Starting phenix.real_space_refine (version: dev) on Sun Feb 19 18:25:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_27336.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_27336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_27336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_27336.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/02_2023/8dd8_27336.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A PHE 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "B GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: 6.35, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.67 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: 3.41 Time building geometry restraints manager: 4.75 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: 97.93 - 105.15: 183 105.15 - 112.37: 5304 112.37 - 119.59: 3761 119.59 - 126.80: 5047 126.80 - 134.02: 152 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 2.440 nonbonded pdb=" O GLN B 497 " pdb=" OG1 THR B 500 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASN A 157 " pdb=" OG SER A 161 " model vdw 2.279 2.440 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 432 " model vdw 2.291 2.440 nonbonded pdb=" NH2 ARG A 916 " pdb=" O ASP A 933 " model vdw 2.292 2.520 ... (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 ========== 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 14.300 Check model and map are aligned: 0.160 Process input model: 31.210 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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= 0.221 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 : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2227 time to fit residues: 33.7363 Evaluate side-chains 89 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 385 HIS B 415 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0845 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= 0.205 Angle : 0.515 7.414 14447 Z= 0.270 Chirality : 0.042 0.150 1558 Planarity : 0.004 0.052 1854 Dihedral : 4.095 17.792 1393 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1258 helix: 0.92 (0.22), residues: 549 sheet: -0.13 (0.43), residues: 139 loop : -1.04 (0.25), residues: 570 *********************** 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 102 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.348 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 99 average time/residue: 0.2435 time to fit residues: 35.1716 Evaluate side-chains 91 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1084 time to fit residues: 2.2647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- 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 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 10715 Z= 0.251 Angle : 0.518 7.021 14447 Z= 0.267 Chirality : 0.042 0.164 1558 Planarity : 0.003 0.049 1854 Dihedral : 4.116 17.871 1393 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1258 helix: 1.02 (0.22), residues: 557 sheet: -0.29 (0.43), residues: 139 loop : -1.09 (0.25), residues: 562 *********************** 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 101 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.428 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.2376 time to fit residues: 33.4257 Evaluate side-chains 95 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2148 time to fit residues: 3.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 33 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: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10715 Z= 0.146 Angle : 0.468 7.074 14447 Z= 0.245 Chirality : 0.041 0.158 1558 Planarity : 0.003 0.047 1854 Dihedral : 3.955 17.754 1393 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1258 helix: 1.22 (0.22), residues: 551 sheet: -0.28 (0.43), residues: 139 loop : -0.99 (0.26), residues: 568 *********************** 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 98 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.311 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.2392 time to fit residues: 33.8122 Evaluate side-chains 86 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1244 time to fit residues: 2.2999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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** A1044 ASN B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1399 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= 0.213 Angle : 0.504 7.236 14447 Z= 0.260 Chirality : 0.042 0.172 1558 Planarity : 0.003 0.047 1854 Dihedral : 3.972 17.696 1393 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1258 helix: 1.18 (0.22), residues: 557 sheet: -0.38 (0.42), residues: 139 loop : -1.02 (0.26), residues: 562 *********************** 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 94 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.471 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 0.2480 time to fit residues: 33.9012 Evaluate side-chains 86 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0999 time to fit residues: 2.2176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 10715 Z= 0.300 Angle : 0.551 7.568 14447 Z= 0.281 Chirality : 0.043 0.166 1558 Planarity : 0.003 0.045 1854 Dihedral : 4.155 18.015 1393 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1258 helix: 1.11 (0.22), residues: 553 sheet: -0.41 (0.43), residues: 135 loop : -1.02 (0.25), residues: 570 *********************** 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 90 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.394 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.2382 time to fit residues: 31.7992 Evaluate side-chains 87 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1241 time to fit residues: 2.3192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1635 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= 0.167 Angle : 0.490 7.919 14447 Z= 0.252 Chirality : 0.041 0.171 1558 Planarity : 0.003 0.046 1854 Dihedral : 4.004 17.797 1393 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.03 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1258 helix: 1.25 (0.22), residues: 556 sheet: -0.37 (0.42), residues: 139 loop : -0.97 (0.26), residues: 563 *********************** 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 93 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.409 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 92 average time/residue: 0.2408 time to fit residues: 32.7029 Evaluate side-chains 85 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0994 time to fit residues: 1.8657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 10715 Z= 0.237 Angle : 0.527 9.099 14447 Z= 0.266 Chirality : 0.042 0.158 1558 Planarity : 0.003 0.045 1854 Dihedral : 4.030 17.759 1393 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1258 helix: 1.23 (0.22), residues: 557 sheet: -0.40 (0.42), residues: 139 loop : -1.01 (0.26), residues: 562 *********************** 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 92 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.489 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 0.2369 time to fit residues: 32.5210 Evaluate side-chains 86 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3193 time to fit residues: 3.1719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10715 Z= 0.254 Angle : 0.538 10.762 14447 Z= 0.271 Chirality : 0.043 0.161 1558 Planarity : 0.003 0.046 1854 Dihedral : 4.077 17.780 1393 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1258 helix: 1.19 (0.22), residues: 555 sheet: -0.37 (0.43), residues: 135 loop : -1.02 (0.25), residues: 568 *********************** 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 85 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.417 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.2301 time to fit residues: 29.1266 Evaluate side-chains 85 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1250 time to fit residues: 2.0569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 126 optimal weight: 0.0980 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10715 Z= 0.151 Angle : 0.495 10.253 14447 Z= 0.251 Chirality : 0.041 0.156 1558 Planarity : 0.003 0.048 1854 Dihedral : 3.929 17.588 1393 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1258 helix: 1.43 (0.22), residues: 551 sheet: -0.24 (0.43), residues: 138 loop : -0.91 (0.26), residues: 569 ********************** 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 88 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2401 time to fit residues: 31.8956 Evaluate side-chains 84 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 0.0670 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 0.0170 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A1047 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102941 restraints weight = 21662.454| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.45 r_work: 0.3233 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10715 Z= 0.130 Angle : 0.496 10.612 14447 Z= 0.250 Chirality : 0.041 0.179 1558 Planarity : 0.003 0.047 1854 Dihedral : 3.802 17.226 1393 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1258 helix: 1.53 (0.23), residues: 551 sheet: 0.01 (0.44), residues: 133 loop : -0.89 (0.26), residues: 574 =============================================================================== Job complete usr+sys time: 2111.36 seconds wall clock time: 39 minutes 49.45 seconds (2389.45 seconds total)