Starting phenix.real_space_refine on Thu Jul 2 05:36:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_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_14227/07_2026/7r11_14227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r11_14227/07_2026/7r11_14227.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 chiralities: 2 Time building chain proxies: 2.54, per 1000 atoms: 0.37 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: 0.46 Conformation dependent library (CDL) restraints added in 691.7 milliseconds 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: 0.20 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: 1.04 Time building geometry restraints manager: 0.67 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: 3786 17.22 - 34.44: 277 34.44 - 51.66: 43 51.66 - 68.89: 6 68.89 - 86.11: 1 Dihedral angle restraints: 4113 sinusoidal: 1658 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 4110 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: 4.150 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.950 Find NCS groups from input model: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 7071 Z= 0.202 Angle : 0.563 6.131 9625 Z= 0.309 Chirality : 0.046 0.279 1036 Planarity : 0.004 0.058 1230 Dihedral : 11.599 86.106 2513 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG D 514 TYR 0.015 0.001 TYR D 385 PHE 0.010 0.001 PHE D 369 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.000 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 ( 7055) covalent geometry : angle 0.55752 / 0.31 ( 9588) SS BOND : bond 0.00192 / 0.14 ( 8) SS BOND : angle 0.64488 / 0.36 ( 16) hydrogen bonds : bond 0.14029 / 9.61 ( 302) hydrogen bonds : angle 5.23148 / 3.90 ( 855) metal coordination : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : bond 0.00471 / 0.23 ( 7) link_NAG-ASN : angle 1.80383 / 1.06 ( 21) *********************** 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 : 0.219 Fit side-chains REVERT: D 168 TRP cc_start: 0.7965 (t-100) cc_final: 0.7464 (t-100) REVERT: D 223 ILE cc_start: 0.7665 (mt) cc_final: 0.6865 (mt) REVERT: D 300 GLN cc_start: 0.6498 (mm110) cc_final: 0.6022 (tm-30) REVERT: D 547 SER cc_start: 0.7753 (t) cc_final: 0.7486 (t) REVERT: A 428 ASP cc_start: 0.5576 (p0) cc_final: 0.5334 (p0) REVERT: A 578 ASP cc_start: 0.6644 (t0) cc_final: 0.6175 (t70) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.0950 time to fit residues: 16.5077 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4185 r_free = 0.4185 target = 0.195872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.172174 restraints weight = 17447.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171470 restraints weight = 27148.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.170211 restraints weight = 9939.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.171779 restraints weight = 5983.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171997 restraints weight = 4471.134| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7071 Z= 0.144 Angle : 0.598 12.562 9625 Z= 0.296 Chirality : 0.043 0.173 1036 Planarity : 0.004 0.053 1230 Dihedral : 4.043 15.389 908 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.90 % Allowed : 10.98 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.29), residues: 830 helix: 0.99 (0.26), residues: 392 sheet: -0.03 (0.63), residues: 58 loop : -0.66 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.021 0.002 TYR D 50 PHE 0.020 0.001 PHE D 504 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7055) covalent geometry : angle 0.59245 / 0.29 ( 9588) SS BOND : bond 0.00239 / 0.12 ( 8) SS BOND : angle 1.16609 / 0.62 ( 16) hydrogen bonds : bond 0.04899 / 3.28 ( 302) hydrogen bonds : angle 4.44659 / 3.29 ( 855) metal coordination : bond 0.00117 / 0.06 ( 1) link_NAG-ASN : bond 0.00413 / 0.20 ( 7) link_NAG-ASN : angle 1.57398 / 1.02 ( 21) *********************** 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 105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: D 300 GLN cc_start: 0.6119 (mm110) cc_final: 0.5896 (tm-30) REVERT: A 584 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6287 (tt) outliers start: 14 outliers final: 1 residues processed: 101 average time/residue: 0.0822 time to fit residues: 11.2537 Evaluate side-chains 85 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU 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 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 6 optimal weight: 0.0000 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 GLN ** 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 = 0.4193 r_free = 0.4193 target = 0.197848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165305 restraints weight = 8914.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.163591 restraints weight = 16085.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165566 restraints weight = 14048.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165648 restraints weight = 8786.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166130 restraints weight = 8873.740| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7071 Z= 0.141 Angle : 0.565 8.117 9625 Z= 0.283 Chirality : 0.042 0.180 1036 Planarity : 0.004 0.052 1230 Dihedral : 3.997 15.170 908 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.22 % Allowed : 12.87 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.29), residues: 830 helix: 1.00 (0.26), residues: 391 sheet: 0.02 (0.62), residues: 58 loop : -0.70 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 306 TYR 0.020 0.001 TYR D 50 PHE 0.022 0.001 PHE A 486 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7055) covalent geometry : angle 0.56050 / 0.28 ( 9588) SS BOND : bond 0.00465 / 0.32 ( 8) SS BOND : angle 0.96426 / 0.52 ( 16) hydrogen bonds : bond 0.04794 / 3.17 ( 302) hydrogen bonds : angle 4.30215 / 3.17 ( 855) metal coordination : bond 0.00182 / 0.10 ( 1) link_NAG-ASN : bond 0.00398 / 0.19 ( 7) link_NAG-ASN : angle 1.44952 / 0.98 ( 21) *********************** 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 : 0.256 Fit side-chains REVERT: A 370 ASN cc_start: 0.6141 (OUTLIER) cc_final: 0.5838 (p0) REVERT: A 584 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6350 (tt) outliers start: 9 outliers final: 2 residues processed: 102 average time/residue: 0.0737 time to fit residues: 10.5517 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 chunk 40 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.198520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175486 restraints weight = 17357.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.173927 restraints weight = 26006.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172833 restraints weight = 10850.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.173303 restraints weight = 9137.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174370 restraints weight = 4989.407| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7071 Z= 0.108 Angle : 0.550 8.355 9625 Z= 0.272 Chirality : 0.041 0.161 1036 Planarity : 0.004 0.051 1230 Dihedral : 3.791 13.614 908 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.49 % Allowed : 13.55 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.29), residues: 830 helix: 1.16 (0.26), residues: 391 sheet: 0.23 (0.67), residues: 53 loop : -0.63 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.011 0.001 TYR D 385 PHE 0.018 0.001 PHE D 504 TRP 0.029 0.001 TRP D 168 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7055) covalent geometry : angle 0.54307 / 0.27 ( 9588) SS BOND : bond 0.00197 / 0.12 ( 8) SS BOND : angle 1.76645 / 0.92 ( 16) hydrogen bonds : bond 0.04078 / 2.66 ( 302) hydrogen bonds : angle 4.12175 / 3.06 ( 855) metal coordination : bond 0.00103 / 0.05 ( 1) link_NAG-ASN : bond 0.00395 / 0.19 ( 7) link_NAG-ASN : angle 1.30711 / 0.90 ( 21) *********************** 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 102 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.206 Fit side-chains REVERT: D 50 TYR cc_start: 0.6838 (t80) cc_final: 0.6571 (t80) REVERT: D 323 MET cc_start: 0.7738 (mmt) cc_final: 0.7493 (mpp) REVERT: A 370 ASN cc_start: 0.6025 (OUTLIER) cc_final: 0.5724 (p0) REVERT: A 584 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6284 (tt) outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.0654 time to fit residues: 9.1644 Evaluate side-chains 92 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4167 r_free = 0.4167 target = 0.194004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161364 restraints weight = 20851.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163199 restraints weight = 25383.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163199 restraints weight = 11909.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163199 restraints weight = 11909.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163199 restraints weight = 11909.001| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7071 Z= 0.170 Angle : 0.599 8.058 9625 Z= 0.302 Chirality : 0.043 0.158 1036 Planarity : 0.004 0.050 1230 Dihedral : 4.076 16.212 908 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.76 % Allowed : 13.82 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 830 helix: 0.95 (0.26), residues: 388 sheet: 0.53 (0.67), residues: 48 loop : -0.82 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 306 TYR 0.023 0.002 TYR D 385 PHE 0.019 0.002 PHE A 486 TRP 0.033 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 7055) covalent geometry : angle 0.59411 / 0.30 ( 9588) SS BOND : bond 0.00341 / 0.20 ( 8) SS BOND : angle 0.90870 / 0.50 ( 16) hydrogen bonds : bond 0.04990 / 3.24 ( 302) hydrogen bonds : angle 4.33329 / 3.19 ( 855) metal coordination : bond 0.00152 / 0.08 ( 1) link_NAG-ASN : bond 0.00403 / 0.19 ( 7) link_NAG-ASN : angle 1.57795 / 1.06 ( 21) *********************** 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 101 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.205 Fit side-chains REVERT: D 50 TYR cc_start: 0.6886 (t80) cc_final: 0.6604 (t80) REVERT: A 370 ASN cc_start: 0.6416 (OUTLIER) cc_final: 0.6076 (p0) REVERT: A 578 ASP cc_start: 0.7230 (t0) cc_final: 0.6888 (t70) outliers start: 13 outliers final: 5 residues processed: 98 average time/residue: 0.0730 time to fit residues: 9.7696 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 : 0.194 ------------------------------------------------------------------------------- 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 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 67 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4171 r_free = 0.4171 target = 0.194549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171065 restraints weight = 10919.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170331 restraints weight = 20631.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168929 restraints weight = 12993.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168105 restraints weight = 10140.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169368 restraints weight = 8566.925| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7071 Z= 0.150 Angle : 0.588 8.456 9625 Z= 0.294 Chirality : 0.042 0.157 1036 Planarity : 0.004 0.039 1230 Dihedral : 4.016 15.747 908 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.36 % Allowed : 14.23 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 830 helix: 0.97 (0.26), residues: 388 sheet: 0.26 (0.66), residues: 53 loop : -0.81 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.019 0.001 TYR D 385 PHE 0.017 0.001 PHE A 486 TRP 0.058 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7055) covalent geometry : angle 0.58358 / 0.29 ( 9588) SS BOND : bond 0.00262 / 0.14 ( 8) SS BOND : angle 0.82048 / 0.46 ( 16) hydrogen bonds : bond 0.04692 / 3.05 ( 302) hydrogen bonds : angle 4.28864 / 3.17 ( 855) metal coordination : bond 0.00207 / 0.11 ( 1) link_NAG-ASN : bond 0.00416 / 0.20 ( 7) link_NAG-ASN : angle 1.49764 / 1.01 ( 21) *********************** 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 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.305 Fit side-chains REVERT: D 50 TYR cc_start: 0.7028 (t80) cc_final: 0.6699 (t80) REVERT: A 370 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5759 (p0) REVERT: A 472 ILE cc_start: 0.7468 (mt) cc_final: 0.7252 (mt) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.0706 time to fit residues: 9.4163 Evaluate side-chains 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 0.0050 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4169 r_free = 0.4169 target = 0.194114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162702 restraints weight = 10870.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.162953 restraints weight = 19490.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164765 restraints weight = 14802.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165141 restraints weight = 8936.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165997 restraints weight = 7855.740| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- 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 = 0.36 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7071 Z= 0.150 Angle : 0.591 8.827 9625 Z= 0.296 Chirality : 0.044 0.347 1036 Planarity : 0.004 0.049 1230 Dihedral : 4.024 15.575 908 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.90 % Allowed : 13.69 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 830 helix: 0.94 (0.26), residues: 389 sheet: 0.49 (0.66), residues: 48 loop : -0.88 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.019 0.001 TYR D 385 PHE 0.015 0.001 PHE D 327 TRP 0.046 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7055) covalent geometry : angle 0.58680 / 0.29 ( 9588) SS BOND : bond 0.00266 / 0.13 ( 8) SS BOND : angle 0.78395 / 0.44 ( 16) hydrogen bonds : bond 0.04730 / 3.06 ( 302) hydrogen bonds : angle 4.27214 / 3.16 ( 855) metal coordination : bond 0.00207 / 0.11 ( 1) link_NAG-ASN : bond 0.00424 / 0.20 ( 7) link_NAG-ASN : angle 1.46578 / 1.00 ( 21) *********************** 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: 14 poor density : 87 time to evaluate : 0.305 Fit side-chains REVERT: A 370 ASN cc_start: 0.6095 (OUTLIER) cc_final: 0.5805 (p0) REVERT: A 472 ILE cc_start: 0.7504 (mt) cc_final: 0.7291 (mt) REVERT: A 578 ASP cc_start: 0.6718 (t0) cc_final: 0.6488 (t70) outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.0781 time to fit residues: 10.7862 Evaluate side-chains 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4169 r_free = 0.4169 target = 0.194197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174911 restraints weight = 16090.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.168512 restraints weight = 21258.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165393 restraints weight = 20646.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.166696 restraints weight = 14910.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167869 restraints weight = 10311.540| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7071 Z= 0.157 Angle : 0.614 13.044 9625 Z= 0.305 Chirality : 0.044 0.340 1036 Planarity : 0.004 0.050 1230 Dihedral : 4.060 16.537 908 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 13.55 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 830 helix: 0.92 (0.26), residues: 389 sheet: -0.36 (0.63), residues: 56 loop : -0.84 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 161 TYR 0.019 0.001 TYR D 385 PHE 0.015 0.001 PHE D 327 TRP 0.039 0.002 TRP D 168 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7055) covalent geometry : angle 0.61073 / 0.30 ( 9588) SS BOND : bond 0.00293 / 0.15 ( 8) SS BOND : angle 0.77810 / 0.44 ( 16) hydrogen bonds : bond 0.04824 / 3.16 ( 302) hydrogen bonds : angle 4.28605 / 3.15 ( 855) metal coordination : bond 0.00175 / 0.09 ( 1) link_NAG-ASN : bond 0.00433 / 0.21 ( 7) link_NAG-ASN : angle 1.47456 / 1.01 ( 21) *********************** 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 99 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 370 ASN cc_start: 0.6071 (OUTLIER) cc_final: 0.5782 (p0) REVERT: A 472 ILE cc_start: 0.7493 (mt) cc_final: 0.7281 (mt) REVERT: A 578 ASP cc_start: 0.6584 (t0) cc_final: 0.6382 (t70) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.0752 time to fit residues: 10.2128 Evaluate side-chains 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 203 TRP 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 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4159 r_free = 0.4159 target = 0.193176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172274 restraints weight = 13344.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167245 restraints weight = 24216.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162400 restraints weight = 12970.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163107 restraints weight = 14124.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164703 restraints weight = 8178.939| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7071 Z= 0.176 Angle : 0.641 14.614 9625 Z= 0.317 Chirality : 0.044 0.332 1036 Planarity : 0.004 0.050 1230 Dihedral : 4.149 16.063 908 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.22 % Allowed : 14.09 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.28), residues: 830 helix: 0.85 (0.26), residues: 388 sheet: -0.42 (0.64), residues: 56 loop : -0.96 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 161 TYR 0.022 0.002 TYR D 50 PHE 0.018 0.002 PHE D 327 TRP 0.037 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 7055) covalent geometry : angle 0.63695 / 0.32 ( 9588) SS BOND : bond 0.00318 / 0.15 ( 8) SS BOND : angle 0.90598 / 0.50 ( 16) hydrogen bonds : bond 0.05087 / 3.33 ( 302) hydrogen bonds : angle 4.37602 / 3.23 ( 855) metal coordination : bond 0.00207 / 0.11 ( 1) link_NAG-ASN : bond 0.00447 / 0.21 ( 7) link_NAG-ASN : angle 1.52691 / 1.04 ( 21) *********************** 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 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 370 ASN cc_start: 0.6199 (OUTLIER) cc_final: 0.5875 (p0) REVERT: A 472 ILE cc_start: 0.7507 (mt) cc_final: 0.7305 (mt) REVERT: A 578 ASP cc_start: 0.6751 (t0) cc_final: 0.6399 (t70) outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.0755 time to fit residues: 9.9337 Evaluate side-chains 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 203 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4172 r_free = 0.4172 target = 0.195369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172348 restraints weight = 16359.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169487 restraints weight = 25277.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168015 restraints weight = 10429.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169369 restraints weight = 6754.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169742 restraints weight = 4933.657| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7071 Z= 0.169 Angle : 0.637 14.129 9625 Z= 0.315 Chirality : 0.044 0.325 1036 Planarity : 0.004 0.050 1230 Dihedral : 4.174 16.002 908 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.36 % Allowed : 14.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 830 helix: 0.78 (0.26), residues: 389 sheet: -0.51 (0.63), residues: 56 loop : -1.00 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 161 TYR 0.023 0.002 TYR D 50 PHE 0.017 0.001 PHE D 327 TRP 0.033 0.002 TRP D 168 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7055) covalent geometry : angle 0.63282 / 0.31 ( 9588) SS BOND : bond 0.00296 / 0.14 ( 8) SS BOND : angle 0.84424 / 0.47 ( 16) hydrogen bonds : bond 0.05008 / 3.27 ( 302) hydrogen bonds : angle 4.36913 / 3.23 ( 855) metal coordination : bond 0.00193 / 0.10 ( 1) link_NAG-ASN : bond 0.00458 / 0.22 ( 7) link_NAG-ASN : angle 1.52402 / 1.03 ( 21) ********************** 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 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 370 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5714 (p0) REVERT: A 386 LYS cc_start: 0.6956 (mmtm) cc_final: 0.5885 (pttt) REVERT: A 472 ILE cc_start: 0.7534 (mt) cc_final: 0.7329 (mt) REVERT: A 578 ASP cc_start: 0.6681 (t0) cc_final: 0.6374 (t70) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.0746 time to fit residues: 10.1842 Evaluate side-chains 93 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 203 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4179 r_free = 0.4179 target = 0.195118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171734 restraints weight = 11363.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171215 restraints weight = 20415.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.171501 restraints weight = 14294.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171425 restraints weight = 9090.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171578 restraints weight = 8531.020| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7071 Z= 0.136 Angle : 0.616 13.561 9625 Z= 0.304 Chirality : 0.043 0.322 1036 Planarity : 0.004 0.052 1230 Dihedral : 4.046 15.231 908 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 14.63 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.28), residues: 830 helix: 0.92 (0.26), residues: 384 sheet: -0.33 (0.60), residues: 63 loop : -1.01 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 161 TYR 0.024 0.001 TYR D 50 PHE 0.025 0.001 PHE D 603 TRP 0.036 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7055) covalent geometry : angle 0.61313 / 0.30 ( 9588) SS BOND : bond 0.00218 / 0.11 ( 8) SS BOND : angle 0.79465 / 0.45 ( 16) hydrogen bonds : bond 0.04598 / 3.00 ( 302) hydrogen bonds : angle 4.27197 / 3.16 ( 855) metal coordination : bond 0.00136 / 0.07 ( 1) link_NAG-ASN : bond 0.00455 / 0.22 ( 7) link_NAG-ASN : angle 1.42115 / 0.97 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.34 seconds wall clock time: 24 minutes 5.78 seconds (1445.78 seconds total)