Starting phenix.real_space_refine on Tue Feb 11 20:17:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.map" model { file = "/net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dma_27532/02_2025/8dma_27532.cif" } resolution = 2.79 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4142 2.51 5 N 1089 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: 4.53, per 1000 atoms: 0.70 Number of scatterers: 6487 At special positions: 0 Unit cell: (77, 87, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1219 8.00 N 1089 7.00 C 4142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.781A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.301A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 21 through 52 removed outlier: 4.051A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.547A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.749A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.700A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.092A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.706A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.658A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.622A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.557A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.709A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.868A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.615A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.449A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.605A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.743A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.242A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.159A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.539A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.993A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.273A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 882 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: 1.75 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.47: 1743 1.47 - 1.59: 2791 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6669 Sorted by residual: bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" CB VAL D 573 " pdb=" CG2 VAL D 573 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8675 1.82 - 3.63: 315 3.63 - 5.45: 42 5.45 - 7.27: 19 7.27 - 9.08: 7 Bond angle restraints: 9058 Sorted by residual: angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C VAL D 364 " pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " ideal model delta sigma weight residual 113.22 116.94 -3.72 1.12e+00 7.97e-01 1.10e+01 angle pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " pdb=" CG1 VAL D 364 " ideal model delta sigma weight residual 110.40 115.87 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.44 -7.04 2.30e+00 1.89e-01 9.38e+00 ... (remaining 9053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3592 17.14 - 34.28: 334 34.28 - 51.42: 51 51.42 - 68.56: 9 68.56 - 85.70: 8 Dihedral angle restraints: 3994 sinusoidal: 1657 harmonic: 2337 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR D 445 " pdb=" C THR D 445 " pdb=" N ILE D 446 " pdb=" CA ILE D 446 " ideal model delta harmonic sigma weight residual 180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 619 0.046 - 0.092: 234 0.092 - 0.138: 81 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 951 Sorted by residual: chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU D 182 " pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CB GLU D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 558 " pdb=" CB LEU D 558 " pdb=" CD1 LEU D 558 " pdb=" CD2 LEU D 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 948 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 373 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 224 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLU D 224 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU D 224 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO D 469 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " 0.034 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1333 2.78 - 3.31: 5871 3.31 - 3.84: 11379 3.84 - 4.37: 13370 4.37 - 4.90: 22664 Nonbonded interactions: 54617 Sorted by model distance: nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.244 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.340 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.350 3.120 ... (remaining 54612 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6669 Z= 0.341 Angle : 0.833 9.082 9058 Z= 0.441 Chirality : 0.055 0.230 951 Planarity : 0.007 0.067 1172 Dihedral : 13.455 85.700 2474 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 790 helix: -1.27 (0.22), residues: 399 sheet: 0.24 (0.64), residues: 60 loop : -0.69 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 163 HIS 0.005 0.002 HIS D 241 PHE 0.021 0.002 PHE D 369 TYR 0.029 0.002 TYR D 385 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.724 Fit side-chains REVERT: A 386 LYS cc_start: 0.9051 (mttt) cc_final: 0.8823 (mptt) REVERT: A 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8478 (m-30) REVERT: D 564 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8453 (mm-30) REVERT: D 597 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 607 ASN cc_start: 0.8700 (t0) cc_final: 0.8418 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 1.4187 time to fit residues: 161.7975 Evaluate side-chains 68 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.070183 restraints weight = 13188.796| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.84 r_work: 0.2826 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6669 Z= 0.257 Angle : 0.579 6.324 9058 Z= 0.298 Chirality : 0.043 0.179 951 Planarity : 0.005 0.046 1172 Dihedral : 5.882 57.060 932 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 8.65 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 790 helix: 0.23 (0.25), residues: 395 sheet: 0.13 (0.65), residues: 59 loop : -0.22 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.018 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.006 0.001 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.741 Fit side-chains REVERT: D 23 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8261 (mp0) REVERT: D 149 ASP cc_start: 0.8538 (m-30) cc_final: 0.8334 (p0) REVERT: D 163 TRP cc_start: 0.8466 (t60) cc_final: 0.8133 (t60) REVERT: D 564 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8943 (mm-30) REVERT: D 597 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8303 (tm-30) REVERT: D 607 ASN cc_start: 0.8859 (t0) cc_final: 0.8415 (t0) outliers start: 10 outliers final: 4 residues processed: 77 average time/residue: 1.3169 time to fit residues: 107.0561 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3323 r_free = 0.3323 target = 0.091561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.071257 restraints weight = 13289.578| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.86 r_work: 0.2843 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6669 Z= 0.180 Angle : 0.528 6.777 9058 Z= 0.270 Chirality : 0.042 0.176 951 Planarity : 0.004 0.038 1172 Dihedral : 5.323 56.324 932 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.73 % Allowed : 10.66 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 790 helix: 0.75 (0.26), residues: 395 sheet: 0.14 (0.66), residues: 59 loop : 0.06 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.735 Fit side-chains REVERT: A 385 THR cc_start: 0.9406 (p) cc_final: 0.9184 (p) REVERT: A 386 LYS cc_start: 0.9321 (mttt) cc_final: 0.8895 (mptt) REVERT: A 496 SER cc_start: 0.8333 (p) cc_final: 0.8048 (m) REVERT: D 149 ASP cc_start: 0.8547 (m-30) cc_final: 0.8316 (p0) REVERT: D 471 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 597 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8411 (tm-30) REVERT: D 607 ASN cc_start: 0.8900 (t0) cc_final: 0.8452 (t0) outliers start: 12 outliers final: 2 residues processed: 83 average time/residue: 1.3469 time to fit residues: 117.5311 Evaluate side-chains 69 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 471 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071713 restraints weight = 13343.761| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.86 r_work: 0.2858 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6669 Z= 0.174 Angle : 0.534 7.376 9058 Z= 0.269 Chirality : 0.042 0.179 951 Planarity : 0.004 0.037 1172 Dihedral : 5.010 55.283 932 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 12.25 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.30), residues: 790 helix: 1.13 (0.26), residues: 389 sheet: 0.14 (0.66), residues: 59 loop : 0.15 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.008 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.791 Fit side-chains REVERT: A 385 THR cc_start: 0.9411 (p) cc_final: 0.9204 (p) REVERT: A 386 LYS cc_start: 0.9317 (mttt) cc_final: 0.8875 (mptt) REVERT: A 440 LYS cc_start: 0.9256 (mppt) cc_final: 0.9000 (mppt) REVERT: A 496 SER cc_start: 0.8254 (p) cc_final: 0.8013 (m) REVERT: D 149 ASP cc_start: 0.8563 (m-30) cc_final: 0.8338 (p0) REVERT: D 471 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: D 597 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8446 (tm-30) REVERT: D 607 ASN cc_start: 0.8849 (t0) cc_final: 0.8449 (t0) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 1.3223 time to fit residues: 114.1569 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.089907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069856 restraints weight = 13314.597| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.84 r_work: 0.2809 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6669 Z= 0.253 Angle : 0.565 7.436 9058 Z= 0.287 Chirality : 0.043 0.190 951 Planarity : 0.004 0.042 1172 Dihedral : 5.071 55.462 932 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 13.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 790 helix: 1.14 (0.26), residues: 396 sheet: 0.12 (0.65), residues: 59 loop : 0.23 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.017 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.009 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9331 (mttt) cc_final: 0.8866 (mptt) REVERT: A 440 LYS cc_start: 0.9295 (mppt) cc_final: 0.9041 (mppt) REVERT: D 149 ASP cc_start: 0.8628 (m-30) cc_final: 0.8395 (p0) REVERT: D 171 GLU cc_start: 0.7905 (mp0) cc_final: 0.7532 (mp0) REVERT: D 471 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: D 472 GLN cc_start: 0.8318 (mp10) cc_final: 0.8013 (mp-120) REVERT: D 579 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8873 (ttp) REVERT: D 597 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8486 (tm-30) REVERT: D 607 ASN cc_start: 0.8807 (t0) cc_final: 0.8379 (t0) outliers start: 13 outliers final: 4 residues processed: 78 average time/residue: 1.4093 time to fit residues: 115.3883 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069300 restraints weight = 13204.597| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.83 r_work: 0.2812 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6669 Z= 0.256 Angle : 0.569 7.766 9058 Z= 0.288 Chirality : 0.043 0.200 951 Planarity : 0.004 0.044 1172 Dihedral : 5.059 55.716 932 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 13.40 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 790 helix: 1.18 (0.26), residues: 396 sheet: 0.04 (0.64), residues: 59 loop : 0.29 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.017 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.009 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8152 (mtpm) REVERT: A 386 LYS cc_start: 0.9353 (mttt) cc_final: 0.8897 (mptt) REVERT: A 440 LYS cc_start: 0.9315 (mppt) cc_final: 0.9061 (mppt) REVERT: D 149 ASP cc_start: 0.8634 (m-30) cc_final: 0.8416 (p0) REVERT: D 171 GLU cc_start: 0.7912 (mp0) cc_final: 0.7508 (mp0) REVERT: D 471 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: D 472 GLN cc_start: 0.8309 (mp10) cc_final: 0.8032 (mp-120) REVERT: D 597 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 607 ASN cc_start: 0.8794 (t0) cc_final: 0.8350 (t0) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 1.6184 time to fit residues: 130.4691 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.088109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067845 restraints weight = 13162.467| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.83 r_work: 0.2781 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6669 Z= 0.314 Angle : 0.605 8.144 9058 Z= 0.306 Chirality : 0.045 0.219 951 Planarity : 0.004 0.052 1172 Dihedral : 5.193 56.984 932 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.45 % Allowed : 13.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 790 helix: 1.20 (0.26), residues: 390 sheet: -0.04 (0.63), residues: 59 loop : 0.30 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.005 0.001 HIS D 241 PHE 0.017 0.001 PHE D 369 TYR 0.016 0.001 TYR D 385 ARG 0.011 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.795 Fit side-chains REVERT: A 378 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8227 (mtpm) REVERT: A 386 LYS cc_start: 0.9392 (mttt) cc_final: 0.9032 (mtmm) REVERT: A 493 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8425 (mpt90) REVERT: D 171 GLU cc_start: 0.7980 (mp0) cc_final: 0.7579 (mp0) REVERT: D 471 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: D 472 GLN cc_start: 0.8366 (mp10) cc_final: 0.8074 (mp-120) REVERT: D 597 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8476 (tm-30) REVERT: D 607 ASN cc_start: 0.8791 (t0) cc_final: 0.8303 (t0) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 1.4140 time to fit residues: 120.1985 Evaluate side-chains 73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.090915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.071039 restraints weight = 13221.020| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.83 r_work: 0.2845 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6669 Z= 0.175 Angle : 0.564 8.894 9058 Z= 0.282 Chirality : 0.042 0.207 951 Planarity : 0.004 0.054 1172 Dihedral : 4.878 54.873 932 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.16 % Allowed : 14.27 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.30), residues: 790 helix: 1.33 (0.26), residues: 391 sheet: -0.10 (0.64), residues: 59 loop : 0.42 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.012 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8243 (mtpm) REVERT: A 386 LYS cc_start: 0.9396 (mttt) cc_final: 0.9082 (mmmm) REVERT: A 493 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8260 (mmm160) REVERT: D 142 LEU cc_start: 0.8510 (mt) cc_final: 0.8268 (mt) REVERT: D 171 GLU cc_start: 0.7989 (mp0) cc_final: 0.7540 (mp0) REVERT: D 471 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: D 472 GLN cc_start: 0.8240 (mp10) cc_final: 0.7849 (mp10) REVERT: D 597 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 607 ASN cc_start: 0.8730 (t0) cc_final: 0.8311 (t0) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 1.4953 time to fit residues: 122.7183 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.089756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069788 restraints weight = 13375.342| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.84 r_work: 0.2820 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6669 Z= 0.230 Angle : 0.599 8.704 9058 Z= 0.298 Chirality : 0.043 0.215 951 Planarity : 0.004 0.060 1172 Dihedral : 4.924 55.310 932 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 14.84 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 790 helix: 1.39 (0.26), residues: 391 sheet: -0.10 (0.63), residues: 59 loop : 0.39 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 594 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 493 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8199 (mmt180) REVERT: D 171 GLU cc_start: 0.7936 (mp0) cc_final: 0.7491 (mp0) REVERT: D 471 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: D 472 GLN cc_start: 0.8331 (mp10) cc_final: 0.7980 (mp-120) REVERT: D 597 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 607 ASN cc_start: 0.8700 (t0) cc_final: 0.8251 (t0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 1.3527 time to fit residues: 99.9028 Evaluate side-chains 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3314 r_free = 0.3314 target = 0.090639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.070531 restraints weight = 13426.556| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.87 r_work: 0.2836 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6669 Z= 0.194 Angle : 0.577 9.183 9058 Z= 0.286 Chirality : 0.042 0.213 951 Planarity : 0.004 0.062 1172 Dihedral : 4.811 54.966 932 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.87 % Allowed : 14.70 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.31), residues: 790 helix: 1.44 (0.26), residues: 391 sheet: -0.07 (0.63), residues: 59 loop : 0.44 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8176 (mtpm) REVERT: A 386 LYS cc_start: 0.9410 (mttt) cc_final: 0.8916 (mptt) REVERT: A 440 LYS cc_start: 0.9278 (mppt) cc_final: 0.8998 (mppt) REVERT: A 493 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8165 (mmm160) REVERT: A 496 SER cc_start: 0.8024 (m) cc_final: 0.7049 (p) REVERT: D 171 GLU cc_start: 0.7935 (mp0) cc_final: 0.7497 (mp0) REVERT: D 471 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: D 472 GLN cc_start: 0.8232 (mp10) cc_final: 0.7886 (mp-120) REVERT: D 479 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8549 (mt-10) REVERT: D 597 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 607 ASN cc_start: 0.8661 (t0) cc_final: 0.8298 (t0) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 1.4349 time to fit residues: 115.7826 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3289 r_free = 0.3289 target = 0.089186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.069100 restraints weight = 13511.410| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.87 r_work: 0.2805 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6669 Z= 0.261 Angle : 0.604 9.108 9058 Z= 0.302 Chirality : 0.044 0.222 951 Planarity : 0.004 0.065 1172 Dihedral : 4.964 55.875 932 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.73 % Allowed : 15.13 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.31), residues: 790 helix: 1.35 (0.26), residues: 392 sheet: -0.16 (0.62), residues: 59 loop : 0.41 (0.38), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.015 0.000 ARG D 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.98 seconds wall clock time: 76 minutes 39.73 seconds (4599.73 seconds total)