Starting phenix.real_space_refine on Wed Mar 4 03:33:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd8_27336/03_2026/8dd8_27336.cif" } resolution = 3.4 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6683 2.51 5 N 1810 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 10492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8265 Classifications: {'peptide': 1011} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 963} Chain breaks: 3 Chain: "B" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2227 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 256} Chain breaks: 2 Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10492 At special positions: 0 Unit cell: (89.024, 109.824, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1924 8.00 N 1810 7.00 C 6683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 495.7 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 48.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.660A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.540A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 133 through 154 removed outlier: 3.580A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.726A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.888A pdb=" N ARG A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 removed outlier: 3.747A pdb=" N VAL A 243 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 245 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.501A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.705A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.631A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.668A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.725A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 723 removed outlier: 4.487A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 863 removed outlier: 4.021A pdb=" N LYS A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 974 through 994 Processing helix chain 'A' and resid 994 through 1006 removed outlier: 3.979A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.808A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1026 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.545A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.005A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 504 removed outlier: 3.796A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 565 removed outlier: 3.872A pdb=" N MET B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 526 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.699A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 593 through 598 removed outlier: 4.263A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 3.709A pdb=" N MET A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 34 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 101 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 4.005A pdb=" N GLN A 205 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 288 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.084A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.853A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.594A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.594A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.857A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 381 removed outlier: 3.655A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1338 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: 1.82 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3437 1.35 - 1.46: 2385 1.46 - 1.58: 4776 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10715 Sorted by residual: bond pdb=" CB CYS A 901 " pdb=" SG CYS A 901 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG1 ILE A1022 " pdb=" CD1 ILE A1022 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CG LEU A 327 " pdb=" CD1 LEU A 327 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CA ILE A 197 " pdb=" CB ILE A 197 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.60e-01 bond pdb=" CG LEU A 929 " pdb=" CD2 LEU A 929 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.32e-01 ... (remaining 10710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 14261 2.18 - 4.35: 153 4.35 - 6.53: 28 6.53 - 8.70: 4 8.70 - 10.88: 1 Bond angle restraints: 14447 Sorted by residual: angle pdb=" CB MET A 489 " pdb=" CG MET A 489 " pdb=" SD MET A 489 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C LYS B 419 " pdb=" N LEU B 420 " pdb=" CA LEU B 420 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.97e+00 angle pdb=" C VAL A 196 " pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 121.97 126.99 -5.02 1.80e+00 3.09e-01 7.77e+00 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 108.07 110.28 -2.21 8.90e-01 1.26e+00 6.17e+00 angle pdb=" C LEU A 234 " pdb=" N SER A 235 " pdb=" CA SER A 235 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.07e+00 ... (remaining 14442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5632 16.67 - 33.35: 716 33.35 - 50.02: 157 50.02 - 66.69: 32 66.69 - 83.36: 16 Dihedral angle restraints: 6553 sinusoidal: 2801 harmonic: 3752 Sorted by residual: dihedral pdb=" CA ALA A 775 " pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 560 " pdb=" CB ASP B 560 " pdb=" CG ASP B 560 " pdb=" OD1 ASP B 560 " ideal model delta sinusoidal sigma weight residual -30.00 -87.52 57.52 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP B 367 " pdb=" C ASP B 367 " pdb=" N TYR B 368 " pdb=" CA TYR B 368 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1059 0.039 - 0.078: 372 0.078 - 0.118: 104 0.118 - 0.157: 22 0.157 - 0.196: 1 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 216 " pdb=" N VAL A 216 " pdb=" C VAL A 216 " pdb=" CB VAL A 216 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CG LEU A 956 " pdb=" CB LEU A 956 " pdb=" CD1 LEU A 956 " pdb=" CD2 LEU A 956 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 1555 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 16 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO A 17 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 217 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 420 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 421 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.026 5.00e-02 4.00e+02 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1145 2.75 - 3.29: 10361 3.29 - 3.82: 17182 3.82 - 4.36: 20438 4.36 - 4.90: 35207 Nonbonded interactions: 84333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 970 " pdb=" OG1 THR A 972 " model vdw 2.211 3.040 nonbonded pdb=" O GLN B 497 " pdb=" OG1 THR B 500 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN A 157 " pdb=" OG SER A 161 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 432 " model vdw 2.291 3.040 nonbonded pdb=" NH2 ARG A 916 " pdb=" O ASP A 933 " model vdw 2.292 3.120 ... (remaining 84328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.140 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.003 0.042 10715 Z= 0.147 Angle : 0.600 10.879 14447 Z= 0.300 Chirality : 0.044 0.196 1558 Planarity : 0.004 0.063 1854 Dihedral : 15.623 83.365 4119 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.65 (0.22), residues: 1258 helix: 0.30 (0.22), residues: 520 sheet: -0.20 (0.43), residues: 141 loop : -1.11 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.014 0.001 TYR B 508 PHE 0.012 0.001 PHE A 954 TRP 0.017 0.001 TRP A 780 HIS 0.015 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00349 (10715) covalent geometry : angle 0.59992 (14447) hydrogen bonds : bond 0.19768 ( 461) hydrogen bonds : angle 6.73188 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.406 Fit side-chains REVERT: A 216 VAL cc_start: 0.8536 (t) cc_final: 0.8293 (t) REVERT: A 599 MET cc_start: 0.8164 (ttp) cc_final: 0.7946 (ttp) REVERT: A 961 LEU cc_start: 0.7271 (mm) cc_final: 0.6972 (mt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0954 time to fit residues: 14.4417 Evaluate side-chains 89 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 676 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.128703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102183 restraints weight = 21928.312| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.82 r_work: 0.3172 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10715 Z= 0.146 Angle : 0.534 6.677 14447 Z= 0.281 Chirality : 0.042 0.155 1558 Planarity : 0.004 0.058 1854 Dihedral : 4.131 17.490 1393 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 0.26 % Allowed : 5.64 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 0.83 (0.22), residues: 550 sheet: -0.31 (0.42), residues: 141 loop : -1.04 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.020 0.001 TYR A 246 PHE 0.016 0.001 PHE B 512 TRP 0.014 0.001 TRP A 780 HIS 0.016 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00339 (10715) covalent geometry : angle 0.53381 (14447) hydrogen bonds : bond 0.04519 ( 461) hydrogen bonds : angle 4.70139 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.387 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 98 average time/residue: 0.1006 time to fit residues: 14.6671 Evaluate side-chains 90 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 0.0060 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102294 restraints weight = 21946.720| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.49 r_work: 0.3204 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10715 Z= 0.132 Angle : 0.502 7.102 14447 Z= 0.261 Chirality : 0.042 0.156 1558 Planarity : 0.003 0.058 1854 Dihedral : 4.039 17.865 1393 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 0.51 % Allowed : 9.32 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 0.97 (0.22), residues: 558 sheet: -0.28 (0.42), residues: 139 loop : -1.08 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.020 0.001 TYR B 508 PHE 0.011 0.001 PHE A 50 TRP 0.015 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00308 (10715) covalent geometry : angle 0.50155 (14447) hydrogen bonds : bond 0.04032 ( 461) hydrogen bonds : angle 4.40405 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.426 Fit side-chains REVERT: A 30 MET cc_start: 0.7007 (mtp) cc_final: 0.6790 (mtt) REVERT: A 34 LEU cc_start: 0.8655 (mm) cc_final: 0.8291 (mt) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.0949 time to fit residues: 14.0801 Evaluate side-chains 96 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.125643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099251 restraints weight = 22097.615| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.59 r_work: 0.3140 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10715 Z= 0.234 Angle : 0.587 7.492 14447 Z= 0.301 Chirality : 0.045 0.159 1558 Planarity : 0.004 0.060 1854 Dihedral : 4.274 17.953 1393 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.51 % Allowed : 12.48 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.30 (0.23), residues: 1258 helix: 0.86 (0.22), residues: 557 sheet: -0.60 (0.42), residues: 141 loop : -1.14 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 818 TYR 0.013 0.001 TYR B 508 PHE 0.019 0.002 PHE B 456 TRP 0.020 0.002 TRP A 780 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00563 (10715) covalent geometry : angle 0.58674 (14447) hydrogen bonds : bond 0.04474 ( 461) hydrogen bonds : angle 4.51861 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.503 Fit side-chains REVERT: A 34 LEU cc_start: 0.8746 (mm) cc_final: 0.8336 (mt) REVERT: A 232 MET cc_start: 0.7541 (ptp) cc_final: 0.6843 (ptm) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.1043 time to fit residues: 14.2346 Evaluate side-chains 87 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 HIS A 920 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101236 restraints weight = 22028.651| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.48 r_work: 0.3188 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10715 Z= 0.125 Angle : 0.500 7.496 14447 Z= 0.261 Chirality : 0.042 0.157 1558 Planarity : 0.003 0.060 1854 Dihedral : 4.092 18.078 1393 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 0.60 % Allowed : 14.19 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.11 (0.23), residues: 1258 helix: 1.04 (0.22), residues: 556 sheet: -0.50 (0.42), residues: 139 loop : -1.08 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.017 0.001 TYR B 508 PHE 0.023 0.001 PHE B 456 TRP 0.013 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00294 (10715) covalent geometry : angle 0.50007 (14447) hydrogen bonds : bond 0.03806 ( 461) hydrogen bonds : angle 4.27877 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 161 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 232 MET cc_start: 0.7514 (ptp) cc_final: 0.6871 (ptm) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.1006 time to fit residues: 14.2775 Evaluate side-chains 90 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 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 = 0.3884 r_free = 0.3884 target = 0.127251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101157 restraints weight = 22094.336| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.78 r_work: 0.3165 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10715 Z= 0.146 Angle : 0.512 7.333 14447 Z= 0.263 Chirality : 0.042 0.159 1558 Planarity : 0.003 0.059 1854 Dihedral : 4.050 17.823 1393 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.11 % Allowed : 14.70 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.07 (0.23), residues: 1258 helix: 1.09 (0.22), residues: 556 sheet: -0.51 (0.42), residues: 139 loop : -1.06 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.017 0.001 TYR B 508 PHE 0.020 0.001 PHE B 456 TRP 0.014 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00349 (10715) covalent geometry : angle 0.51244 (14447) hydrogen bonds : bond 0.03794 ( 461) hydrogen bonds : angle 4.25748 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7116 (ppp) REVERT: A 161 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8747 (p) REVERT: A 232 MET cc_start: 0.7463 (ptp) cc_final: 0.6833 (ptm) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 0.0938 time to fit residues: 13.6995 Evaluate side-chains 91 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 917 HIS ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099692 restraints weight = 22042.646| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.94 r_work: 0.3124 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10715 Z= 0.198 Angle : 0.556 7.666 14447 Z= 0.284 Chirality : 0.044 0.159 1558 Planarity : 0.004 0.059 1854 Dihedral : 4.179 18.029 1393 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.94 % Allowed : 15.73 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 1.05 (0.22), residues: 553 sheet: -0.66 (0.42), residues: 141 loop : -1.03 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 818 TYR 0.016 0.001 TYR B 508 PHE 0.018 0.001 PHE B 456 TRP 0.018 0.001 TRP A 780 HIS 0.005 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00475 (10715) covalent geometry : angle 0.55609 (14447) hydrogen bonds : bond 0.04073 ( 461) hydrogen bonds : angle 4.35729 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 47 HIS cc_start: 0.8102 (m-70) cc_final: 0.7885 (m-70) REVERT: A 123 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7114 (ppp) REVERT: A 161 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 232 MET cc_start: 0.7613 (ptp) cc_final: 0.7037 (ptm) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.1020 time to fit residues: 14.1906 Evaluate side-chains 93 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 86 optimal weight: 0.0980 chunk 83 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.125180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098985 restraints weight = 22083.250| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.10 r_work: 0.3104 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10715 Z= 0.236 Angle : 0.595 8.070 14447 Z= 0.304 Chirality : 0.045 0.159 1558 Planarity : 0.004 0.058 1854 Dihedral : 4.349 18.064 1393 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 1.37 % Allowed : 15.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 0.93 (0.22), residues: 553 sheet: -0.72 (0.42), residues: 137 loop : -1.08 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 818 TYR 0.014 0.001 TYR B 508 PHE 0.018 0.002 PHE B 456 TRP 0.020 0.002 TRP A 780 HIS 0.004 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00569 (10715) covalent geometry : angle 0.59498 (14447) hydrogen bonds : bond 0.04298 ( 461) hydrogen bonds : angle 4.46880 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.7193 (ppp) REVERT: A 161 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 232 MET cc_start: 0.7782 (ptp) cc_final: 0.7237 (ptm) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 0.0964 time to fit residues: 13.9613 Evaluate side-chains 93 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 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 = 0.3881 r_free = 0.3881 target = 0.126936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100244 restraints weight = 21930.416| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.76 r_work: 0.3142 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10715 Z= 0.135 Angle : 0.534 10.428 14447 Z= 0.272 Chirality : 0.043 0.232 1558 Planarity : 0.003 0.061 1854 Dihedral : 4.206 17.964 1393 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 1.11 % Allowed : 16.15 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.03 (0.24), residues: 1258 helix: 1.14 (0.22), residues: 553 sheet: -0.61 (0.42), residues: 137 loop : -1.00 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.014 0.001 TYR B 508 PHE 0.017 0.001 PHE B 456 TRP 0.012 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00320 (10715) covalent geometry : angle 0.53389 (14447) hydrogen bonds : bond 0.03745 ( 461) hydrogen bonds : angle 4.31350 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7107 (ppp) REVERT: A 161 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 232 MET cc_start: 0.7729 (ptp) cc_final: 0.7194 (ptm) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.1037 time to fit residues: 14.4406 Evaluate side-chains 93 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101486 restraints weight = 21835.815| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.73 r_work: 0.3180 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10715 Z= 0.114 Angle : 0.527 10.869 14447 Z= 0.267 Chirality : 0.042 0.205 1558 Planarity : 0.003 0.061 1854 Dihedral : 4.084 17.731 1393 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 0.77 % Allowed : 16.24 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.14 (0.24), residues: 1258 helix: 1.32 (0.22), residues: 547 sheet: -0.47 (0.42), residues: 139 loop : -0.96 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.014 0.001 TYR B 508 PHE 0.016 0.001 PHE B 456 TRP 0.011 0.001 TRP A 780 HIS 0.006 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00267 (10715) covalent geometry : angle 0.52686 (14447) hydrogen bonds : bond 0.03605 ( 461) hydrogen bonds : angle 4.24494 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7075 (ppp) REVERT: A 161 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8774 (p) REVERT: A 232 MET cc_start: 0.7625 (ptp) cc_final: 0.7063 (ptm) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.0938 time to fit residues: 13.3381 Evaluate side-chains 94 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.0070 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099045 restraints weight = 22130.305| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.99 r_work: 0.3101 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10715 Z= 0.118 Angle : 0.530 10.677 14447 Z= 0.269 Chirality : 0.042 0.200 1558 Planarity : 0.003 0.061 1854 Dihedral : 4.064 21.454 1393 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 0.77 % Allowed : 16.50 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.20 (0.24), residues: 1258 helix: 1.31 (0.22), residues: 552 sheet: -0.38 (0.43), residues: 138 loop : -0.89 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 358 TYR 0.013 0.001 TYR B 508 PHE 0.016 0.001 PHE B 456 TRP 0.011 0.001 TRP A 780 HIS 0.006 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00277 (10715) covalent geometry : angle 0.53039 (14447) hydrogen bonds : bond 0.03553 ( 461) hydrogen bonds : angle 4.21309 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.62 seconds wall clock time: 40 minutes 10.99 seconds (2410.99 seconds total)