Starting phenix.real_space_refine on Sat Aug 23 17:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8om9_16971/08_2025/8om9_16971.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8317 2.51 5 N 2286 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5783 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 22, 'TRANS': 709} Chain breaks: 7 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6566 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.78, per 1000 atoms: 0.21 Number of scatterers: 13314 At special positions: 0 Unit cell: (95.0768, 170.041, 134.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 48 15.00 Mg 2 11.99 O 2599 8.00 N 2286 7.00 C 8317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 418.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 56.5% alpha, 9.6% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.012A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.593A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.564A pdb=" N ASN A 285 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.914A pdb=" N GLN A 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.543A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.875A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 436 through 456 removed outlier: 4.704A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 475 through 503 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.869A pdb=" N GLU A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 553 through 615 removed outlier: 3.780A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.438A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 785 through 788 Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.676A pdb=" N ALA A 831 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 877 through 894 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.881A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.907A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.933A pdb=" N GLU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.550A pdb=" N PHE B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 546 removed outlier: 3.673A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.612A pdb=" N GLY B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 663 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 667 through 680 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 688 removed outlier: 3.557A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 688 " --> pdb=" O HIS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 709 through 737 removed outlier: 4.216A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 762 Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 843 Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 918 Processing helix chain 'B' and resid 951 through 964 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.986A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1076 removed outlier: 3.504A pdb=" N ASN B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1112 removed outlier: 3.827A pdb=" N THR B1112 " --> pdb=" O ALA B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.662A pdb=" N THR B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.804A pdb=" N VAL A 148 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.519A pdb=" N LEU A 173 " --> pdb=" O THR A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.832A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.508A pdb=" N CYS A 697 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 637 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 708 through 711 removed outlier: 3.716A pdb=" N ILE A 747 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LEU A 805 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 814 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.164A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.526A pdb=" N THR B 282 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 454 through 458 removed outlier: 6.507A pdb=" N LEU B 369 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE B 371 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 370 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 372 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 880 through 884 removed outlier: 6.972A pdb=" N THR B 882 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS B 860 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 884 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 858 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 858 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 934 through 937 removed outlier: 6.740A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 970 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU B1006 " --> pdb=" O SER B 970 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 892 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2681 1.33 - 1.46: 4196 1.46 - 1.58: 6562 1.58 - 1.71: 91 1.71 - 1.83: 99 Bond restraints: 13629 Sorted by residual: bond pdb=" C LEU A 414 " pdb=" N PRO A 415 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.64e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B2000 " pdb=" C5 ADP B2000 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 1.470 1.417 0.053 1.01e-02 9.80e+03 2.77e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.72: 18561 7.72 - 15.43: 13 15.43 - 23.15: 0 23.15 - 30.86: 2 30.86 - 38.58: 2 Bond angle restraints: 18578 Sorted by residual: angle pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 110.00 140.87 -30.87 1.12e+00 7.97e-01 7.60e+02 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 102.17 75.57 26.60 1.05e+00 9.07e-01 6.42e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 74.69 28.51 1.50e+00 4.44e-01 3.61e+02 angle pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 106.10 67.52 38.58 3.20e+00 9.77e-02 1.45e+02 angle pdb=" C LEU A 414 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 121.00 109.91 11.09 1.16e+00 7.43e-01 9.14e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 7694 33.71 - 67.43: 476 67.43 - 101.14: 15 101.14 - 134.85: 2 134.85 - 168.56: 1 Dihedral angle restraints: 8188 sinusoidal: 3661 harmonic: 4527 Sorted by residual: dihedral pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual 115.10 86.80 28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C PRO A 415 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual -120.70 -139.41 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" O1B ADP B2000 " pdb=" O3A ADP B2000 " pdb=" PB ADP B2000 " pdb=" PA ADP B2000 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.56 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1966 0.146 - 0.293: 162 0.293 - 0.439: 4 0.439 - 0.585: 0 0.585 - 0.731: 1 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C3' DG C 36 " pdb=" C4' DG C 36 " pdb=" O3' DG C 36 " pdb=" C2' DG C 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2130 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 415 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO A 415 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO A 415 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 416 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " -0.039 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 415 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2000 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.62e+00 pdb=" C2 ADP B2000 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP B2000 " 0.006 2.00e-02 2.50e+03 pdb=" C5 ADP B2000 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP B2000 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP B2000 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP B2000 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ADP B2000 " -0.008 2.00e-02 2.50e+03 pdb=" N7 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ADP B2000 " 0.022 2.00e-02 2.50e+03 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 178 2.60 - 3.18: 11938 3.18 - 3.75: 23146 3.75 - 4.33: 31652 4.33 - 4.90: 48445 Nonbonded interactions: 115359 Sorted by model distance: nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 2.025 2.170 nonbonded pdb=" OH TYR A 757 " pdb=" CD1 ILE B1097 " model vdw 2.056 3.460 nonbonded pdb=" O2B ADP B2000 " pdb="MG MG B2001 " model vdw 2.073 2.170 nonbonded pdb=" OG SER B 903 " pdb=" OD2 ASP B 975 " model vdw 2.079 3.040 nonbonded pdb=" O HIS A 785 " pdb=" OG1 THR A 788 " model vdw 2.118 3.040 ... (remaining 115354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.008 0.188 13629 Z= 0.483 Angle : 1.286 38.579 18578 Z= 0.843 Chirality : 0.088 0.731 2133 Planarity : 0.005 0.057 2201 Dihedral : 18.878 168.563 5240 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.76 % Allowed : 22.53 % Favored : 74.71 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.21), residues: 1518 helix: 0.15 (0.18), residues: 766 sheet: -2.38 (0.36), residues: 172 loop : -1.92 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 593 TYR 0.027 0.004 TYR B1021 PHE 0.027 0.004 PHE B 784 TRP 0.019 0.005 TRP A 764 HIS 0.011 0.003 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00761 (13629) covalent geometry : angle 1.28647 (18578) hydrogen bonds : bond 0.14384 ( 694) hydrogen bonds : angle 6.54300 ( 1963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.6585 (mp10) cc_final: 0.6260 (mp10) REVERT: A 347 LYS cc_start: 0.8169 (pttp) cc_final: 0.7923 (pttp) REVERT: A 364 GLU cc_start: 0.7710 (tp30) cc_final: 0.7506 (tp30) REVERT: A 429 GLN cc_start: 0.7845 (mt0) cc_final: 0.7541 (mt0) REVERT: A 480 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 482 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8484 (tpm170) REVERT: A 626 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 647 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7987 (tm-30) REVERT: A 817 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 818 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7361 (mttp) REVERT: A 846 GLN cc_start: 0.7773 (mt0) cc_final: 0.7514 (mm110) REVERT: A 850 GLU cc_start: 0.7825 (mp0) cc_final: 0.7509 (mp0) REVERT: B 434 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8543 (pm20) REVERT: B 526 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 626 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 860 LYS cc_start: 0.8413 (mttt) cc_final: 0.8185 (mmmt) REVERT: B 883 ASP cc_start: 0.7686 (t0) cc_final: 0.7395 (t0) REVERT: B 1015 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (t) REVERT: B 1085 LYS cc_start: 0.8252 (tttt) cc_final: 0.8014 (tttt) REVERT: B 1091 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7994 (mmmm) outliers start: 38 outliers final: 16 residues processed: 298 average time/residue: 0.1157 time to fit residues: 48.6660 Evaluate side-chains 279 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 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 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 550 ASN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.200538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161849 restraints weight = 20682.663| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.00 r_work: 0.4009 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13629 Z= 0.240 Angle : 0.688 6.811 18578 Z= 0.364 Chirality : 0.044 0.168 2133 Planarity : 0.005 0.053 2201 Dihedral : 18.022 152.633 2176 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.16 % Allowed : 19.91 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.22), residues: 1518 helix: 0.29 (0.18), residues: 784 sheet: -2.53 (0.34), residues: 185 loop : -1.72 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 752 TYR 0.029 0.002 TYR B 846 PHE 0.021 0.002 PHE A 836 TRP 0.009 0.002 TRP A 764 HIS 0.010 0.002 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00523 (13629) covalent geometry : angle 0.68784 (18578) hydrogen bonds : bond 0.05295 ( 694) hydrogen bonds : angle 5.48482 ( 1963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6386 (mp) REVERT: A 337 GLN cc_start: 0.6714 (mm-40) cc_final: 0.5910 (tp40) REVERT: A 353 LYS cc_start: 0.8212 (tttp) cc_final: 0.7921 (tttp) REVERT: A 357 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 364 GLU cc_start: 0.6554 (tp30) cc_final: 0.6203 (tp30) REVERT: A 429 GLN cc_start: 0.7817 (mt0) cc_final: 0.7556 (mt0) REVERT: A 452 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7501 (pt0) REVERT: A 459 ASP cc_start: 0.6620 (p0) cc_final: 0.6241 (p0) REVERT: A 480 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 502 ASP cc_start: 0.6638 (m-30) cc_final: 0.6367 (m-30) REVERT: A 503 LEU cc_start: 0.2626 (OUTLIER) cc_final: 0.2300 (tp) REVERT: A 566 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.5277 (p0) REVERT: A 590 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8167 (mm-30) REVERT: A 685 ILE cc_start: 0.8324 (mm) cc_final: 0.7896 (tt) REVERT: A 728 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5529 (pm20) REVERT: A 784 PHE cc_start: 0.7073 (m-80) cc_final: 0.6793 (m-80) REVERT: A 817 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 850 GLU cc_start: 0.7030 (mp0) cc_final: 0.6588 (mp0) REVERT: B 281 MET cc_start: 0.5969 (tpp) cc_final: 0.5699 (tpp) REVERT: B 367 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6832 (t80) REVERT: B 407 ASP cc_start: 0.6487 (m-30) cc_final: 0.6237 (m-30) REVERT: B 526 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7527 (mmmm) REVERT: B 580 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6616 (t) REVERT: B 626 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7490 (t) REVERT: B 630 HIS cc_start: 0.7091 (m90) cc_final: 0.6525 (m90) REVERT: B 713 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7515 (mmtt) REVERT: B 720 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7689 (tp-100) REVERT: B 883 ASP cc_start: 0.7245 (t0) cc_final: 0.6872 (t0) REVERT: B 938 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.4703 (tpm-80) REVERT: B 1085 LYS cc_start: 0.7762 (tttt) cc_final: 0.7447 (tttt) REVERT: B 1091 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7299 (mmmm) REVERT: B 1093 LEU cc_start: 0.7270 (tp) cc_final: 0.6947 (tp) REVERT: B 1094 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6624 (mt-10) outliers start: 71 outliers final: 32 residues processed: 319 average time/residue: 0.1090 time to fit residues: 49.4708 Evaluate side-chains 298 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1066 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 0.0000 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 127 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS A 629 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 692 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN B1071 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.202826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.164347 restraints weight = 20931.674| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.08 r_work: 0.4043 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13629 Z= 0.158 Angle : 0.631 7.007 18578 Z= 0.330 Chirality : 0.042 0.209 2133 Planarity : 0.004 0.057 2201 Dihedral : 17.923 147.008 2159 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.65 % Allowed : 21.08 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.22), residues: 1518 helix: 0.59 (0.19), residues: 778 sheet: -2.43 (0.35), residues: 181 loop : -1.59 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 669 TYR 0.015 0.001 TYR B1011 PHE 0.014 0.002 PHE A 468 TRP 0.007 0.001 TRP B1122 HIS 0.006 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00346 (13629) covalent geometry : angle 0.63055 (18578) hydrogen bonds : bond 0.04675 ( 694) hydrogen bonds : angle 5.12381 ( 1963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6092 (mm-40) REVERT: A 364 GLU cc_start: 0.6455 (tp30) cc_final: 0.5977 (tp30) REVERT: A 452 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7439 (pt0) REVERT: A 459 ASP cc_start: 0.6814 (p0) cc_final: 0.6486 (p0) REVERT: A 482 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7708 (tpm170) REVERT: A 566 ASN cc_start: 0.5729 (OUTLIER) cc_final: 0.5127 (p0) REVERT: A 590 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 685 ILE cc_start: 0.8332 (mm) cc_final: 0.7893 (tt) REVERT: A 784 PHE cc_start: 0.7022 (m-80) cc_final: 0.6767 (m-80) REVERT: A 850 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6603 (mp0) REVERT: A 886 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: A 894 MET cc_start: 0.6378 (tmm) cc_final: 0.6137 (tmm) REVERT: B 264 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: B 281 MET cc_start: 0.6125 (tpp) cc_final: 0.5909 (tpp) REVERT: B 367 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6879 (t80) REVERT: B 526 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7455 (mmmm) REVERT: B 544 ASN cc_start: 0.7621 (m-40) cc_final: 0.7098 (m-40) REVERT: B 626 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (t) REVERT: B 637 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6959 (mt-10) REVERT: B 642 VAL cc_start: 0.8248 (m) cc_final: 0.8036 (t) REVERT: B 713 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7339 (mmtt) REVERT: B 714 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8209 (tmmt) REVERT: B 812 GLU cc_start: 0.7262 (tp30) cc_final: 0.6915 (tp30) REVERT: B 883 ASP cc_start: 0.7192 (t0) cc_final: 0.6817 (t0) REVERT: B 1030 MET cc_start: 0.4284 (mmm) cc_final: 0.3771 (mmm) REVERT: B 1085 LYS cc_start: 0.7716 (tttt) cc_final: 0.7378 (tttt) REVERT: B 1091 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7285 (mmmm) REVERT: B 1094 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6642 (mt-10) outliers start: 64 outliers final: 32 residues processed: 304 average time/residue: 0.1070 time to fit residues: 46.2309 Evaluate side-chains 290 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 636 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.200605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.161713 restraints weight = 20833.691| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.02 r_work: 0.4010 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13629 Z= 0.226 Angle : 0.673 11.169 18578 Z= 0.351 Chirality : 0.043 0.169 2133 Planarity : 0.005 0.058 2201 Dihedral : 17.904 146.471 2155 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.81 % Allowed : 21.22 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.22), residues: 1518 helix: 0.50 (0.18), residues: 768 sheet: -2.21 (0.37), residues: 173 loop : -1.62 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 796 TYR 0.025 0.002 TYR B1011 PHE 0.018 0.002 PHE A 836 TRP 0.011 0.002 TRP A 764 HIS 0.014 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00489 (13629) covalent geometry : angle 0.67290 (18578) hydrogen bonds : bond 0.04868 ( 694) hydrogen bonds : angle 5.21407 ( 1963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 337 GLN cc_start: 0.6962 (mm110) cc_final: 0.6068 (mm110) REVERT: A 364 GLU cc_start: 0.6496 (tp30) cc_final: 0.5919 (tp30) REVERT: A 372 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8538 (pt) REVERT: A 452 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7434 (pt0) REVERT: A 459 ASP cc_start: 0.6781 (p0) cc_final: 0.6345 (p0) REVERT: A 480 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 566 ASN cc_start: 0.5670 (OUTLIER) cc_final: 0.5075 (p0) REVERT: A 590 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 624 ILE cc_start: 0.7671 (mm) cc_final: 0.7405 (tt) REVERT: A 685 ILE cc_start: 0.8366 (mm) cc_final: 0.7936 (tt) REVERT: A 711 ARG cc_start: 0.6623 (tpt170) cc_final: 0.6393 (tpt90) REVERT: A 784 PHE cc_start: 0.7043 (m-80) cc_final: 0.6759 (m-80) REVERT: A 817 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 838 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7961 (mmmm) REVERT: A 850 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6484 (mp0) REVERT: A 881 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.4970 (tm-30) REVERT: A 886 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: A 894 MET cc_start: 0.6251 (tmm) cc_final: 0.5969 (tmm) REVERT: B 264 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 290 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5452 (pp) REVERT: B 367 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6888 (t80) REVERT: B 514 ASN cc_start: 0.7985 (t0) cc_final: 0.7650 (t0) REVERT: B 526 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7490 (mmmm) REVERT: B 544 ASN cc_start: 0.7735 (m-40) cc_final: 0.7452 (m-40) REVERT: B 626 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7717 (t) REVERT: B 636 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7416 (tp40) REVERT: B 713 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7423 (mmtt) REVERT: B 714 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8252 (tmmt) REVERT: B 720 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7596 (tp-100) REVERT: B 728 MET cc_start: 0.7358 (tmm) cc_final: 0.7101 (tmm) REVERT: B 812 GLU cc_start: 0.7355 (tp30) cc_final: 0.6977 (tp30) REVERT: B 848 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6715 (ttt90) REVERT: B 883 ASP cc_start: 0.7203 (t0) cc_final: 0.6804 (t0) REVERT: B 938 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5515 (tpm-80) REVERT: B 1030 MET cc_start: 0.4641 (mmm) cc_final: 0.4132 (mmm) REVERT: B 1058 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6493 (pt0) REVERT: B 1085 LYS cc_start: 0.7755 (tttt) cc_final: 0.7492 (tttt) REVERT: B 1091 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7433 (mmmm) outliers start: 80 outliers final: 37 residues processed: 318 average time/residue: 0.1087 time to fit residues: 48.8742 Evaluate side-chains 309 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 149 optimal weight: 0.0370 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 37 optimal weight: 4.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.203274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.164827 restraints weight = 20818.925| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.11 r_work: 0.4047 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13629 Z= 0.147 Angle : 0.626 11.667 18578 Z= 0.326 Chirality : 0.042 0.354 2133 Planarity : 0.004 0.063 2201 Dihedral : 17.730 145.586 2153 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.45 % Allowed : 22.31 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.22), residues: 1518 helix: 0.68 (0.19), residues: 775 sheet: -2.24 (0.36), residues: 188 loop : -1.66 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 796 TYR 0.015 0.001 TYR B1011 PHE 0.019 0.002 PHE A 286 TRP 0.041 0.002 TRP B 768 HIS 0.014 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00325 (13629) covalent geometry : angle 0.62644 (18578) hydrogen bonds : bond 0.04399 ( 694) hydrogen bonds : angle 4.97031 ( 1963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 264 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7004 (mp) REVERT: A 337 GLN cc_start: 0.6852 (mm110) cc_final: 0.6249 (mm-40) REVERT: A 348 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7161 (mm110) REVERT: A 364 GLU cc_start: 0.6414 (tp30) cc_final: 0.5786 (tp30) REVERT: A 452 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7396 (pt0) REVERT: A 459 ASP cc_start: 0.6986 (p0) cc_final: 0.6368 (p0) REVERT: A 482 ARG cc_start: 0.8057 (tpm170) cc_final: 0.7337 (tpm170) REVERT: A 566 ASN cc_start: 0.5684 (OUTLIER) cc_final: 0.5154 (p0) REVERT: A 579 LYS cc_start: 0.8225 (mttt) cc_final: 0.7945 (mttt) REVERT: A 590 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 685 ILE cc_start: 0.8328 (mm) cc_final: 0.7992 (tt) REVERT: A 698 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 784 PHE cc_start: 0.6995 (m-80) cc_final: 0.6769 (m-80) REVERT: A 817 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7673 (p) REVERT: A 850 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6502 (mp0) REVERT: A 886 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: A 894 MET cc_start: 0.6170 (tmm) cc_final: 0.5886 (tmm) REVERT: B 264 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: B 290 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5571 (pp) REVERT: B 367 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6962 (t80) REVERT: B 508 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7532 (mmtm) REVERT: B 514 ASN cc_start: 0.7945 (t0) cc_final: 0.7519 (t0) REVERT: B 626 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7422 (t) REVERT: B 630 HIS cc_start: 0.7049 (m90) cc_final: 0.6408 (m90) REVERT: B 632 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7565 (mmtm) REVERT: B 636 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7380 (tp40) REVERT: B 687 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7160 (mmmt) REVERT: B 713 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7411 (mmtt) REVERT: B 812 GLU cc_start: 0.7279 (tp30) cc_final: 0.6912 (tp30) REVERT: B 848 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6763 (ttt90) REVERT: B 883 ASP cc_start: 0.7240 (t0) cc_final: 0.6903 (t0) REVERT: B 938 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5407 (tpm-80) REVERT: B 1085 LYS cc_start: 0.7725 (tttt) cc_final: 0.7416 (tttt) REVERT: B 1091 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7343 (mmtt) REVERT: B 1094 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6673 (mt-10) outliers start: 75 outliers final: 38 residues processed: 316 average time/residue: 0.1220 time to fit residues: 53.9154 Evaluate side-chains 308 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.202722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164106 restraints weight = 20904.892| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.09 r_work: 0.4034 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13629 Z= 0.160 Angle : 0.636 11.078 18578 Z= 0.330 Chirality : 0.042 0.374 2133 Planarity : 0.004 0.066 2201 Dihedral : 17.692 153.189 2153 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.87 % Allowed : 23.76 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.22), residues: 1518 helix: 0.70 (0.19), residues: 777 sheet: -2.13 (0.37), residues: 193 loop : -1.69 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 669 TYR 0.018 0.001 TYR B1011 PHE 0.015 0.002 PHE A 468 TRP 0.010 0.001 TRP B 768 HIS 0.013 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00353 (13629) covalent geometry : angle 0.63625 (18578) hydrogen bonds : bond 0.04367 ( 694) hydrogen bonds : angle 4.92369 ( 1963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (mp) REVERT: A 337 GLN cc_start: 0.6991 (mm110) cc_final: 0.6360 (mm-40) REVERT: A 452 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7393 (pt0) REVERT: A 460 MET cc_start: 0.6346 (mtm) cc_final: 0.5584 (mtm) REVERT: A 482 ARG cc_start: 0.8067 (tpm170) cc_final: 0.7517 (tpm170) REVERT: A 566 ASN cc_start: 0.5705 (OUTLIER) cc_final: 0.5127 (p0) REVERT: A 685 ILE cc_start: 0.8391 (mm) cc_final: 0.8052 (tt) REVERT: A 691 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7737 (tt) REVERT: A 784 PHE cc_start: 0.6998 (m-80) cc_final: 0.6746 (m-80) REVERT: A 817 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 850 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6533 (mp0) REVERT: A 886 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: A 894 MET cc_start: 0.6080 (tmm) cc_final: 0.5790 (tmm) REVERT: B 264 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 290 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5544 (pp) REVERT: B 367 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.6962 (t80) REVERT: B 514 ASN cc_start: 0.7968 (t0) cc_final: 0.7592 (t0) REVERT: B 544 ASN cc_start: 0.7599 (m-40) cc_final: 0.7283 (m-40) REVERT: B 626 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (t) REVERT: B 632 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7607 (mmtm) REVERT: B 713 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7645 (mmtt) REVERT: B 812 GLU cc_start: 0.7278 (tp30) cc_final: 0.6908 (tp30) REVERT: B 839 LYS cc_start: 0.7256 (mppt) cc_final: 0.6952 (mppt) REVERT: B 848 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6725 (ttt90) REVERT: B 883 ASP cc_start: 0.7215 (t0) cc_final: 0.6864 (t0) REVERT: B 938 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5473 (tpm-80) REVERT: B 1085 LYS cc_start: 0.7743 (tttt) cc_final: 0.7446 (tttt) REVERT: B 1091 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7331 (mmtt) REVERT: B 1094 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6725 (mt-10) outliers start: 67 outliers final: 41 residues processed: 311 average time/residue: 0.1166 time to fit residues: 50.5732 Evaluate side-chains 311 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.200922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.162211 restraints weight = 20631.121| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.02 r_work: 0.4016 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13629 Z= 0.213 Angle : 0.687 11.228 18578 Z= 0.354 Chirality : 0.044 0.387 2133 Planarity : 0.005 0.066 2201 Dihedral : 17.763 156.139 2153 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.23 % Allowed : 23.76 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1518 helix: 0.48 (0.18), residues: 780 sheet: -2.09 (0.38), residues: 185 loop : -1.78 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 796 TYR 0.030 0.002 TYR B1011 PHE 0.018 0.002 PHE A 468 TRP 0.041 0.002 TRP B 768 HIS 0.010 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00465 (13629) covalent geometry : angle 0.68696 (18578) hydrogen bonds : bond 0.04691 ( 694) hydrogen bonds : angle 5.06815 ( 1963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7074 (mp) REVERT: A 337 GLN cc_start: 0.7131 (mm110) cc_final: 0.6185 (tp40) REVERT: A 372 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8535 (pt) REVERT: A 452 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7402 (pt0) REVERT: A 566 ASN cc_start: 0.5705 (OUTLIER) cc_final: 0.5133 (p0) REVERT: A 681 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 685 ILE cc_start: 0.8351 (mm) cc_final: 0.8036 (tt) REVERT: A 691 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 817 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 850 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6565 (mp0) REVERT: A 886 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: A 894 MET cc_start: 0.6110 (tmm) cc_final: 0.5840 (tmm) REVERT: B 264 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: B 290 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5494 (pp) REVERT: B 367 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 407 ASP cc_start: 0.6718 (m-30) cc_final: 0.6461 (m-30) REVERT: B 514 ASN cc_start: 0.8025 (t0) cc_final: 0.7614 (t0) REVERT: B 544 ASN cc_start: 0.7647 (m-40) cc_final: 0.7378 (m-40) REVERT: B 562 TRP cc_start: 0.8033 (t60) cc_final: 0.7747 (t60) REVERT: B 626 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7426 (t) REVERT: B 630 HIS cc_start: 0.7095 (m90) cc_final: 0.6470 (m90) REVERT: B 632 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7619 (mmtm) REVERT: B 713 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7640 (mmtt) REVERT: B 715 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: B 812 GLU cc_start: 0.7379 (tp30) cc_final: 0.6982 (tp30) REVERT: B 839 LYS cc_start: 0.7294 (mppt) cc_final: 0.6901 (mppt) REVERT: B 848 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6654 (ttt90) REVERT: B 883 ASP cc_start: 0.7223 (t0) cc_final: 0.6858 (t0) REVERT: B 938 ARG cc_start: 0.5799 (OUTLIER) cc_final: 0.5328 (tpm-80) REVERT: B 1066 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7140 (mtp85) REVERT: B 1085 LYS cc_start: 0.7744 (tttt) cc_final: 0.7453 (tttt) REVERT: B 1091 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7262 (mmtt) REVERT: B 1093 LEU cc_start: 0.7308 (tp) cc_final: 0.6856 (tp) REVERT: B 1094 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6765 (mt-10) outliers start: 72 outliers final: 42 residues processed: 306 average time/residue: 0.1133 time to fit residues: 48.1802 Evaluate side-chains 309 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.202408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.163716 restraints weight = 20753.221| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.09 r_work: 0.4037 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13629 Z= 0.160 Angle : 0.655 10.834 18578 Z= 0.339 Chirality : 0.043 0.413 2133 Planarity : 0.005 0.069 2201 Dihedral : 17.703 161.045 2153 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.01 % Allowed : 23.84 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.22), residues: 1518 helix: 0.62 (0.19), residues: 781 sheet: -2.09 (0.37), residues: 192 loop : -1.77 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 796 TYR 0.019 0.001 TYR B1011 PHE 0.028 0.002 PHE B 780 TRP 0.017 0.001 TRP B 768 HIS 0.010 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00357 (13629) covalent geometry : angle 0.65536 (18578) hydrogen bonds : bond 0.04317 ( 694) hydrogen bonds : angle 4.97162 ( 1963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7053 (mp) REVERT: A 337 GLN cc_start: 0.7030 (mm110) cc_final: 0.6404 (mm-40) REVERT: A 372 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8508 (pt) REVERT: A 402 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7597 (mm-40) REVERT: A 446 ASP cc_start: 0.7797 (m-30) cc_final: 0.7507 (m-30) REVERT: A 452 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7254 (pt0) REVERT: A 482 ARG cc_start: 0.7918 (tpm170) cc_final: 0.7224 (tpm170) REVERT: A 566 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5234 (p0) REVERT: A 681 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6500 (tt0) REVERT: A 685 ILE cc_start: 0.8324 (mm) cc_final: 0.7936 (tt) REVERT: A 691 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 850 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6575 (mp0) REVERT: A 886 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: A 894 MET cc_start: 0.6098 (tmm) cc_final: 0.5813 (tmm) REVERT: B 264 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: B 290 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5516 (pp) REVERT: B 367 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6945 (t80) REVERT: B 514 ASN cc_start: 0.7989 (t0) cc_final: 0.7604 (t0) REVERT: B 544 ASN cc_start: 0.7565 (m-40) cc_final: 0.7339 (m-40) REVERT: B 626 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7310 (t) REVERT: B 630 HIS cc_start: 0.7015 (m90) cc_final: 0.6441 (m90) REVERT: B 632 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7586 (mmtm) REVERT: B 713 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7608 (mmtt) REVERT: B 715 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7947 (mmm-85) REVERT: B 722 VAL cc_start: 0.8452 (m) cc_final: 0.8215 (p) REVERT: B 732 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6932 (mp0) REVERT: B 780 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 812 GLU cc_start: 0.7300 (tp30) cc_final: 0.6927 (tp30) REVERT: B 839 LYS cc_start: 0.7192 (mppt) cc_final: 0.6756 (mppt) REVERT: B 848 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6738 (ttt90) REVERT: B 859 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6904 (mt) REVERT: B 938 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.5386 (tpm-80) REVERT: B 1030 MET cc_start: 0.4604 (mmm) cc_final: 0.3576 (mmm) REVERT: B 1085 LYS cc_start: 0.7745 (tttt) cc_final: 0.7470 (tttt) REVERT: B 1091 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7277 (mmtt) REVERT: B 1094 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6733 (mt-10) outliers start: 69 outliers final: 49 residues processed: 304 average time/residue: 0.1170 time to fit residues: 49.6165 Evaluate side-chains 316 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.202257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.163513 restraints weight = 20871.071| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.10 r_work: 0.4032 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13629 Z= 0.171 Angle : 0.670 10.881 18578 Z= 0.346 Chirality : 0.043 0.420 2133 Planarity : 0.005 0.075 2201 Dihedral : 17.712 164.949 2153 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.38 % Allowed : 24.13 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.22), residues: 1518 helix: 0.57 (0.19), residues: 787 sheet: -2.12 (0.37), residues: 189 loop : -1.83 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 796 TYR 0.023 0.001 TYR B1011 PHE 0.022 0.002 PHE B 780 TRP 0.013 0.001 TRP B 768 HIS 0.010 0.001 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00380 (13629) covalent geometry : angle 0.67020 (18578) hydrogen bonds : bond 0.04375 ( 694) hydrogen bonds : angle 4.95619 ( 1963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 253 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7072 (mp) REVERT: A 337 GLN cc_start: 0.7076 (mm110) cc_final: 0.6493 (mm110) REVERT: A 372 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8499 (pt) REVERT: A 430 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8309 (ptpp) REVERT: A 446 ASP cc_start: 0.7804 (m-30) cc_final: 0.7495 (m-30) REVERT: A 452 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7270 (pt0) REVERT: A 482 ARG cc_start: 0.7921 (tpm170) cc_final: 0.7318 (tpm170) REVERT: A 485 MET cc_start: 0.7459 (mtt) cc_final: 0.7189 (mmm) REVERT: A 566 ASN cc_start: 0.6069 (OUTLIER) cc_final: 0.4849 (p0) REVERT: A 579 LYS cc_start: 0.8153 (mttt) cc_final: 0.7868 (mttt) REVERT: A 681 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: A 685 ILE cc_start: 0.8326 (mm) cc_final: 0.8007 (tt) REVERT: A 691 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 850 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6580 (mp0) REVERT: A 886 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: A 894 MET cc_start: 0.6052 (tmm) cc_final: 0.5785 (tmm) REVERT: B 264 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: B 290 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5523 (pp) REVERT: B 367 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 514 ASN cc_start: 0.7999 (t0) cc_final: 0.7619 (t0) REVERT: B 544 ASN cc_start: 0.7544 (m-40) cc_final: 0.7291 (m-40) REVERT: B 626 CYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7372 (t) REVERT: B 630 HIS cc_start: 0.7036 (m90) cc_final: 0.6483 (m90) REVERT: B 632 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7601 (mmtm) REVERT: B 647 HIS cc_start: 0.6911 (t-90) cc_final: 0.6653 (t-90) REVERT: B 713 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7628 (mmtt) REVERT: B 715 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: B 732 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6870 (mp0) REVERT: B 812 GLU cc_start: 0.7325 (tp30) cc_final: 0.6942 (tp30) REVERT: B 839 LYS cc_start: 0.7272 (mppt) cc_final: 0.6842 (mppt) REVERT: B 848 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6724 (ttt90) REVERT: B 859 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6924 (mt) REVERT: B 938 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.5350 (tpm-80) REVERT: B 1030 MET cc_start: 0.4645 (mmm) cc_final: 0.3592 (mmm) REVERT: B 1085 LYS cc_start: 0.7742 (tttt) cc_final: 0.7474 (tttt) REVERT: B 1091 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7260 (mmtt) REVERT: B 1094 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6799 (mt-10) outliers start: 74 outliers final: 50 residues processed: 302 average time/residue: 0.1230 time to fit residues: 51.4639 Evaluate side-chains 312 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.201674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.162813 restraints weight = 20801.176| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.05 r_work: 0.4025 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13629 Z= 0.192 Angle : 0.691 11.051 18578 Z= 0.357 Chirality : 0.044 0.410 2133 Planarity : 0.005 0.068 2201 Dihedral : 17.736 169.041 2153 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.80 % Allowed : 24.49 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1518 helix: 0.48 (0.19), residues: 784 sheet: -2.14 (0.38), residues: 182 loop : -1.78 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 669 TYR 0.037 0.002 TYR A 678 PHE 0.021 0.002 PHE B 780 TRP 0.011 0.001 TRP B 768 HIS 0.013 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00425 (13629) covalent geometry : angle 0.69070 (18578) hydrogen bonds : bond 0.04509 ( 694) hydrogen bonds : angle 5.00197 ( 1963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 251 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7098 (mp) REVERT: A 337 GLN cc_start: 0.7107 (mm110) cc_final: 0.5648 (mm-40) REVERT: A 340 ARG cc_start: 0.7328 (tpp80) cc_final: 0.6915 (tpp80) REVERT: A 372 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8638 (pt) REVERT: A 430 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8311 (ptpp) REVERT: A 446 ASP cc_start: 0.7782 (m-30) cc_final: 0.7460 (m-30) REVERT: A 452 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7368 (pt0) REVERT: A 482 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7502 (tpm170) REVERT: A 485 MET cc_start: 0.7477 (mtt) cc_final: 0.7130 (mmm) REVERT: A 566 ASN cc_start: 0.6058 (OUTLIER) cc_final: 0.4780 (p0) REVERT: A 595 LEU cc_start: 0.8200 (tp) cc_final: 0.7935 (tp) REVERT: A 643 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7349 (tp30) REVERT: A 678 TYR cc_start: 0.7181 (t80) cc_final: 0.6749 (t80) REVERT: A 681 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6703 (tt0) REVERT: A 685 ILE cc_start: 0.8289 (mm) cc_final: 0.7995 (tt) REVERT: A 691 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 698 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 850 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6574 (mp0) REVERT: A 886 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: A 894 MET cc_start: 0.6061 (tmm) cc_final: 0.5788 (tmm) REVERT: B 264 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: B 290 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5412 (pp) REVERT: B 367 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6904 (t80) REVERT: B 514 ASN cc_start: 0.8020 (t0) cc_final: 0.7548 (t0) REVERT: B 544 ASN cc_start: 0.7569 (m-40) cc_final: 0.7350 (m-40) REVERT: B 626 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7385 (t) REVERT: B 630 HIS cc_start: 0.7085 (m90) cc_final: 0.6524 (m90) REVERT: B 632 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7747 (mmtm) REVERT: B 636 GLN cc_start: 0.8043 (tp40) cc_final: 0.7562 (tp40) REVERT: B 647 HIS cc_start: 0.6953 (t-90) cc_final: 0.6672 (t-90) REVERT: B 713 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7649 (mmtt) REVERT: B 715 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7957 (mmm-85) REVERT: B 722 VAL cc_start: 0.8436 (m) cc_final: 0.8206 (p) REVERT: B 732 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6863 (mp0) REVERT: B 792 LEU cc_start: 0.8770 (tp) cc_final: 0.8396 (tp) REVERT: B 812 GLU cc_start: 0.7369 (tp30) cc_final: 0.6964 (tp30) REVERT: B 839 LYS cc_start: 0.7281 (mppt) cc_final: 0.6841 (mppt) REVERT: B 848 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6724 (ttt90) REVERT: B 859 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6907 (mt) REVERT: B 938 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5134 (tpm-80) REVERT: B 1030 MET cc_start: 0.4741 (mmm) cc_final: 0.3501 (mmm) REVERT: B 1085 LYS cc_start: 0.7734 (tttt) cc_final: 0.7441 (tttt) REVERT: B 1091 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7249 (mmtt) REVERT: B 1094 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6786 (mt-10) outliers start: 66 outliers final: 49 residues processed: 295 average time/residue: 0.1174 time to fit residues: 48.5153 Evaluate side-chains 312 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 ASN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.203169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.164514 restraints weight = 20920.712| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.12 r_work: 0.4047 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13629 Z= 0.147 Angle : 0.666 10.522 18578 Z= 0.343 Chirality : 0.043 0.392 2133 Planarity : 0.005 0.068 2201 Dihedral : 17.667 171.531 2153 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.58 % Allowed : 25.29 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.22), residues: 1518 helix: 0.65 (0.19), residues: 780 sheet: -2.22 (0.36), residues: 195 loop : -1.69 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 796 TYR 0.027 0.001 TYR A 678 PHE 0.015 0.002 PHE B 780 TRP 0.010 0.001 TRP B 768 HIS 0.012 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00331 (13629) covalent geometry : angle 0.66642 (18578) hydrogen bonds : bond 0.04201 ( 694) hydrogen bonds : angle 4.89820 ( 1963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.44 seconds wall clock time: 65 minutes 1.06 seconds (3901.06 seconds total)