Starting phenix.real_space_refine on Tue Mar 3 16:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r11_14227/03_2026/7r11_14227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r11_14227/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2026/7r11_14227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2026/7r11_14227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2026/7r11_14227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r11_14227/03_2026/7r11_14227.map" } 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-5986/lib/python3.9/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 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: 1.88, per 1000 atoms: 0.27 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: 0.49 Conformation dependent library (CDL) restraints added in 263.9 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: 0.15 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: 0.94 Time building geometry restraints manager: 0.61 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: 2.610 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.610 Find NCS groups from input model: 0.020 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- 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 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 : 11.822 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 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 covalent geometry : bond 0.00358 ( 7055) covalent geometry : angle 0.55752 ( 9588) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.64488 ( 16) hydrogen bonds : bond 0.14029 ( 302) hydrogen bonds : angle 5.23148 ( 855) metal coordination : bond 0.00116 ( 1) link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 1.80383 ( 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: 0.0859 time to fit residues: 14.8454 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 : 0.260 ------------------------------------------------------------------------------- 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... 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 = 0.4185 r_free = 0.4185 target = 0.195862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171754 restraints weight = 17458.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.171469 restraints weight = 27556.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.170173 restraints weight = 10039.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.171734 restraints weight = 6042.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.171961 restraints weight = 4474.326| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 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 = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1319 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= 0.147 Angle : 0.599 12.745 9625 Z= 0.296 Chirality : 0.042 0.188 1036 Planarity : 0.004 0.053 1230 Dihedral : 6.203 57.503 1055 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.63 % Allowed : 11.25 % 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: 0.23 (0.29), residues: 830 helix: 1.00 (0.26), residues: 392 sheet: -0.02 (0.63), residues: 58 loop : -0.66 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 457 TYR 0.022 0.002 TYR D 50 PHE 0.019 0.001 PHE D 504 TRP 0.015 0.002 TRP A 436 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7055) covalent geometry : angle 0.59285 ( 9588) SS BOND : bond 0.00310 ( 8) SS BOND : angle 1.21788 ( 16) hydrogen bonds : bond 0.04960 ( 302) hydrogen bonds : angle 4.45804 ( 855) metal coordination : bond 0.00120 ( 1) link_NAG-ASN : bond 0.00431 ( 7) link_NAG-ASN : angle 1.62380 ( 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 107 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: D 300 GLN cc_start: 0.6086 (mm110) cc_final: 0.5859 (tm-30) REVERT: A 584 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6156 (tt) outliers start: 12 outliers final: 1 residues processed: 103 average time/residue: 0.0710 time to fit residues: 9.7992 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 : 0.226 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 77 optimal weight: 0.0020 chunk 6 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4217 r_free = 0.4217 target = 0.200496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167602 restraints weight = 8885.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164951 restraints weight = 14969.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167296 restraints weight = 13014.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167191 restraints weight = 8638.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168168 restraints weight = 8151.175| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1640 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= 0.115 Angle : 0.552 9.055 9625 Z= 0.275 Chirality : 0.041 0.174 1036 Planarity : 0.004 0.049 1230 Dihedral : 5.509 55.665 1055 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 12.47 % Favored : 86.04 % 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: 1.15 (0.26), residues: 391 sheet: 0.17 (0.66), residues: 53 loop : -0.59 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.021 0.001 TYR D 50 PHE 0.024 0.001 PHE A 486 TRP 0.014 0.001 TRP D 168 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7055) covalent geometry : angle 0.54571 ( 9588) SS BOND : bond 0.00202 ( 8) SS BOND : angle 1.68967 ( 16) hydrogen bonds : bond 0.04291 ( 302) hydrogen bonds : angle 4.20556 ( 855) metal coordination : bond 0.00074 ( 1) link_NAG-ASN : bond 0.00410 ( 7) link_NAG-ASN : angle 1.32161 ( 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: 11 poor density : 92 time to evaluate : 0.248 Fit side-chains REVERT: A 370 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5713 (p0) REVERT: A 584 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6319 (tt) outliers start: 11 outliers final: 2 residues processed: 102 average time/residue: 0.0691 time to fit residues: 9.8540 Evaluate side-chains 86 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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: 0.0670 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 40 optimal weight: 0.0370 chunk 37 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.1172 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.203354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180356 restraints weight = 17770.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.179282 restraints weight = 25656.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178330 restraints weight = 9190.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.180440 restraints weight = 5576.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181300 restraints weight = 4083.645| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7071 Z= 0.103 Angle : 0.526 8.271 9625 Z= 0.261 Chirality : 0.040 0.169 1036 Planarity : 0.004 0.048 1230 Dihedral : 4.981 55.012 1055 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 13.41 % Favored : 85.50 % 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: 0.54 (0.29), residues: 830 helix: 1.31 (0.27), residues: 391 sheet: 0.42 (0.67), residues: 48 loop : -0.60 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.008 0.001 TYR D 385 PHE 0.019 0.001 PHE D 504 TRP 0.023 0.001 TRP D 168 HIS 0.002 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7055) covalent geometry : angle 0.52381 ( 9588) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.58825 ( 16) hydrogen bonds : bond 0.03755 ( 302) hydrogen bonds : angle 3.99229 ( 855) metal coordination : bond 0.00044 ( 1) link_NAG-ASN : bond 0.00385 ( 7) link_NAG-ASN : angle 1.22423 ( 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 93 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.253 Fit side-chains REVERT: D 297 MET cc_start: 0.7013 (mtm) cc_final: 0.6744 (mtp) REVERT: A 584 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6249 (tt) outliers start: 8 outliers final: 1 residues processed: 92 average time/residue: 0.0709 time to fit residues: 9.1048 Evaluate side-chains 81 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 LEU 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: 0.0470 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.200765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177180 restraints weight = 21185.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.175921 restraints weight = 26794.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.174650 restraints weight = 10167.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.176042 restraints weight = 5698.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.176006 restraints weight = 4340.868| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7071 Z= 0.121 Angle : 0.544 8.246 9625 Z= 0.272 Chirality : 0.041 0.172 1036 Planarity : 0.004 0.050 1230 Dihedral : 5.027 56.439 1055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.81 % Allowed : 14.36 % Favored : 84.82 % 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: 0.48 (0.29), residues: 830 helix: 1.25 (0.27), residues: 394 sheet: 0.17 (0.69), residues: 50 loop : -0.60 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.022 0.001 TYR D 50 PHE 0.015 0.001 PHE D 504 TRP 0.026 0.001 TRP D 168 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7055) covalent geometry : angle 0.54071 ( 9588) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.69466 ( 16) hydrogen bonds : bond 0.04151 ( 302) hydrogen bonds : angle 4.02299 ( 855) metal coordination : bond 0.00089 ( 1) link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 1.30223 ( 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 86 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.208 Fit side-chains REVERT: A 584 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6263 (tt) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.0722 time to fit residues: 8.4785 Evaluate side-chains 81 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.194264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169424 restraints weight = 10914.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168418 restraints weight = 19199.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169343 restraints weight = 16162.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169160 restraints weight = 9382.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170386 restraints weight = 8820.016| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 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 = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7071 Z= 0.169 Angle : 0.597 9.067 9625 Z= 0.300 Chirality : 0.043 0.169 1036 Planarity : 0.004 0.054 1230 Dihedral : 5.389 59.975 1055 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.95 % Allowed : 14.91 % 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 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: 0.17 (0.28), residues: 830 helix: 0.96 (0.26), residues: 394 sheet: 0.11 (0.72), residues: 46 loop : -0.72 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 306 TYR 0.022 0.002 TYR D 385 PHE 0.017 0.002 PHE D 327 TRP 0.020 0.002 TRP D 168 HIS 0.002 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7055) covalent geometry : angle 0.59255 ( 9588) SS BOND : bond 0.00375 ( 8) SS BOND : angle 0.87713 ( 16) hydrogen bonds : bond 0.04950 ( 302) hydrogen bonds : angle 4.25646 ( 855) metal coordination : bond 0.00119 ( 1) link_NAG-ASN : bond 0.00403 ( 7) link_NAG-ASN : angle 1.50603 ( 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 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.192 Fit side-chains REVERT: A 472 ILE cc_start: 0.7463 (mt) cc_final: 0.7252 (mt) REVERT: A 584 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6185 (tt) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.0771 time to fit residues: 9.5318 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.194816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164273 restraints weight = 10895.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166271 restraints weight = 19682.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167287 restraints weight = 12024.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167337 restraints weight = 8141.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168248 restraints weight = 7236.189| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7071 Z= 0.150 Angle : 0.592 12.960 9625 Z= 0.293 Chirality : 0.042 0.170 1036 Planarity : 0.004 0.050 1230 Dihedral : 5.317 58.581 1055 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.36 % Allowed : 14.36 % 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: 0.13 (0.28), residues: 830 helix: 0.94 (0.26), residues: 394 sheet: 0.04 (0.71), residues: 46 loop : -0.75 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.020 0.002 TYR D 385 PHE 0.014 0.001 PHE D 327 TRP 0.030 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7055) covalent geometry : angle 0.58898 ( 9588) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.78573 ( 16) hydrogen bonds : bond 0.04666 ( 302) hydrogen bonds : angle 4.23387 ( 855) metal coordination : bond 0.00101 ( 1) link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 1.42672 ( 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 92 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.261 Fit side-chains REVERT: D 94 LYS cc_start: 0.8330 (tttt) cc_final: 0.8112 (ttmm) REVERT: A 472 ILE cc_start: 0.7482 (mt) cc_final: 0.7276 (mt) REVERT: A 584 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6230 (tt) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.0740 time to fit residues: 9.5210 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 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 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 584 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.198638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175228 restraints weight = 16367.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.172923 restraints weight = 25333.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171235 restraints weight = 9656.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.172567 restraints weight = 6226.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172911 restraints weight = 4788.632| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7071 Z= 0.127 Angle : 0.582 13.954 9625 Z= 0.284 Chirality : 0.041 0.164 1036 Planarity : 0.004 0.040 1230 Dihedral : 5.135 56.987 1055 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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 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: 0.19 (0.28), residues: 830 helix: 0.99 (0.26), residues: 393 sheet: 0.04 (0.71), residues: 46 loop : -0.72 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.019 0.001 TYR D 50 PHE 0.014 0.001 PHE D 504 TRP 0.055 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7055) covalent geometry : angle 0.57875 ( 9588) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.67119 ( 16) hydrogen bonds : bond 0.04330 ( 302) hydrogen bonds : angle 4.14511 ( 855) metal coordination : bond 0.00071 ( 1) link_NAG-ASN : bond 0.00418 ( 7) link_NAG-ASN : angle 1.32751 ( 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 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.243 Fit side-chains REVERT: D 376 MET cc_start: 0.7940 (mtt) cc_final: 0.7740 (mtp) REVERT: A 472 ILE cc_start: 0.7432 (mt) cc_final: 0.7223 (mt) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.0742 time to fit residues: 9.4843 Evaluate side-chains 90 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.197493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172140 restraints weight = 13509.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.170182 restraints weight = 22685.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.168347 restraints weight = 10912.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169148 restraints weight = 9255.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170191 restraints weight = 5903.192| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 0.048 7071 Z= 0.148 Angle : 0.606 13.889 9625 Z= 0.300 Chirality : 0.042 0.164 1036 Planarity : 0.004 0.048 1230 Dihedral : 5.276 58.430 1055 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.36 % Allowed : 15.18 % Favored : 83.47 % 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: 394 sheet: 0.03 (0.71), residues: 46 loop : -0.76 (0.30), residues: 390 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 0.013 0.001 PHE D 504 TRP 0.051 0.002 TRP D 168 HIS 0.002 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7055) covalent geometry : angle 0.60281 ( 9588) SS BOND : bond 0.00269 ( 8) SS BOND : angle 0.73170 ( 16) hydrogen bonds : bond 0.04661 ( 302) hydrogen bonds : angle 4.21662 ( 855) metal coordination : bond 0.00144 ( 1) link_NAG-ASN : bond 0.00420 ( 7) link_NAG-ASN : angle 1.39637 ( 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 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.247 Fit side-chains REVERT: D 183 TYR cc_start: 0.8143 (t80) cc_final: 0.7939 (t80) REVERT: A 472 ILE cc_start: 0.7481 (mt) cc_final: 0.7272 (mt) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.0743 time to fit residues: 9.8155 Evaluate side-chains 93 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 18 optimal weight: 0.0040 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 overall best weight: 0.2868 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.196826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171553 restraints weight = 15986.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.171915 restraints weight = 27590.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171133 restraints weight = 9501.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.172486 restraints weight = 6215.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.172760 restraints weight = 4689.327| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7071 Z= 0.126 Angle : 0.587 13.279 9625 Z= 0.291 Chirality : 0.042 0.165 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.153 56.899 1055 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.08 % Allowed : 15.04 % 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 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: 0.24 (0.28), residues: 830 helix: 1.12 (0.27), residues: 387 sheet: -0.35 (0.64), residues: 56 loop : -0.72 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.017 0.001 TYR D 50 PHE 0.024 0.001 PHE D 603 TRP 0.047 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7055) covalent geometry : angle 0.58452 ( 9588) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.63261 ( 16) hydrogen bonds : bond 0.04307 ( 302) hydrogen bonds : angle 4.10716 ( 855) metal coordination : bond 0.00129 ( 1) link_NAG-ASN : bond 0.00424 ( 7) link_NAG-ASN : angle 1.31122 ( 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 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.242 Fit side-chains REVERT: A 386 LYS cc_start: 0.6827 (mmtm) cc_final: 0.5737 (pttt) REVERT: A 472 ILE cc_start: 0.7436 (mt) cc_final: 0.7224 (mt) outliers start: 8 outliers final: 8 residues processed: 90 average time/residue: 0.0765 time to fit residues: 9.6362 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 324 THR 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 68 optimal weight: 0.3980 chunk 37 optimal weight: 0.0000 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 overall best weight: 0.2584 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.199727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167790 restraints weight = 11497.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169334 restraints weight = 20245.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171457 restraints weight = 12664.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171751 restraints weight = 7679.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172965 restraints weight = 6547.886| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2539 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= 0.123 Angle : 0.581 12.925 9625 Z= 0.288 Chirality : 0.041 0.164 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.055 56.405 1055 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.95 % Allowed : 15.18 % 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 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: 0.36 (0.28), residues: 830 helix: 1.27 (0.27), residues: 381 sheet: 0.09 (0.62), residues: 57 loop : -0.75 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 219 TYR 0.017 0.001 TYR D 50 PHE 0.014 0.001 PHE D 504 TRP 0.044 0.001 TRP D 168 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7055) covalent geometry : angle 0.57887 ( 9588) SS BOND : bond 0.00186 ( 8) SS BOND : angle 0.65479 ( 16) hydrogen bonds : bond 0.04144 ( 302) hydrogen bonds : angle 4.04361 ( 855) metal coordination : bond 0.00087 ( 1) link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 1.26316 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.39 seconds wall clock time: 22 minutes 24.55 seconds (1344.55 seconds total)