Starting phenix.real_space_refine on Tue Feb 11 19:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuu_60914/02_2025/9iuu_60914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuu_60914/02_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_60914/02_2025/9iuu_60914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuu_60914/02_2025/9iuu_60914.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuu_60914/02_2025/9iuu_60914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuu_60914/02_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-5592/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: 4.78, per 1000 atoms: 0.73 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: 1.62 Conformation dependent library (CDL) restraints added in 924.4 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: 0.72 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: 1.80 Time building geometry restraints manager: 1.91 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: 2.560 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.280 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- 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 : 0.576 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: 0.1661 time to fit residues: 17.6062 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 : 0.685 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125811 restraints weight = 8581.914| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.78 r_work: 0.3393 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.735 Fit side-chains REVERT: A 33 ASN cc_start: 0.8718 (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: 0.6979 (t60) cc_final: 0.6645 (t60) REVERT: A 313 LYS cc_start: 0.8019 (tttt) cc_final: 0.7805 (ttpt) REVERT: B 400 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: B 428 ASP cc_start: 0.8909 (p0) cc_final: 0.8694 (p0) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.1525 time to fit residues: 20.9164 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 : 0.688 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.145197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124848 restraints weight = 8517.709| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.81 r_work: 0.3391 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6700 Z= 0.193 Angle : 0.504 7.981 9107 Z= 0.269 Chirality : 0.041 0.191 963 Planarity : 0.004 0.051 1172 Dihedral : 5.048 51.489 989 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.74 % Allowed : 14.96 % Favored : 81.29 % 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: 0.18 (0.29), residues: 787 helix: 1.24 (0.26), residues: 381 sheet: -1.39 (0.74), residues: 43 loop : -0.89 (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 0.014 0.001 PHE A 369 TYR 0.012 0.001 TYR A 237 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 109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.756 Fit side-chains REVERT: A 35 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 129 THR cc_start: 0.8114 (t) cc_final: 0.7895 (t) REVERT: A 163 TRP cc_start: 0.6905 (t60) cc_final: 0.6553 (t60) REVERT: A 435 GLU cc_start: 0.7535 (pt0) cc_final: 0.6999 (mt-10) REVERT: B 400 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8625 (m-10) outliers start: 26 outliers final: 16 residues processed: 103 average time/residue: 0.1371 time to fit residues: 20.8548 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 447 VAL 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 361 CYS 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 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: 1.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.144318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123900 restraints weight = 8560.936| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.81 r_work: 0.3377 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1271 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= 0.213 Angle : 0.514 7.130 9107 Z= 0.273 Chirality : 0.042 0.188 963 Planarity : 0.004 0.050 1172 Dihedral : 4.927 46.790 989 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.60 % Allowed : 15.54 % Favored : 80.86 % 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: 0.22 (0.29), residues: 787 helix: 1.28 (0.26), residues: 382 sheet: -1.33 (0.73), residues: 43 loop : -0.88 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.015 0.001 PHE A 369 TYR 0.013 0.001 TYR A 237 ARG 0.002 0.000 ARG B 498 *********************** 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 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.734 Fit side-chains REVERT: A 35 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 73 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 129 THR cc_start: 0.8109 (t) cc_final: 0.7904 (t) REVERT: A 163 TRP cc_start: 0.6928 (t60) cc_final: 0.6659 (t60) REVERT: A 435 GLU cc_start: 0.7575 (pt0) cc_final: 0.7088 (mp0) REVERT: B 400 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8622 (m-10) outliers start: 25 outliers final: 16 residues processed: 100 average time/residue: 0.1368 time to fit residues: 20.1975 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.141512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121096 restraints weight = 8494.314| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.78 r_work: 0.3279 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6700 Z= 0.288 Angle : 0.558 6.847 9107 Z= 0.296 Chirality : 0.044 0.190 963 Planarity : 0.004 0.050 1172 Dihedral : 5.044 46.235 989 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.32 % Allowed : 14.24 % 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: 0.07 (0.29), residues: 787 helix: 1.14 (0.25), residues: 382 sheet: -1.40 (0.73), residues: 43 loop : -0.93 (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 0.017 0.001 PHE A 369 TYR 0.016 0.001 TYR A 237 ARG 0.002 0.000 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 107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.854 Fit side-chains REVERT: A 35 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 73 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 129 THR cc_start: 0.8113 (t) cc_final: 0.7905 (t) REVERT: B 400 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8720 (m-10) outliers start: 30 outliers final: 18 residues processed: 100 average time/residue: 0.1345 time to fit residues: 20.1474 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL 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 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118547 restraints weight = 8612.653| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.08 r_work: 0.3277 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6700 Z= 0.174 Angle : 0.502 7.373 9107 Z= 0.267 Chirality : 0.041 0.189 963 Planarity : 0.004 0.049 1172 Dihedral : 4.747 44.401 989 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 0.29 (0.29), residues: 787 helix: 1.38 (0.25), residues: 383 sheet: -1.41 (0.73), residues: 43 loop : -0.89 (0.32), residues: 361 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 369 TYR 0.010 0.001 TYR A 41 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 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.692 Fit side-chains REVERT: A 35 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 129 THR cc_start: 0.8007 (t) cc_final: 0.7796 (t) REVERT: A 163 TRP cc_start: 0.6794 (t60) cc_final: 0.6518 (t60) REVERT: A 435 GLU cc_start: 0.7859 (pt0) cc_final: 0.7194 (mp0) REVERT: B 400 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8589 (m-10) outliers start: 20 outliers final: 14 residues processed: 95 average time/residue: 0.1363 time to fit residues: 19.2978 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS 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 361 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 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 = 0.3659 r_free = 0.3659 target = 0.141053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118637 restraints weight = 8720.435| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.12 r_work: 0.3307 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1653 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= 0.167 Angle : 0.496 6.585 9107 Z= 0.264 Chirality : 0.041 0.186 963 Planarity : 0.004 0.049 1172 Dihedral : 4.370 41.811 987 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 15.83 % 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: 0.42 (0.29), residues: 787 helix: 1.49 (0.26), residues: 383 sheet: -1.37 (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 A 165 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 230 TYR 0.010 0.001 TYR A 41 ARG 0.001 0.000 ARG B 498 *********************** 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 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.708 Fit side-chains REVERT: A 129 THR cc_start: 0.8011 (t) cc_final: 0.7808 (t) REVERT: A 163 TRP cc_start: 0.6796 (t60) cc_final: 0.6546 (t60) REVERT: A 297 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7573 (mmt) REVERT: A 474 MET cc_start: 0.8229 (mmp) cc_final: 0.7718 (mmp) REVERT: B 400 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8610 (m-10) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.1344 time to fit residues: 17.6018 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS 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 356 THR Chi-restraints excluded: chain B residue 361 CYS 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 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: 4.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 0.0370 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.143416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122338 restraints weight = 8543.646| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.88 r_work: 0.3273 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6700 Z= 0.224 Angle : 0.528 7.360 9107 Z= 0.281 Chirality : 0.042 0.191 963 Planarity : 0.004 0.049 1172 Dihedral : 4.249 37.158 984 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.02 % Allowed : 16.26 % 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: 0.37 (0.29), residues: 787 helix: 1.42 (0.26), residues: 383 sheet: -1.36 (0.73), residues: 43 loop : -0.82 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.008 0.001 HIS A 34 PHE 0.014 0.001 PHE A 369 TYR 0.015 0.001 TYR A 202 ARG 0.001 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 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.735 Fit side-chains REVERT: A 163 TRP cc_start: 0.6808 (t60) cc_final: 0.6555 (t60) REVERT: A 297 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: A 474 MET cc_start: 0.8192 (mmp) cc_final: 0.7615 (mmp) REVERT: B 400 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8701 (m-10) outliers start: 21 outliers final: 17 residues processed: 90 average time/residue: 0.1401 time to fit residues: 18.9794 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL 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 335 LEU 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 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.143978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122658 restraints weight = 8634.005| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.94 r_work: 0.3291 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1715 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= 0.188 Angle : 0.515 6.733 9107 Z= 0.274 Chirality : 0.041 0.190 963 Planarity : 0.004 0.049 1172 Dihedral : 4.182 36.782 984 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.02 % Allowed : 16.12 % Favored : 80.86 % 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: 0.45 (0.29), residues: 787 helix: 1.49 (0.26), residues: 384 sheet: -1.32 (0.73), residues: 43 loop : -0.79 (0.32), residues: 360 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 0.011 0.001 TYR A 237 ARG 0.001 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: 21 poor density : 74 time to evaluate : 0.744 Fit side-chains REVERT: A 163 TRP cc_start: 0.6839 (t60) cc_final: 0.6588 (t60) REVERT: A 297 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7522 (mmt) REVERT: A 474 MET cc_start: 0.8162 (mmp) cc_final: 0.7691 (mmp) REVERT: B 400 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8642 (m-10) outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.1406 time to fit residues: 19.0146 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL 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 335 LEU 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 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 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 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 = 0.3706 r_free = 0.3706 target = 0.144917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123694 restraints weight = 8689.424| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.95 r_work: 0.3334 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6700 Z= 0.186 Angle : 0.519 6.577 9107 Z= 0.275 Chirality : 0.042 0.189 963 Planarity : 0.004 0.049 1172 Dihedral : 4.158 36.864 984 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.02 % Allowed : 16.26 % 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: 0.44 (0.29), residues: 787 helix: 1.47 (0.26), residues: 385 sheet: -1.29 (0.74), residues: 43 loop : -0.78 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.007 0.001 HIS A 34 PHE 0.013 0.001 PHE A 230 TYR 0.014 0.001 TYR A 202 ARG 0.001 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 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.783 Fit side-chains REVERT: A 297 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7447 (mmt) REVERT: A 474 MET cc_start: 0.8149 (mmp) cc_final: 0.7691 (mmp) REVERT: B 400 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8643 (m-10) outliers start: 21 outliers final: 18 residues processed: 90 average time/residue: 0.1315 time to fit residues: 17.8905 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 318 VAL Chi-restraints excluded: chain A residue 343 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 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 335 LEU 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 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.144947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123973 restraints weight = 8715.677| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.92 r_work: 0.3328 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6700 Z= 0.186 Angle : 0.514 6.435 9107 Z= 0.272 Chirality : 0.041 0.187 963 Planarity : 0.004 0.049 1172 Dihedral : 4.143 36.961 984 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 16.40 % 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: 0.47 (0.30), residues: 787 helix: 1.49 (0.26), residues: 385 sheet: -1.25 (0.74), residues: 43 loop : -0.77 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.007 0.001 HIS A 34 PHE 0.013 0.001 PHE A 230 TYR 0.012 0.001 TYR A 237 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: 3331.83 seconds wall clock time: 59 minutes 53.33 seconds (3593.33 seconds total)