Starting phenix.real_space_refine on Mon Jul 22 23:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu6_41617/07_2024/8tu6_41617.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 C 6474 2.51 5 N 1751 2.21 5 O 1869 1.98 5 H 10170 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ASP 806": "OD1" <-> "OD2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A PHE 960": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "A PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "A GLU 1037": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B ASP 569": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 16079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 16079 Classifications: {'peptide': 981} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935} Chain breaks: 4 Chain: "B" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4259 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain breaks: 1 Time building chain proxies: 9.77, per 1000 atoms: 0.48 Number of scatterers: 20338 At special positions: 0 Unit cell: (90.909, 113.022, 135.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 O 1869 8.00 N 1751 7.00 C 6474 6.00 H 10170 1.00 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: 16.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 54.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 54 through 62 Proline residue: A 57 - end of helix removed outlier: 4.282A pdb=" N GLN A 60 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.000A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.590A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.517A pdb=" N GLY A 248 " --> pdb=" O LEU A 244 " (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 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 413 through 417 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.698A 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 570 removed outlier: 3.614A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 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 673 removed outlier: 3.865A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 4.715A pdb=" N GLN A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.215A 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 removed outlier: 3.698A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 Processing helix chain 'A' and resid 809 through 827 Processing helix chain 'A' and resid 856 through 862 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 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.625A pdb=" N LYS A 942 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 943 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 4.047A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.611A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.765A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.953A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.745A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 445 through 516 removed outlier: 3.880A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 586 Proline residue: B 568 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 7.254A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212 removed outlier: 5.584A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.098A 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: 6.724A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.640A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 400 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN A 428 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (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 Processing sheet with id=AA9, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AB1, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 removed outlier: 4.399A pdb=" N TYR B 334 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP B 359 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 336 " --> pdb=" O ASP B 359 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1491 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: 7.61 Time building geometry restraints manager: 17.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10137 1.03 - 1.23: 50 1.23 - 1.42: 4304 1.42 - 1.62: 5944 1.62 - 1.81: 115 Bond restraints: 20550 Sorted by residual: bond pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.88e+00 bond pdb=" N MET B 326 " pdb=" CA MET B 326 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET B 326 " pdb=" H MET B 326 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" CA LYS A 973 " pdb=" CB LYS A 973 " ideal model delta sigma weight residual 1.533 1.550 -0.018 1.60e-02 3.91e+03 1.21e+00 bond pdb=" CB GLU B 403 " pdb=" CG GLU B 403 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.28e-01 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 274 106.25 - 113.18: 24073 113.18 - 120.12: 6656 120.12 - 127.06: 6045 127.06 - 134.00: 123 Bond angle restraints: 37171 Sorted by residual: angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA ILE A 561 " pdb=" CB ILE A 561 " pdb=" CG1 ILE A 561 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.43e+00 angle pdb=" C ILE A 561 " pdb=" CA ILE A 561 " pdb=" CB ILE A 561 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.82e+00 3.02e-01 6.60e+00 angle pdb=" CB LYS A 973 " pdb=" CG LYS A 973 " pdb=" CD LYS A 973 " ideal model delta sigma weight residual 111.30 117.04 -5.74 2.30e+00 1.89e-01 6.23e+00 angle pdb=" CA LYS A 973 " pdb=" CB LYS A 973 " pdb=" CG LYS A 973 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.94e+00 ... (remaining 37166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 8493 17.74 - 35.48: 787 35.48 - 53.23: 246 53.23 - 70.97: 57 70.97 - 88.71: 18 Dihedral angle restraints: 9601 sinusoidal: 5294 harmonic: 4307 Sorted by residual: dihedral pdb=" CA ARG B 358 " pdb=" C ARG B 358 " pdb=" N ASP B 359 " pdb=" CA ASP B 359 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CG ARG A 93 " pdb=" CD ARG A 93 " pdb=" NE ARG A 93 " pdb=" CZ ARG A 93 " ideal model delta sinusoidal sigma weight residual 90.00 41.31 48.69 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA ARG A 808 " pdb=" C ARG A 808 " pdb=" N GLN A 809 " pdb=" CA GLN A 809 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 981 0.031 - 0.061: 372 0.061 - 0.092: 93 0.092 - 0.122: 63 0.122 - 0.153: 7 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA ILE A 921 " pdb=" N ILE A 921 " pdb=" C ILE A 921 " pdb=" CB ILE A 921 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL A 952 " pdb=" N VAL A 952 " pdb=" C VAL A 952 " pdb=" CB VAL A 952 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1513 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 93 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.08e+00 pdb=" NE ARG A 93 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 93 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 93 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 93 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 93 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 93 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 93 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 93 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 741 " 0.153 9.50e-02 1.11e+02 5.13e-02 3.41e+00 pdb=" NE ARG A 741 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 741 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 741 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 741 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 741 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 741 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 741 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 741 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 561 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 562 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.021 5.00e-02 4.00e+02 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1393 2.20 - 2.80: 42495 2.80 - 3.40: 57246 3.40 - 4.00: 74662 4.00 - 4.60: 116551 Nonbonded interactions: 292347 Sorted by model distance: nonbonded pdb=" O ASN A 345 " pdb="HD22 ASN B 564 " model vdw 1.601 1.850 nonbonded pdb=" HH TYR A 584 " pdb=" OD2 ASP A 608 " model vdw 1.613 1.850 nonbonded pdb="HH21 ARG A 612 " pdb=" OE2 GLU A 642 " model vdw 1.618 1.850 nonbonded pdb="HH12 ARG A 398 " pdb=" OD1 ASP A 434 " model vdw 1.639 1.850 nonbonded pdb=" HG SER A 405 " pdb=" O LEU A 455 " model vdw 1.640 1.850 ... (remaining 292342 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 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: 1.440 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: 0.310 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 66.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 10380 Z= 0.243 Angle : 0.591 7.415 13994 Z= 0.325 Chirality : 0.039 0.153 1516 Planarity : 0.005 0.094 1796 Dihedral : 16.954 88.712 3995 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 20.62 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.51 (0.24), residues: 1219 helix: 0.77 (0.22), residues: 588 sheet: -0.19 (0.39), residues: 156 loop : 0.19 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.008 0.001 HIS B 450 PHE 0.011 0.001 PHE A 667 TYR 0.012 0.001 TYR A 904 ARG 0.013 0.001 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7697 (mttm) cc_final: 0.7408 (tttp) REVERT: A 288 MET cc_start: 0.7256 (ttm) cc_final: 0.6871 (ttt) REVERT: A 488 ASP cc_start: 0.7293 (t0) cc_final: 0.6768 (p0) REVERT: A 573 LYS cc_start: 0.7697 (mmmm) cc_final: 0.7337 (mmtt) REVERT: A 733 LYS cc_start: 0.8406 (ttmp) cc_final: 0.8188 (ttmt) REVERT: A 811 MET cc_start: 0.8099 (ttm) cc_final: 0.7815 (ttp) REVERT: A 979 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6512 (ttt-90) REVERT: A 1010 MET cc_start: 0.8399 (mtt) cc_final: 0.8032 (mtm) REVERT: B 496 GLU cc_start: 0.8607 (tp30) cc_final: 0.8333 (tp30) REVERT: B 525 MET cc_start: 0.8595 (mtt) cc_final: 0.8389 (tmm) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 0.6792 time to fit residues: 141.2762 Evaluate side-chains 136 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 965 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10380 Z= 0.180 Angle : 0.525 5.388 13994 Z= 0.276 Chirality : 0.038 0.145 1516 Planarity : 0.004 0.053 1796 Dihedral : 5.018 55.398 1361 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.38 % Allowed : 16.92 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.85 (0.24), residues: 1219 helix: 1.12 (0.21), residues: 597 sheet: -0.17 (0.39), residues: 154 loop : 0.28 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.006 0.001 HIS A 59 PHE 0.010 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.005 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.7855 (p90) cc_final: 0.7601 (p90) REVERT: A 184 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7876 (mmtt) REVERT: A 264 LYS cc_start: 0.7741 (mttm) cc_final: 0.7447 (tttp) REVERT: A 282 MET cc_start: 0.7708 (mtp) cc_final: 0.7365 (ttm) REVERT: A 288 MET cc_start: 0.7404 (ttm) cc_final: 0.6960 (ttt) REVERT: A 573 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7283 (mmtt) REVERT: A 811 MET cc_start: 0.8020 (ttm) cc_final: 0.7779 (ttp) REVERT: A 937 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8061 (p90) REVERT: A 979 ARG cc_start: 0.6683 (ttp80) cc_final: 0.6445 (ttt-90) REVERT: A 1010 MET cc_start: 0.8267 (mtm) cc_final: 0.7852 (mtm) REVERT: B 525 MET cc_start: 0.8601 (mtt) cc_final: 0.8399 (tmm) outliers start: 27 outliers final: 16 residues processed: 164 average time/residue: 0.5951 time to fit residues: 131.3029 Evaluate side-chains 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10380 Z= 0.229 Angle : 0.512 6.177 13994 Z= 0.267 Chirality : 0.038 0.141 1516 Planarity : 0.004 0.052 1796 Dihedral : 4.886 56.345 1359 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 16.21 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.88 (0.24), residues: 1219 helix: 1.23 (0.21), residues: 596 sheet: -0.29 (0.40), residues: 147 loop : 0.20 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6768 (pp) REVERT: A 59 HIS cc_start: 0.7819 (p90) cc_final: 0.7580 (p90) REVERT: A 184 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7832 (mmtt) REVERT: A 219 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6312 (mp10) REVERT: A 264 LYS cc_start: 0.7761 (mttm) cc_final: 0.7468 (tttp) REVERT: A 573 LYS cc_start: 0.7690 (mmmm) cc_final: 0.7319 (mmtt) REVERT: A 675 MET cc_start: 0.8248 (tpp) cc_final: 0.7897 (tpp) REVERT: A 811 MET cc_start: 0.8137 (ttm) cc_final: 0.7935 (ttp) REVERT: A 979 ARG cc_start: 0.6715 (ttp80) cc_final: 0.6467 (ttt-90) REVERT: B 421 ASP cc_start: 0.7933 (t0) cc_final: 0.7424 (t0) REVERT: B 525 MET cc_start: 0.8601 (mtt) cc_final: 0.8390 (tmm) outliers start: 27 outliers final: 19 residues processed: 167 average time/residue: 0.6150 time to fit residues: 136.9819 Evaluate side-chains 161 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10380 Z= 0.262 Angle : 0.516 5.107 13994 Z= 0.269 Chirality : 0.039 0.144 1516 Planarity : 0.004 0.046 1796 Dihedral : 4.887 55.528 1359 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.91 % Allowed : 16.04 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.82 (0.24), residues: 1219 helix: 1.22 (0.21), residues: 600 sheet: -0.38 (0.40), residues: 147 loop : 0.15 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE A 930 TYR 0.008 0.001 TYR A 904 ARG 0.005 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6809 (pp) REVERT: A 59 HIS cc_start: 0.7847 (p90) cc_final: 0.7620 (p90) REVERT: A 155 ASP cc_start: 0.7315 (m-30) cc_final: 0.6468 (t0) REVERT: A 184 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7823 (mmtt) REVERT: A 219 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6376 (mp10) REVERT: A 264 LYS cc_start: 0.7786 (mttm) cc_final: 0.7490 (tttp) REVERT: A 448 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 573 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7342 (mmtt) REVERT: A 979 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6452 (ttt-90) REVERT: B 421 ASP cc_start: 0.7988 (t0) cc_final: 0.7383 (t0) REVERT: B 525 MET cc_start: 0.8603 (mtt) cc_final: 0.8382 (tmm) outliers start: 33 outliers final: 24 residues processed: 163 average time/residue: 0.5689 time to fit residues: 126.8722 Evaluate side-chains 166 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 0.0050 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10380 Z= 0.211 Angle : 0.492 5.517 13994 Z= 0.256 Chirality : 0.038 0.141 1516 Planarity : 0.004 0.051 1796 Dihedral : 4.766 54.576 1359 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.00 % Allowed : 15.59 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.96 (0.24), residues: 1219 helix: 1.39 (0.21), residues: 599 sheet: -0.44 (0.41), residues: 147 loop : 0.18 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.005 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.7841 (p90) cc_final: 0.7613 (p90) REVERT: A 155 ASP cc_start: 0.7246 (m-30) cc_final: 0.6571 (t0) REVERT: A 219 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 264 LYS cc_start: 0.7793 (mttm) cc_final: 0.7502 (tttp) REVERT: A 336 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 448 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 549 ASP cc_start: 0.7278 (m-30) cc_final: 0.7047 (m-30) REVERT: A 675 MET cc_start: 0.8162 (tpp) cc_final: 0.7875 (tpp) REVERT: A 979 ARG cc_start: 0.6713 (ttp80) cc_final: 0.6458 (ttt-90) REVERT: B 380 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8341 (mt) REVERT: B 421 ASP cc_start: 0.8027 (t0) cc_final: 0.7410 (t0) REVERT: B 422 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8193 (p) REVERT: B 525 MET cc_start: 0.8612 (mtt) cc_final: 0.8382 (tmm) outliers start: 34 outliers final: 26 residues processed: 163 average time/residue: 0.5565 time to fit residues: 124.8452 Evaluate side-chains 168 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10380 Z= 0.235 Angle : 0.499 5.702 13994 Z= 0.260 Chirality : 0.038 0.144 1516 Planarity : 0.004 0.055 1796 Dihedral : 4.748 53.010 1359 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.08 % Allowed : 16.21 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.92 (0.24), residues: 1219 helix: 1.38 (0.21), residues: 599 sheet: -0.48 (0.41), residues: 147 loop : 0.13 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.012 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.010 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6833 (pp) REVERT: A 59 HIS cc_start: 0.7846 (p90) cc_final: 0.7608 (p90) REVERT: A 155 ASP cc_start: 0.7247 (m-30) cc_final: 0.6571 (t0) REVERT: A 219 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6409 (mp10) REVERT: A 264 LYS cc_start: 0.7776 (mttm) cc_final: 0.7508 (tttp) REVERT: A 336 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 448 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 549 ASP cc_start: 0.7314 (m-30) cc_final: 0.7042 (m-30) REVERT: A 973 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8306 (mmtp) REVERT: A 979 ARG cc_start: 0.6739 (ttp80) cc_final: 0.6463 (ttt-90) REVERT: A 1029 ASP cc_start: 0.7749 (p0) cc_final: 0.7459 (m-30) REVERT: B 380 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 421 ASP cc_start: 0.8059 (t0) cc_final: 0.7435 (t0) REVERT: B 422 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (p) REVERT: B 525 MET cc_start: 0.8612 (mtt) cc_final: 0.8382 (tmm) outliers start: 35 outliers final: 26 residues processed: 164 average time/residue: 0.5588 time to fit residues: 126.5279 Evaluate side-chains 168 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10380 Z= 0.178 Angle : 0.478 6.038 13994 Z= 0.248 Chirality : 0.038 0.139 1516 Planarity : 0.004 0.055 1796 Dihedral : 4.624 52.527 1359 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.08 % Allowed : 16.12 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.09 (0.25), residues: 1219 helix: 1.52 (0.21), residues: 599 sheet: -0.45 (0.41), residues: 147 loop : 0.24 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.009 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.008 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6856 (pp) REVERT: A 59 HIS cc_start: 0.7900 (p90) cc_final: 0.7647 (p90) REVERT: A 155 ASP cc_start: 0.7261 (m-30) cc_final: 0.6559 (t0) REVERT: A 219 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6432 (mp10) REVERT: A 264 LYS cc_start: 0.7749 (mttm) cc_final: 0.7529 (tttp) REVERT: A 336 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 549 ASP cc_start: 0.7307 (m-30) cc_final: 0.7030 (m-30) REVERT: A 675 MET cc_start: 0.8096 (tpp) cc_final: 0.7858 (tpp) REVERT: A 825 GLN cc_start: 0.7262 (mm-40) cc_final: 0.7042 (mm-40) REVERT: A 886 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8162 (mtmm) REVERT: A 973 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8323 (mmtp) REVERT: A 979 ARG cc_start: 0.6742 (ttp80) cc_final: 0.6465 (ttt-90) REVERT: B 380 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 421 ASP cc_start: 0.8070 (t0) cc_final: 0.7457 (t0) REVERT: B 422 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 525 MET cc_start: 0.8615 (mtt) cc_final: 0.8380 (tmm) outliers start: 35 outliers final: 27 residues processed: 167 average time/residue: 0.5474 time to fit residues: 125.7731 Evaluate side-chains 173 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10380 Z= 0.162 Angle : 0.469 5.944 13994 Z= 0.243 Chirality : 0.037 0.138 1516 Planarity : 0.004 0.058 1796 Dihedral : 4.505 51.648 1359 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.25 (0.25), residues: 1219 helix: 1.65 (0.21), residues: 600 sheet: -0.41 (0.41), residues: 147 loop : 0.32 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.008 0.001 PHE A 930 TYR 0.010 0.001 TYR A 904 ARG 0.008 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6851 (pp) REVERT: A 155 ASP cc_start: 0.7241 (m-30) cc_final: 0.6542 (t0) REVERT: A 264 LYS cc_start: 0.7778 (mttm) cc_final: 0.7525 (tttp) REVERT: A 336 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 549 ASP cc_start: 0.7302 (m-30) cc_final: 0.7002 (m-30) REVERT: A 675 MET cc_start: 0.8102 (tpp) cc_final: 0.7884 (tpp) REVERT: A 825 GLN cc_start: 0.7226 (mm-40) cc_final: 0.7020 (mm-40) REVERT: A 886 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8141 (mtmm) REVERT: A 973 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8411 (mmtp) REVERT: A 979 ARG cc_start: 0.6738 (ttp80) cc_final: 0.6410 (ttt-90) REVERT: B 380 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 421 ASP cc_start: 0.8075 (t0) cc_final: 0.7457 (t0) REVERT: B 422 VAL cc_start: 0.8557 (p) cc_final: 0.8306 (p) REVERT: B 497 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6619 (tp-100) REVERT: B 525 MET cc_start: 0.8620 (mtt) cc_final: 0.8371 (tmm) outliers start: 29 outliers final: 22 residues processed: 158 average time/residue: 0.5544 time to fit residues: 120.2265 Evaluate side-chains 162 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10380 Z= 0.206 Angle : 0.481 6.107 13994 Z= 0.250 Chirality : 0.038 0.142 1516 Planarity : 0.004 0.060 1796 Dihedral : 4.474 50.939 1358 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 17.09 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.16 (0.25), residues: 1219 helix: 1.59 (0.21), residues: 603 sheet: -0.44 (0.42), residues: 147 loop : 0.24 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 665 PHE 0.011 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.010 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6866 (pp) REVERT: A 59 HIS cc_start: 0.7891 (p90) cc_final: 0.7597 (p90) REVERT: A 336 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 549 ASP cc_start: 0.7277 (m-30) cc_final: 0.6967 (m-30) REVERT: A 675 MET cc_start: 0.8130 (tpp) cc_final: 0.7907 (tpp) REVERT: A 886 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8143 (mtmm) REVERT: A 973 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8430 (mmtp) REVERT: A 979 ARG cc_start: 0.6662 (ttp80) cc_final: 0.6397 (ttt-90) REVERT: B 380 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 421 ASP cc_start: 0.8108 (t0) cc_final: 0.7488 (t0) REVERT: B 422 VAL cc_start: 0.8577 (p) cc_final: 0.8329 (p) REVERT: B 525 MET cc_start: 0.8629 (mtt) cc_final: 0.8373 (tmm) outliers start: 26 outliers final: 22 residues processed: 154 average time/residue: 0.5538 time to fit residues: 116.2255 Evaluate side-chains 161 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10380 Z= 0.152 Angle : 0.467 6.289 13994 Z= 0.241 Chirality : 0.037 0.140 1516 Planarity : 0.004 0.061 1796 Dihedral : 4.350 50.521 1358 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.03 % Allowed : 17.36 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.36 (0.25), residues: 1219 helix: 1.76 (0.21), residues: 603 sheet: -0.39 (0.42), residues: 147 loop : 0.34 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.007 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.009 0.000 ARG A 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6891 (pp) REVERT: A 59 HIS cc_start: 0.7884 (p90) cc_final: 0.7592 (p90) REVERT: A 336 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (mt) REVERT: A 549 ASP cc_start: 0.7276 (m-30) cc_final: 0.6974 (m-30) REVERT: A 675 MET cc_start: 0.8078 (tpp) cc_final: 0.7873 (tpp) REVERT: A 820 MET cc_start: 0.7794 (ptp) cc_final: 0.7431 (ptp) REVERT: A 886 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8119 (mtmm) REVERT: A 973 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8462 (mmtp) REVERT: A 979 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6427 (ttt-90) REVERT: B 380 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 421 ASP cc_start: 0.8105 (t0) cc_final: 0.7500 (t0) REVERT: B 422 VAL cc_start: 0.8600 (p) cc_final: 0.8358 (p) REVERT: B 497 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: B 525 MET cc_start: 0.8604 (mtt) cc_final: 0.8359 (tmm) outliers start: 23 outliers final: 17 residues processed: 154 average time/residue: 0.5625 time to fit residues: 118.8236 Evaluate side-chains 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 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 = 0.3937 r_free = 0.3937 target = 0.160225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122821 restraints weight = 35229.298| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.01 r_work: 0.3337 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10380 Z= 0.234 Angle : 0.493 6.124 13994 Z= 0.256 Chirality : 0.038 0.143 1516 Planarity : 0.004 0.062 1796 Dihedral : 4.393 49.679 1357 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.11 % Allowed : 17.27 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.21 (0.25), residues: 1219 helix: 1.64 (0.21), residues: 603 sheet: -0.43 (0.42), residues: 147 loop : 0.25 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE A 930 TYR 0.009 0.001 TYR B 470 ARG 0.008 0.000 ARG A 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.97 seconds wall clock time: 82 minutes 53.78 seconds (4973.78 seconds total)