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114200 restraints weight = 8729.732| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.10 r_work: 0.3248 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6700 Z= 0.217 Angle : 0.522 8.046 9107 Z= 0.276 Chirality : 0.042 0.185 963 Planarity : 0.004 0.049 1172 Dihedral : 4.850 45.137 989 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.32 % Allowed : 14.68 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.19 (0.29), residues: 787 helix: 1.29 (0.25), residues: 382 sheet: -1.54 (0.72), residues: 43 loop : -0.91 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 369 TYR 0.013 0.001 TYR A 237 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.737 Fit side-chains REVERT: A 35 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 73 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 435 GLU cc_start: 0.7866 (pt0) cc_final: 0.7223 (mp0) REVERT: A 474 MET cc_start: 0.8263 (mmp) cc_final: 0.7996 (mmp) REVERT: B 400 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8680 (m-10) outliers start: 30 outliers final: 19 residues processed: 96 average time/residue: 0.1375 time to fit residues: 19.9363 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124485 restraints weight = 8618.019| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.95 r_work: 0.3347 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6700 Z= 0.159 Angle : 0.491 6.491 9107 Z= 0.260 Chirality : 0.041 0.180 963 Planarity : 0.004 0.048 1172 Dihedral : 4.544 43.527 989 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.31 % Allowed : 15.25 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.43 (0.29), residues: 787 helix: 1.52 (0.26), residues: 383 sheet: -1.51 (0.73), residues: 43 loop : -0.83 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 369 TYR 0.010 0.001 TYR A 41 ARG 0.002 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.797 Fit side-chains REVERT: A 163 TRP cc_start: 0.6829 (t60) cc_final: 0.6531 (t60) REVERT: A 435 GLU cc_start: 0.7793 (pt0) cc_final: 0.7193 (mp0) REVERT: A 474 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7859 (mmp) REVERT: B 400 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8539 (m-10) outliers start: 23 outliers final: 19 residues processed: 94 average time/residue: 0.1411 time to fit residues: 19.9149 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 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 = 0.3583 r_free = 0.3583 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112123 restraints weight = 8760.917| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.08 r_work: 0.3235 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6700 Z= 0.315 Angle : 0.585 8.297 9107 Z= 0.309 Chirality : 0.045 0.188 963 Planarity : 0.004 0.049 1172 Dihedral : 4.461 38.539 984 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.03 % Allowed : 15.25 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.19 (0.29), residues: 787 helix: 1.27 (0.25), residues: 382 sheet: -1.45 (0.73), residues: 43 loop : -0.90 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.010 0.001 HIS A 34 PHE 0.017 0.001 PHE A 369 TYR 0.017 0.002 TYR A 237 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.656 Fit side-chains REVERT: A 297 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7487 (mmt) REVERT: A 364 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (t) REVERT: A 474 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7825 (mmp) REVERT: B 400 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8760 (m-10) outliers start: 28 outliers final: 20 residues processed: 91 average time/residue: 0.1348 time to fit residues: 18.2146 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 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 = 0.3687 r_free = 0.3687 target = 0.143322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122010 restraints weight = 8645.890| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.94 r_work: 0.3285 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6700 Z= 0.197 Angle : 0.531 6.932 9107 Z= 0.281 Chirality : 0.042 0.192 963 Planarity : 0.004 0.048 1172 Dihedral : 4.261 37.406 984 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.45 % Allowed : 16.12 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.34 (0.29), residues: 787 helix: 1.42 (0.25), residues: 384 sheet: -1.45 (0.74), residues: 43 loop : -0.86 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.008 0.001 HIS A 34 PHE 0.012 0.001 PHE A 230 TYR 0.011 0.001 TYR A 237 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.691 Fit side-chains REVERT: A 297 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7539 (mmt) REVERT: A 364 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 474 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7853 (mmp) REVERT: B 400 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8660 (m-10) outliers start: 24 outliers final: 17 residues processed: 87 average time/residue: 0.1390 time to fit residues: 18.1570 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 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 = 0.3697 r_free = 0.3697 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122959 restraints weight = 8674.353| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.95 r_work: 0.3310 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6700 Z= 0.183 Angle : 0.522 6.544 9107 Z= 0.277 Chirality : 0.041 0.191 963 Planarity : 0.004 0.048 1172 Dihedral : 4.150 36.201 984 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 16.12 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.40 (0.29), residues: 787 helix: 1.48 (0.25), residues: 385 sheet: -1.31 (0.74), residues: 43 loop : -0.87 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.008 0.001 HIS A 34 PHE 0.013 0.001 PHE A 230 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.679 Fit side-chains REVERT: A 297 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7498 (mmt) REVERT: A 474 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7785 (mmp) REVERT: B 400 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8620 (m-10) outliers start: 23 outliers final: 18 residues processed: 90 average time/residue: 0.1334 time to fit residues: 18.0524 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 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 = 0.3652 r_free = 0.3652 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118002 restraints weight = 8885.269| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6700 Z= 0.154 Angle : 0.499 5.678 9107 Z= 0.265 Chirality : 0.040 0.188 963 Planarity : 0.004 0.049 1172 Dihedral : 3.994 34.569 984 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.73 % Allowed : 16.69 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.53 (0.30), residues: 787 helix: 1.60 (0.26), residues: 385 sheet: -1.16 (0.76), residues: 43 loop : -0.83 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 163 HIS 0.005 0.001 HIS A 34 PHE 0.011 0.001 PHE A 230 TYR 0.011 0.001 TYR A 158 ARG 0.002 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.76 seconds wall clock time: 60 minutes 57.88 seconds (3657.88 seconds total)