Starting phenix.real_space_refine on Wed Mar 12 01:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.map" model { file = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2025/7r11_14227.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4392 2.51 5 N 1131 2.21 5 O 1307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6870 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 587, 4795 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 587, 4795 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 bond proxies already assigned to first conformer: 4920 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1969 Classifications: {'peptide': 250} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 235} Chain breaks: 1 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: 7.37, per 1000 atoms: 1.07 Number of scatterers: 6870 At special positions: 0 Unit cell: (75.46, 95.942, 141.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 39 16.00 O 1307 8.00 N 1131 7.00 C 4392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG D 701 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 546 " " NAG D 706 " - " ASN D 90 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 374 " 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 51.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.841A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.535A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.169A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.562A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 4.175A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.528A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.676A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.476A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.162A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.589A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.520A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.553A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.692A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 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: 3.688A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.631A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.609A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.716A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.621A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.102A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.460A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.989A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.277A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.032A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.889A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.294A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.460A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 302 hydrogen bonds defined for protein. 855 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: 1.85 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2188 1.34 - 1.46: 1733 1.46 - 1.58: 3074 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 7055 Sorted by residual: bond pdb=" N ARG D 582 " pdb=" CA ARG D 582 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.21e+01 bond pdb=" N ASN D 580 " pdb=" CA ASN D 580 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.32e+00 bond pdb=" N VAL A 539 " pdb=" CA VAL A 539 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.14e-02 7.69e+03 9.14e+00 bond pdb=" N ILE D 54 " pdb=" CA ILE D 54 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N VAL D 581 " pdb=" CA VAL D 581 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.37e-02 5.33e+03 8.74e+00 ... (remaining 7050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 9206 1.23 - 2.45: 281 2.45 - 3.68: 85 3.68 - 4.90: 10 4.90 - 6.13: 6 Bond angle restraints: 9588 Sorted by residual: angle pdb=" CA THR D 55 " pdb=" C THR D 55 " pdb=" O THR D 55 " ideal model delta sigma weight residual 121.60 117.83 3.77 1.21e+00 6.83e-01 9.70e+00 angle pdb=" N GLN D 524 " pdb=" CA GLN D 524 " pdb=" C GLN D 524 " ideal model delta sigma weight residual 111.07 107.92 3.15 1.07e+00 8.73e-01 8.69e+00 angle pdb=" CA ASN D 53 " pdb=" CB ASN D 53 " pdb=" CG ASN D 53 " ideal model delta sigma weight residual 112.60 115.44 -2.84 1.00e+00 1.00e+00 8.08e+00 angle pdb=" N ARG D 245 " pdb=" CA ARG D 245 " pdb=" C ARG D 245 " ideal model delta sigma weight residual 111.07 108.07 3.00 1.07e+00 8.73e-01 7.85e+00 angle pdb=" CA ASN D 580 " pdb=" C ASN D 580 " pdb=" O ASN D 580 " ideal model delta sigma weight residual 121.06 117.85 3.21 1.16e+00 7.43e-01 7.68e+00 ... (remaining 9583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 3918 17.22 - 34.44: 280 34.44 - 51.66: 47 51.66 - 68.89: 14 68.89 - 86.11: 1 Dihedral angle restraints: 4260 sinusoidal: 1805 harmonic: 2455 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.76 -32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ILE D 223 " pdb=" C ILE D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N VAL D 581 " pdb=" CA VAL D 581 " pdb=" CB VAL D 581 " pdb=" CG1 VAL D 581 " ideal model delta sinusoidal sigma weight residual -60.00 -115.06 55.06 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 858 0.056 - 0.112: 152 0.112 - 0.167: 20 0.167 - 0.223: 5 0.223 - 0.279: 1 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA VAL A 551 " pdb=" N VAL A 551 " pdb=" C VAL A 551 " pdb=" CB VAL A 551 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASN D 53 " pdb=" N ASN D 53 " pdb=" C ASN D 53 " pdb=" CB ASN D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 539 " pdb=" CA VAL A 539 " pdb=" CG1 VAL A 539 " pdb=" CG2 VAL A 539 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1033 not shown) Planarity restraints: 1237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO D 146 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 262 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO D 263 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 263 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 263 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 32 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE D 32 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE D 32 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN D 33 " -0.009 2.00e-02 2.50e+03 ... (remaining 1234 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1596 2.79 - 3.32: 6369 3.32 - 3.84: 10763 3.84 - 4.37: 12074 4.37 - 4.90: 21571 Nonbonded interactions: 52373 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.261 3.040 nonbonded pdb=" O ASP D 431 " pdb=" OG1 THR D 434 " model vdw 2.289 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.329 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.333 3.040 ... (remaining 52368 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.580 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7055 Z= 0.224 Angle : 0.558 6.131 9588 Z= 0.308 Chirality : 0.046 0.279 1036 Planarity : 0.004 0.058 1230 Dihedral : 11.822 86.106 2660 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.54 % Allowed : 7.05 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.15 (0.29), residues: 830 helix: 1.00 (0.27), residues: 385 sheet: -0.19 (0.63), residues: 57 loop : -0.73 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.000 HIS D 374 PHE 0.010 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.003 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.764 Fit side-chains REVERT: D 168 TRP cc_start: 0.7965 (t-100) cc_final: 0.7462 (t-100) REVERT: D 223 ILE cc_start: 0.7665 (mt) cc_final: 0.6864 (mt) REVERT: D 300 GLN cc_start: 0.6498 (mm110) cc_final: 0.6021 (tm-30) REVERT: D 547 SER cc_start: 0.7753 (t) cc_final: 0.7487 (t) REVERT: A 428 ASP cc_start: 0.5576 (p0) cc_final: 0.5333 (p0) REVERT: A 578 ASP cc_start: 0.6644 (t0) cc_final: 0.6176 (t70) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.2234 time to fit residues: 38.2698 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 580 ASN ** 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 = 0.4155 r_free = 0.4155 target = 0.192616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160301 restraints weight = 8793.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158267 restraints weight = 14235.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160111 restraints weight = 12716.321| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7055 Z= 0.294 Angle : 0.637 12.683 9588 Z= 0.320 Chirality : 0.044 0.201 1036 Planarity : 0.005 0.054 1230 Dihedral : 6.419 59.332 1055 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.30 % Allowed : 10.70 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.04 (0.28), residues: 830 helix: 0.73 (0.26), residues: 392 sheet: -0.04 (0.62), residues: 58 loop : -0.77 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.003 0.001 HIS D 540 PHE 0.021 0.002 PHE D 327 TYR 0.026 0.002 TYR D 385 ARG 0.005 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: D 300 GLN cc_start: 0.6073 (mm110) cc_final: 0.5869 (tm-30) REVERT: A 584 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6249 (tt) outliers start: 17 outliers final: 2 residues processed: 103 average time/residue: 0.1966 time to fit residues: 27.5848 Evaluate side-chains 85 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.0170 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.196518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172394 restraints weight = 10855.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171892 restraints weight = 19332.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.173122 restraints weight = 15470.121| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7055 Z= 0.179 Angle : 0.554 8.983 9588 Z= 0.278 Chirality : 0.041 0.175 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.702 56.640 1055 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.22 % Allowed : 13.01 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 830 helix: 1.00 (0.26), residues: 391 sheet: -0.17 (0.61), residues: 63 loop : -0.66 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS D 374 PHE 0.018 0.001 PHE D 504 TYR 0.015 0.001 TYR D 385 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.773 Fit side-chains REVERT: D 376 MET cc_start: 0.7909 (mtt) cc_final: 0.7707 (mtp) REVERT: A 370 ASN cc_start: 0.6078 (OUTLIER) cc_final: 0.5784 (p0) REVERT: A 584 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6293 (tt) outliers start: 9 outliers final: 2 residues processed: 102 average time/residue: 0.1810 time to fit residues: 25.4127 Evaluate side-chains 87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS A 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.198110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174655 restraints weight = 17422.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172952 restraints weight = 27433.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.171614 restraints weight = 10625.427| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7055 Z= 0.193 Angle : 0.564 9.431 9588 Z= 0.284 Chirality : 0.042 0.179 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.391 57.462 1055 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.76 % Allowed : 13.69 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 830 helix: 1.00 (0.26), residues: 393 sheet: 0.20 (0.63), residues: 58 loop : -0.78 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 168 HIS 0.002 0.001 HIS D 374 PHE 0.017 0.001 PHE D 504 TYR 0.021 0.001 TYR D 50 ARG 0.004 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.702 Fit side-chains REVERT: D 376 MET cc_start: 0.7913 (mtt) cc_final: 0.7551 (mtp) REVERT: A 370 ASN cc_start: 0.6122 (OUTLIER) cc_final: 0.5822 (p0) REVERT: A 584 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6218 (tt) outliers start: 13 outliers final: 3 residues processed: 98 average time/residue: 0.1783 time to fit residues: 24.0421 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.192019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164655 restraints weight = 11071.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166156 restraints weight = 21107.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166117 restraints weight = 10859.247| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7055 Z= 0.254 Angle : 0.602 9.244 9588 Z= 0.304 Chirality : 0.044 0.331 1036 Planarity : 0.004 0.051 1230 Dihedral : 5.489 59.694 1055 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.36 % Allowed : 14.77 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.28), residues: 830 helix: 0.95 (0.27), residues: 388 sheet: -0.07 (0.62), residues: 63 loop : -0.85 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 168 HIS 0.002 0.001 HIS D 374 PHE 0.013 0.001 PHE D 504 TYR 0.021 0.002 TYR D 385 ARG 0.004 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: D 50 TYR cc_start: 0.6750 (t80) cc_final: 0.6463 (t80) REVERT: D 168 TRP cc_start: 0.7716 (t-100) cc_final: 0.7449 (t-100) REVERT: D 376 MET cc_start: 0.8013 (mtt) cc_final: 0.7752 (mtp) REVERT: A 370 ASN cc_start: 0.6128 (OUTLIER) cc_final: 0.5834 (p0) REVERT: A 472 ILE cc_start: 0.7549 (mt) cc_final: 0.7347 (mt) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.1885 time to fit residues: 24.6391 Evaluate side-chains 93 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161896 restraints weight = 11122.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164149 restraints weight = 20016.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165507 restraints weight = 11276.559| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7055 Z= 0.246 Angle : 0.596 8.204 9588 Z= 0.302 Chirality : 0.044 0.308 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.504 59.746 1055 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 14.50 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.01 (0.28), residues: 830 helix: 0.88 (0.26), residues: 389 sheet: -0.10 (0.62), residues: 63 loop : -0.89 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 PHE 0.018 0.001 PHE D 603 TYR 0.020 0.002 TYR D 385 ARG 0.004 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: D 168 TRP cc_start: 0.7896 (t-100) cc_final: 0.7654 (t-100) REVERT: A 370 ASN cc_start: 0.6116 (OUTLIER) cc_final: 0.5807 (p0) REVERT: A 472 ILE cc_start: 0.7549 (mt) cc_final: 0.7345 (mt) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.1757 time to fit residues: 23.7263 Evaluate side-chains 95 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 382 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170546 restraints weight = 21097.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.169258 restraints weight = 25065.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167720 restraints weight = 9285.479| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7055 Z= 0.284 Angle : 0.630 13.066 9588 Z= 0.317 Chirality : 0.044 0.293 1036 Planarity : 0.004 0.053 1230 Dihedral : 5.622 58.645 1055 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 14.23 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.15 (0.28), residues: 830 helix: 0.79 (0.26), residues: 389 sheet: -0.21 (0.61), residues: 63 loop : -0.99 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.012 0.002 PHE D 504 TYR 0.023 0.002 TYR D 385 ARG 0.003 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: D 168 TRP cc_start: 0.7879 (t-100) cc_final: 0.7653 (t-100) REVERT: A 370 ASN cc_start: 0.6152 (OUTLIER) cc_final: 0.5860 (p0) REVERT: A 472 ILE cc_start: 0.7578 (mt) cc_final: 0.7371 (mt) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.1779 time to fit residues: 24.4694 Evaluate side-chains 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.195984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172882 restraints weight = 15942.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171171 restraints weight = 24545.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.169540 restraints weight = 10240.898| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7055 Z= 0.179 Angle : 0.580 12.613 9588 Z= 0.288 Chirality : 0.042 0.277 1036 Planarity : 0.004 0.053 1230 Dihedral : 5.270 57.043 1055 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.08 % Allowed : 14.91 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.04 (0.28), residues: 830 helix: 1.00 (0.27), residues: 388 sheet: -0.27 (0.61), residues: 63 loop : -0.92 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS D 535 PHE 0.015 0.001 PHE D 504 TYR 0.018 0.001 TYR D 183 ARG 0.003 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: D 168 TRP cc_start: 0.7847 (t-100) cc_final: 0.7589 (t-100) REVERT: A 370 ASN cc_start: 0.5891 (OUTLIER) cc_final: 0.5633 (p0) REVERT: A 472 ILE cc_start: 0.7526 (mt) cc_final: 0.7320 (mt) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.1825 time to fit residues: 25.4141 Evaluate side-chains 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 46 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.195192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171511 restraints weight = 13543.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.169101 restraints weight = 23449.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167389 restraints weight = 10752.126| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7055 Z= 0.247 Angle : 0.619 13.752 9588 Z= 0.310 Chirality : 0.043 0.271 1036 Planarity : 0.004 0.056 1230 Dihedral : 5.462 59.509 1055 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.08 % Allowed : 14.77 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.03 (0.28), residues: 830 helix: 0.96 (0.27), residues: 384 sheet: -0.27 (0.61), residues: 63 loop : -0.96 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS D 374 PHE 0.032 0.001 PHE D 327 TYR 0.020 0.002 TYR D 385 ARG 0.006 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.7586 (mtp) cc_final: 0.7042 (mtp) REVERT: D 323 MET cc_start: 0.7372 (mmm) cc_final: 0.6479 (mmm) REVERT: A 472 ILE cc_start: 0.7572 (mt) cc_final: 0.7362 (mt) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1754 time to fit residues: 23.2017 Evaluate side-chains 92 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 75 optimal weight: 0.4980 chunk 4 optimal weight: 0.0070 chunk 20 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173802 restraints weight = 17488.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.174041 restraints weight = 25775.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.173458 restraints weight = 8803.758| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7055 Z= 0.160 Angle : 0.579 12.344 9588 Z= 0.288 Chirality : 0.041 0.274 1036 Planarity : 0.004 0.056 1230 Dihedral : 5.084 55.669 1055 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.81 % Allowed : 15.45 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.20 (0.29), residues: 830 helix: 1.20 (0.27), residues: 379 sheet: -0.31 (0.61), residues: 63 loop : -0.83 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS D 535 PHE 0.024 0.001 PHE D 327 TYR 0.017 0.001 TYR D 183 ARG 0.005 0.000 ARG D 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.7462 (mtp) cc_final: 0.7246 (mtp) REVERT: D 323 MET cc_start: 0.7081 (mmm) cc_final: 0.6185 (mmm) REVERT: A 386 LYS cc_start: 0.6798 (mmtm) cc_final: 0.5843 (pttt) REVERT: A 472 ILE cc_start: 0.7515 (mt) cc_final: 0.7287 (mt) outliers start: 6 outliers final: 5 residues processed: 91 average time/residue: 0.1694 time to fit residues: 21.9133 Evaluate side-chains 86 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain A residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** 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 = 0.4186 r_free = 0.4186 target = 0.196638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168401 restraints weight = 13217.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170411 restraints weight = 24220.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.169902 restraints weight = 10189.938| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7055 Z= 0.228 Angle : 0.627 12.872 9588 Z= 0.313 Chirality : 0.043 0.271 1036 Planarity : 0.005 0.111 1230 Dihedral : 5.300 57.904 1055 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.68 % Allowed : 15.99 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.15 (0.28), residues: 830 helix: 1.19 (0.27), residues: 376 sheet: -0.31 (0.61), residues: 63 loop : -0.89 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.034 0.002 PHE D 327 TYR 0.027 0.002 TYR D 50 ARG 0.005 0.001 ARG D 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.64 seconds wall clock time: 44 minutes 27.72 seconds (2667.72 seconds total)