Starting phenix.real_space_refine on Thu Sep 26 15:52:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_16971.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_16971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_16971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_16971.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/09_2024/8om9_16971.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.41, per 1000 atoms: 0.63 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: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.42 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: 5.53 Time building geometry restraints manager: 4.12 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.740 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- 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= 0.474 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (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 TRP 0.019 0.005 TRP A 764 HIS 0.011 0.003 HIS A 829 PHE 0.027 0.004 PHE B 784 TYR 0.027 0.004 TYR B1021 ARG 0.013 0.002 ARG B 593 *********************** 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 fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 1.352 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: 0.2895 time to fit residues: 119.9512 Evaluate side-chains 279 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13629 Z= 0.268 Angle : 0.654 6.874 18578 Z= 0.346 Chirality : 0.043 0.164 2133 Planarity : 0.004 0.049 2201 Dihedral : 17.954 153.788 2176 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.58 % Allowed : 20.86 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1518 helix: 0.41 (0.18), residues: 792 sheet: -2.51 (0.33), residues: 200 loop : -1.65 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 764 HIS 0.009 0.001 HIS B 984 PHE 0.020 0.002 PHE A 468 TYR 0.021 0.002 TYR B 846 ARG 0.004 0.001 ARG B 796 *********************** 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 338 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 275 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (p) REVERT: A 337 GLN cc_start: 0.6557 (mm-40) cc_final: 0.6313 (mm-40) REVERT: A 357 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 364 GLU cc_start: 0.7715 (tp30) cc_final: 0.7415 (tp30) REVERT: A 377 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6914 (tp-100) REVERT: A 452 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8038 (pt0) REVERT: A 459 ASP cc_start: 0.7584 (p0) cc_final: 0.7361 (p0) REVERT: A 482 ARG cc_start: 0.8790 (tpm170) cc_final: 0.8355 (tpm170) REVERT: A 566 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 626 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7963 (mp0) REVERT: A 647 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7793 (tm-30) REVERT: A 678 TYR cc_start: 0.7301 (t80) cc_final: 0.7064 (t80) REVERT: A 728 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6431 (pm20) REVERT: A 784 PHE cc_start: 0.7483 (m-80) cc_final: 0.7034 (m-80) REVERT: A 850 GLU cc_start: 0.8059 (mp0) cc_final: 0.7802 (mp0) REVERT: B 281 MET cc_start: 0.6095 (tpp) cc_final: 0.5817 (tpp) REVERT: B 367 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 407 ASP cc_start: 0.7698 (m-30) cc_final: 0.7497 (m-30) REVERT: B 434 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8432 (pm20) REVERT: B 526 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7755 (mmmm) REVERT: B 626 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8303 (t) REVERT: B 630 HIS cc_start: 0.7410 (m90) cc_final: 0.7084 (m90) REVERT: B 673 LEU cc_start: 0.7637 (mt) cc_final: 0.7410 (mp) REVERT: B 674 GLU cc_start: 0.7904 (tp30) cc_final: 0.7644 (mm-30) REVERT: B 732 GLU cc_start: 0.8271 (mp0) cc_final: 0.7928 (tm-30) REVERT: B 938 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6564 (tpm-80) REVERT: B 1030 MET cc_start: 0.4342 (mmm) cc_final: 0.3900 (mmm) REVERT: B 1085 LYS cc_start: 0.8227 (tttt) cc_final: 0.7961 (tttt) REVERT: B 1091 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7908 (mmmm) REVERT: B 1093 LEU cc_start: 0.7627 (tp) cc_final: 0.7309 (tp) REVERT: B 1094 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7764 (mt-10) outliers start: 63 outliers final: 27 residues processed: 314 average time/residue: 0.2917 time to fit residues: 127.8228 Evaluate side-chains 304 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 270 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 414 LEU 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 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 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 425 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 815 SER 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 1066 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13629 Z= 0.253 Angle : 0.632 11.998 18578 Z= 0.331 Chirality : 0.042 0.214 2133 Planarity : 0.004 0.055 2201 Dihedral : 17.937 147.016 2158 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.72 % Allowed : 21.15 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1518 helix: 0.53 (0.18), residues: 783 sheet: -2.30 (0.36), residues: 175 loop : -1.63 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.006 0.001 HIS B 984 PHE 0.016 0.002 PHE B 703 TYR 0.019 0.002 TYR B 846 ARG 0.006 0.001 ARG B 669 *********************** 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 342 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 277 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6252 (mm-40) REVERT: A 357 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 364 GLU cc_start: 0.7672 (tp30) cc_final: 0.7257 (tp30) REVERT: A 452 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7999 (pt0) REVERT: A 480 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 565 LYS cc_start: 0.8628 (pttm) cc_final: 0.8419 (pttp) REVERT: A 595 LEU cc_start: 0.8463 (tp) cc_final: 0.8088 (tt) REVERT: A 626 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7945 (mp0) REVERT: A 647 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7726 (tm-30) REVERT: A 678 TYR cc_start: 0.7264 (t80) cc_final: 0.7016 (t80) REVERT: A 685 ILE cc_start: 0.8634 (mm) cc_final: 0.8050 (tt) REVERT: A 711 ARG cc_start: 0.6883 (tpt170) cc_final: 0.6605 (tpt90) REVERT: A 784 PHE cc_start: 0.7443 (m-80) cc_final: 0.6992 (m-80) REVERT: A 817 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 850 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7897 (mp0) REVERT: B 264 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: B 367 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 434 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8429 (pm20) REVERT: B 526 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7720 (mmmm) REVERT: B 544 ASN cc_start: 0.8021 (m-40) cc_final: 0.7631 (m-40) REVERT: B 580 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.6993 (t) REVERT: B 591 ASN cc_start: 0.8171 (m-40) cc_final: 0.7667 (p0) REVERT: B 626 CYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8273 (t) REVERT: B 630 HIS cc_start: 0.7442 (m90) cc_final: 0.7096 (m90) REVERT: B 642 VAL cc_start: 0.8564 (m) cc_final: 0.8358 (t) REVERT: B 713 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7610 (mmtt) REVERT: B 714 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8759 (tmmt) REVERT: B 729 HIS cc_start: 0.8150 (t-90) cc_final: 0.7875 (t-90) REVERT: B 732 GLU cc_start: 0.8383 (mp0) cc_final: 0.7891 (tm-30) REVERT: B 812 GLU cc_start: 0.7860 (tp30) cc_final: 0.7370 (tp30) REVERT: B 883 ASP cc_start: 0.7932 (t70) cc_final: 0.7384 (t70) REVERT: B 908 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 1030 MET cc_start: 0.4408 (mmm) cc_final: 0.3980 (mmm) REVERT: B 1085 LYS cc_start: 0.8219 (tttt) cc_final: 0.7968 (tttt) REVERT: B 1091 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7911 (mmmm) REVERT: B 1094 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7822 (mt-10) outliers start: 65 outliers final: 35 residues processed: 313 average time/residue: 0.2835 time to fit residues: 123.8096 Evaluate side-chains 306 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 377 GLN 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 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 688 MET 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 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR 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 636 GLN Chi-restraints excluded: chain B residue 678 LEU 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 855 ARG 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 142 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 0.0370 chunk 144 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN B 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13629 Z= 0.191 Angle : 0.609 11.493 18578 Z= 0.317 Chirality : 0.041 0.304 2133 Planarity : 0.004 0.061 2201 Dihedral : 17.782 142.971 2153 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.52 % Allowed : 21.29 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1518 helix: 0.71 (0.19), residues: 788 sheet: -2.26 (0.36), residues: 183 loop : -1.58 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1122 HIS 0.005 0.001 HIS B 729 PHE 0.016 0.001 PHE A 468 TYR 0.017 0.001 TYR B1028 ARG 0.011 0.000 ARG B 796 *********************** 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 342 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 266 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 PHE cc_start: 0.7929 (m-80) cc_final: 0.7702 (m-80) REVERT: A 337 GLN cc_start: 0.6507 (mm-40) cc_final: 0.6162 (mm110) REVERT: A 364 GLU cc_start: 0.7621 (tp30) cc_final: 0.7152 (tp30) REVERT: A 430 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8300 (ptpp) REVERT: A 452 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7958 (pt0) REVERT: A 503 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4000 (tp) REVERT: A 566 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 626 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7888 (mp0) REVERT: A 647 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7730 (tm-30) REVERT: A 678 TYR cc_start: 0.7194 (t80) cc_final: 0.6911 (t80) REVERT: A 685 ILE cc_start: 0.8590 (mm) cc_final: 0.8003 (tt) REVERT: A 850 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7795 (mp0) REVERT: B 264 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: B 281 MET cc_start: 0.5958 (tpp) cc_final: 0.5720 (tpp) REVERT: B 290 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6583 (pp) REVERT: B 367 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7557 (t80) REVERT: B 434 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8398 (pm20) REVERT: B 514 ASN cc_start: 0.8188 (t0) cc_final: 0.7967 (t0) REVERT: B 526 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7671 (mmmm) REVERT: B 626 CYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8192 (t) REVERT: B 630 HIS cc_start: 0.7379 (m90) cc_final: 0.7043 (m90) REVERT: B 636 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (tp40) REVERT: B 713 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7436 (mmtt) REVERT: B 714 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8752 (tmmt) REVERT: B 729 HIS cc_start: 0.8148 (t-90) cc_final: 0.7866 (t-90) REVERT: B 732 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: B 737 LEU cc_start: 0.8105 (tp) cc_final: 0.7885 (mm) REVERT: B 812 GLU cc_start: 0.7814 (tp30) cc_final: 0.7341 (tp30) REVERT: B 848 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6779 (ttt90) REVERT: B 883 ASP cc_start: 0.7971 (t70) cc_final: 0.7473 (t0) REVERT: B 1030 MET cc_start: 0.4264 (mmm) cc_final: 0.3853 (mmm) REVERT: B 1085 LYS cc_start: 0.8227 (tttt) cc_final: 0.7899 (tttt) REVERT: B 1091 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7881 (mmmm) REVERT: B 1094 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7894 (mt-10) outliers start: 76 outliers final: 39 residues processed: 315 average time/residue: 0.2877 time to fit residues: 127.1918 Evaluate side-chains 297 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 503 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 807 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 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 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 732 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.0370 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13629 Z= 0.277 Angle : 0.642 10.896 18578 Z= 0.335 Chirality : 0.043 0.326 2133 Planarity : 0.005 0.062 2201 Dihedral : 17.749 146.360 2153 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.81 % Allowed : 21.88 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1518 helix: 0.64 (0.19), residues: 778 sheet: -2.06 (0.38), residues: 175 loop : -1.61 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.006 0.001 HIS B 864 PHE 0.017 0.002 PHE A 836 TYR 0.027 0.002 TYR B1011 ARG 0.013 0.001 ARG B 796 *********************** 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 349 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 269 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.6975 (mp10) cc_final: 0.6692 (mp10) REVERT: A 357 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 358 GLU cc_start: 0.7921 (pt0) cc_final: 0.7540 (pp20) REVERT: A 452 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7974 (pt0) REVERT: A 460 MET cc_start: 0.7771 (mtm) cc_final: 0.6778 (mtm) REVERT: A 485 MET cc_start: 0.7562 (mmm) cc_final: 0.7322 (mmm) REVERT: A 503 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.4201 (tp) REVERT: A 566 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7542 (p0) REVERT: A 626 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8021 (mp0) REVERT: A 647 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7730 (tm-30) REVERT: A 678 TYR cc_start: 0.7234 (t80) cc_final: 0.7009 (t80) REVERT: A 685 ILE cc_start: 0.8653 (mm) cc_final: 0.8171 (tt) REVERT: A 784 PHE cc_start: 0.7393 (m-80) cc_final: 0.6948 (m-80) REVERT: A 850 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 264 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: B 290 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6549 (pp) REVERT: B 367 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 434 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8438 (pm20) REVERT: B 514 ASN cc_start: 0.8254 (t0) cc_final: 0.8048 (t0) REVERT: B 526 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7721 (mmmm) REVERT: B 544 ASN cc_start: 0.8090 (m-40) cc_final: 0.7779 (m-40) REVERT: B 580 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7031 (t) REVERT: B 594 LEU cc_start: 0.7964 (mt) cc_final: 0.7670 (mt) REVERT: B 626 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 630 HIS cc_start: 0.7489 (m90) cc_final: 0.7175 (m90) REVERT: B 713 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7712 (mmtt) REVERT: B 714 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8783 (tmmt) REVERT: B 729 HIS cc_start: 0.8163 (t-90) cc_final: 0.7864 (t-90) REVERT: B 732 GLU cc_start: 0.8346 (mp0) cc_final: 0.7890 (tm-30) REVERT: B 812 GLU cc_start: 0.7874 (tp30) cc_final: 0.7388 (tp30) REVERT: B 848 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6847 (ttt90) REVERT: B 883 ASP cc_start: 0.7924 (t70) cc_final: 0.7450 (t0) REVERT: B 938 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6461 (tpm-80) REVERT: B 1030 MET cc_start: 0.4653 (mmm) cc_final: 0.4235 (mmm) REVERT: B 1085 LYS cc_start: 0.8252 (tttt) cc_final: 0.8025 (tttt) REVERT: B 1091 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7903 (mmmm) REVERT: B 1094 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7830 (mt-10) outliers start: 80 outliers final: 47 residues processed: 322 average time/residue: 0.2790 time to fit residues: 126.7013 Evaluate side-chains 319 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 263 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN 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 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 788 THR 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 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 406 GLN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 541 THR 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 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 847 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 51 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 0.0770 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 429 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13629 Z= 0.236 Angle : 0.634 12.206 18578 Z= 0.328 Chirality : 0.043 0.390 2133 Planarity : 0.005 0.065 2201 Dihedral : 17.712 152.519 2153 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.23 % Allowed : 22.46 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1518 helix: 0.71 (0.19), residues: 774 sheet: -1.95 (0.39), residues: 181 loop : -1.58 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 768 HIS 0.008 0.001 HIS A 829 PHE 0.023 0.002 PHE A 286 TYR 0.019 0.001 TYR B1011 ARG 0.008 0.001 ARG B 796 *********************** 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 342 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 270 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.6975 (mp10) cc_final: 0.6639 (mp10) REVERT: A 313 PHE cc_start: 0.8105 (m-80) cc_final: 0.7803 (m-80) REVERT: A 337 GLN cc_start: 0.7001 (mm110) cc_final: 0.6799 (mm-40) REVERT: A 357 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 402 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8218 (mm-40) REVERT: A 430 LYS cc_start: 0.8650 (ptpp) cc_final: 0.8357 (ptpp) REVERT: A 452 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7969 (pt0) REVERT: A 503 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4139 (tp) REVERT: A 566 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7548 (p0) REVERT: A 643 GLU cc_start: 0.8520 (tp30) cc_final: 0.8301 (tp30) REVERT: A 647 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7716 (tm-30) REVERT: A 685 ILE cc_start: 0.8613 (mm) cc_final: 0.8136 (tt) REVERT: A 698 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 784 PHE cc_start: 0.7348 (m-80) cc_final: 0.6933 (m-80) REVERT: A 850 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7845 (mp0) REVERT: B 264 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: B 290 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6539 (pp) REVERT: B 367 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7606 (t80) REVERT: B 415 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: B 434 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8434 (pm20) REVERT: B 508 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7527 (tppt) REVERT: B 514 ASN cc_start: 0.8272 (t0) cc_final: 0.7994 (t0) REVERT: B 544 ASN cc_start: 0.8058 (m-40) cc_final: 0.7764 (m-40) REVERT: B 580 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7030 (t) REVERT: B 594 LEU cc_start: 0.7937 (mt) cc_final: 0.7636 (mt) REVERT: B 626 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8284 (t) REVERT: B 630 HIS cc_start: 0.7477 (m90) cc_final: 0.7208 (m-70) REVERT: B 632 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8009 (mmtm) REVERT: B 687 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7552 (mmmt) REVERT: B 713 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7817 (mmtt) REVERT: B 729 HIS cc_start: 0.8165 (t-90) cc_final: 0.7854 (t-90) REVERT: B 732 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: B 812 GLU cc_start: 0.7867 (tp30) cc_final: 0.7374 (tp30) REVERT: B 839 LYS cc_start: 0.7528 (mmtp) cc_final: 0.7320 (mppt) REVERT: B 848 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6821 (ttt90) REVERT: B 859 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7249 (mt) REVERT: B 883 ASP cc_start: 0.7970 (t70) cc_final: 0.7484 (t0) REVERT: B 908 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 938 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6420 (tpm-80) REVERT: B 1030 MET cc_start: 0.4602 (mmm) cc_final: 0.4249 (mmm) REVERT: B 1085 LYS cc_start: 0.8237 (tttt) cc_final: 0.8005 (tttt) REVERT: B 1094 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 72 outliers final: 46 residues processed: 318 average time/residue: 0.2971 time to fit residues: 130.8532 Evaluate side-chains 319 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 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 377 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 503 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 788 THR 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 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 406 GLN Chi-restraints excluded: chain B residue 415 GLU 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 580 VAL 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 732 GLU 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 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 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 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 553 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN B 636 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2435 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= 0.228 Angle : 0.632 11.402 18578 Z= 0.326 Chirality : 0.042 0.415 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.686 158.340 2153 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.52 % Allowed : 22.82 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1518 helix: 0.72 (0.19), residues: 776 sheet: -1.87 (0.39), residues: 186 loop : -1.57 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 768 HIS 0.007 0.001 HIS A 829 PHE 0.016 0.002 PHE B 402 TYR 0.019 0.001 TYR B1011 ARG 0.009 0.000 ARG A 355 *********************** 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 339 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 263 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.7084 (mp10) cc_final: 0.6735 (mp10) REVERT: A 313 PHE cc_start: 0.8090 (m-80) cc_final: 0.7805 (m-80) REVERT: A 337 GLN cc_start: 0.7031 (mm110) cc_final: 0.6827 (mm-40) REVERT: A 357 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 402 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8217 (mm-40) REVERT: A 430 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8324 (ptpp) REVERT: A 452 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7949 (pt0) REVERT: A 503 LEU cc_start: 0.4655 (OUTLIER) cc_final: 0.4112 (tp) REVERT: A 566 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7553 (p0) REVERT: A 643 GLU cc_start: 0.8498 (tp30) cc_final: 0.8267 (tp30) REVERT: A 647 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7915 (tm-30) REVERT: A 678 TYR cc_start: 0.7303 (t80) cc_final: 0.7034 (t80) REVERT: A 685 ILE cc_start: 0.8603 (mm) cc_final: 0.8045 (tt) REVERT: A 698 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 784 PHE cc_start: 0.7337 (m-80) cc_final: 0.6951 (m-80) REVERT: A 850 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 264 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8350 (tm-30) REVERT: B 290 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6550 (pp) REVERT: B 367 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7606 (t80) REVERT: B 415 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: B 434 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8408 (pm20) REVERT: B 514 ASN cc_start: 0.8281 (t0) cc_final: 0.8041 (t0) REVERT: B 544 ASN cc_start: 0.8062 (m-40) cc_final: 0.7778 (m-40) REVERT: B 594 LEU cc_start: 0.7920 (mt) cc_final: 0.7634 (mt) REVERT: B 626 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8112 (t) REVERT: B 630 HIS cc_start: 0.7439 (m90) cc_final: 0.7123 (m90) REVERT: B 687 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7750 (mmmt) REVERT: B 713 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7812 (mmtt) REVERT: B 729 HIS cc_start: 0.8152 (t-90) cc_final: 0.7840 (t-90) REVERT: B 732 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: B 812 GLU cc_start: 0.7857 (tp30) cc_final: 0.7355 (tp30) REVERT: B 839 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7265 (mppt) REVERT: B 848 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6845 (ttt90) REVERT: B 883 ASP cc_start: 0.7966 (t70) cc_final: 0.7452 (t0) REVERT: B 908 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 938 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6372 (tpm-80) REVERT: B 1085 LYS cc_start: 0.8231 (tttt) cc_final: 0.7997 (tttt) REVERT: B 1094 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7818 (mt-10) outliers start: 76 outliers final: 49 residues processed: 314 average time/residue: 0.2976 time to fit residues: 129.2675 Evaluate side-chains 320 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 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 503 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 788 THR 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 849 LEU 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 415 GLU 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 732 GLU 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 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 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 94 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 402 GLN A 429 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13629 Z= 0.261 Angle : 0.655 11.381 18578 Z= 0.338 Chirality : 0.043 0.413 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.710 163.581 2153 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.94 % Allowed : 23.47 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1518 helix: 0.65 (0.19), residues: 776 sheet: -1.93 (0.39), residues: 181 loop : -1.59 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 768 HIS 0.007 0.001 HIS A 829 PHE 0.015 0.002 PHE B 402 TYR 0.023 0.001 TYR B1011 ARG 0.013 0.001 ARG B 796 *********************** 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 335 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 267 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8085 (tt0) cc_final: 0.7828 (tt0) REVERT: A 298 GLN cc_start: 0.7119 (mp10) cc_final: 0.6756 (mp10) REVERT: A 313 PHE cc_start: 0.8064 (m-80) cc_final: 0.7862 (m-80) REVERT: A 357 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 372 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8591 (pt) REVERT: A 430 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8374 (ptpp) REVERT: A 452 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7908 (pt0) REVERT: A 503 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4115 (tp) REVERT: A 566 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7464 (p0) REVERT: A 643 GLU cc_start: 0.8509 (tp30) cc_final: 0.8271 (tp30) REVERT: A 647 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7820 (tm-30) REVERT: A 685 ILE cc_start: 0.8622 (mm) cc_final: 0.8082 (tt) REVERT: A 850 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7845 (mp0) REVERT: B 264 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 290 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6443 (pp) REVERT: B 367 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 415 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: B 434 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8442 (pm20) REVERT: B 514 ASN cc_start: 0.8258 (t0) cc_final: 0.8019 (t0) REVERT: B 544 ASN cc_start: 0.8044 (m-40) cc_final: 0.7828 (m-40) REVERT: B 562 TRP cc_start: 0.8245 (t60) cc_final: 0.7956 (t60) REVERT: B 580 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7076 (t) REVERT: B 594 LEU cc_start: 0.7932 (mt) cc_final: 0.7633 (mt) REVERT: B 626 CYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8097 (t) REVERT: B 630 HIS cc_start: 0.7479 (m90) cc_final: 0.7115 (m90) REVERT: B 632 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8067 (mmtm) REVERT: B 687 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7563 (mmmt) REVERT: B 713 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7819 (mmtt) REVERT: B 722 VAL cc_start: 0.9029 (m) cc_final: 0.8822 (p) REVERT: B 729 HIS cc_start: 0.8149 (t-90) cc_final: 0.7839 (t-90) REVERT: B 732 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: B 812 GLU cc_start: 0.7916 (tp30) cc_final: 0.7412 (tp30) REVERT: B 839 LYS cc_start: 0.7482 (mmtp) cc_final: 0.7259 (mppt) REVERT: B 848 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6849 (ttt90) REVERT: B 883 ASP cc_start: 0.7964 (t70) cc_final: 0.7437 (t0) REVERT: B 908 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 938 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6247 (tpm-80) REVERT: B 1085 LYS cc_start: 0.8242 (tttt) cc_final: 0.8030 (tttt) REVERT: B 1091 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7950 (mmmt) REVERT: B 1094 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7833 (mt-10) outliers start: 68 outliers final: 47 residues processed: 310 average time/residue: 0.2956 time to fit residues: 126.7906 Evaluate side-chains 320 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 414 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE 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 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP 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 688 MET Chi-restraints excluded: chain A residue 788 THR 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 849 LEU 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 415 GLU 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 580 VAL 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 732 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 429 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2708 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= 0.248 Angle : 0.652 11.247 18578 Z= 0.336 Chirality : 0.043 0.415 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.708 167.757 2153 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.65 % Allowed : 23.91 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1518 helix: 0.68 (0.19), residues: 776 sheet: -1.98 (0.38), residues: 181 loop : -1.54 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 768 HIS 0.008 0.001 HIS B 817 PHE 0.016 0.002 PHE A 725 TYR 0.033 0.002 TYR A 678 ARG 0.015 0.001 ARG B 796 *********************** 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 318 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 254 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8111 (tt0) cc_final: 0.7829 (tt0) REVERT: A 298 GLN cc_start: 0.7083 (mp10) cc_final: 0.6716 (mp10) REVERT: A 372 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8578 (pt) REVERT: A 430 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8340 (ptpp) REVERT: A 452 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7863 (pt0) REVERT: A 482 ARG cc_start: 0.8881 (tpm170) cc_final: 0.8512 (tpm170) REVERT: A 566 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7441 (p0) REVERT: A 643 GLU cc_start: 0.8526 (tp30) cc_final: 0.8300 (tp30) REVERT: A 647 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7804 (tm-30) REVERT: A 681 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: A 685 ILE cc_start: 0.8622 (mm) cc_final: 0.8084 (tt) REVERT: A 784 PHE cc_start: 0.7331 (m-80) cc_final: 0.6927 (m-80) REVERT: A 850 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7828 (mp0) REVERT: B 264 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: B 290 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6547 (pp) REVERT: B 367 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 415 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: B 434 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8457 (pm20) REVERT: B 514 ASN cc_start: 0.8263 (t0) cc_final: 0.8034 (t0) REVERT: B 544 ASN cc_start: 0.8028 (m-40) cc_final: 0.7827 (m110) REVERT: B 562 TRP cc_start: 0.8233 (t60) cc_final: 0.7948 (t60) REVERT: B 580 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7062 (t) REVERT: B 594 LEU cc_start: 0.8001 (mt) cc_final: 0.7734 (mt) REVERT: B 626 CYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8116 (t) REVERT: B 630 HIS cc_start: 0.7467 (m90) cc_final: 0.7084 (m90) REVERT: B 632 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7997 (mmtm) REVERT: B 674 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7518 (tp30) REVERT: B 687 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7744 (mmmt) REVERT: B 713 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7820 (mmtt) REVERT: B 715 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8241 (mmm-85) REVERT: B 729 HIS cc_start: 0.8144 (t-90) cc_final: 0.7831 (t-90) REVERT: B 732 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: B 812 GLU cc_start: 0.7884 (tp30) cc_final: 0.7380 (tp30) REVERT: B 839 LYS cc_start: 0.7485 (mmtp) cc_final: 0.7261 (mppt) REVERT: B 848 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6855 (ttt90) REVERT: B 883 ASP cc_start: 0.7974 (t70) cc_final: 0.7449 (t0) REVERT: B 938 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6189 (tpm-80) REVERT: B 1030 MET cc_start: 0.4626 (mmm) cc_final: 0.3895 (mmm) REVERT: B 1085 LYS cc_start: 0.8248 (tttt) cc_final: 0.8035 (tttt) REVERT: B 1094 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 64 outliers final: 48 residues processed: 292 average time/residue: 0.2971 time to fit residues: 119.2375 Evaluate side-chains 312 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 252 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 497 ILE 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 788 THR 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 849 LEU 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 415 GLU 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 580 VAL 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 732 GLU 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 847 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 429 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13629 Z= 0.295 Angle : 0.690 11.474 18578 Z= 0.355 Chirality : 0.044 0.429 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.750 171.855 2153 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.51 % Allowed : 24.71 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1518 helix: 0.51 (0.18), residues: 784 sheet: -2.08 (0.38), residues: 175 loop : -1.62 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 768 HIS 0.009 0.001 HIS B 817 PHE 0.015 0.002 PHE A 836 TYR 0.030 0.002 TYR A 678 ARG 0.011 0.001 ARG B 796 ********************** 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 325 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8151 (tt0) cc_final: 0.7892 (tt0) REVERT: A 298 GLN cc_start: 0.7186 (mp10) cc_final: 0.6823 (mp10) REVERT: A 337 GLN cc_start: 0.7190 (mm110) cc_final: 0.6597 (mm-40) REVERT: A 340 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7631 (tpp80) REVERT: A 347 LYS cc_start: 0.8475 (pttp) cc_final: 0.8103 (tmtt) REVERT: A 354 ASN cc_start: 0.6822 (m-40) cc_final: 0.6358 (p0) REVERT: A 355 ARG cc_start: 0.8016 (ptm160) cc_final: 0.7728 (ptm-80) REVERT: A 372 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8724 (pt) REVERT: A 430 LYS cc_start: 0.8687 (ptpp) cc_final: 0.8380 (ptpp) REVERT: A 446 ASP cc_start: 0.8452 (m-30) cc_final: 0.8223 (m-30) REVERT: A 452 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7913 (pt0) REVERT: A 482 ARG cc_start: 0.8886 (tpm170) cc_final: 0.8466 (tpm170) REVERT: A 566 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7461 (p0) REVERT: A 643 GLU cc_start: 0.8526 (tp30) cc_final: 0.8296 (tp30) REVERT: A 647 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7838 (tm-30) REVERT: A 678 TYR cc_start: 0.7472 (t80) cc_final: 0.5927 (t80) REVERT: A 681 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 685 ILE cc_start: 0.8633 (mm) cc_final: 0.8131 (tt) REVERT: A 784 PHE cc_start: 0.7356 (m-80) cc_final: 0.6945 (m-80) REVERT: A 850 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7824 (mp0) REVERT: B 264 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: B 290 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6401 (pp) REVERT: B 367 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7610 (t80) REVERT: B 399 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7099 (mm-30) REVERT: B 415 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7138 (pt0) REVERT: B 434 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8477 (pm20) REVERT: B 514 ASN cc_start: 0.8299 (t0) cc_final: 0.8080 (t0) REVERT: B 562 TRP cc_start: 0.8253 (t60) cc_final: 0.8001 (t60) REVERT: B 580 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.7073 (t) REVERT: B 594 LEU cc_start: 0.7999 (mt) cc_final: 0.7706 (mt) REVERT: B 626 CYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8145 (t) REVERT: B 630 HIS cc_start: 0.7517 (m90) cc_final: 0.7150 (m90) REVERT: B 632 LYS cc_start: 0.8381 (mmtm) cc_final: 0.8113 (mmtm) REVERT: B 674 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7525 (tp30) REVERT: B 687 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7595 (mmmt) REVERT: B 713 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7864 (mmtt) REVERT: B 715 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: B 720 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8107 (tp-100) REVERT: B 729 HIS cc_start: 0.8150 (t-90) cc_final: 0.7876 (t-90) REVERT: B 732 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 812 GLU cc_start: 0.8043 (tp30) cc_final: 0.7517 (tp30) REVERT: B 839 LYS cc_start: 0.7503 (mmtp) cc_final: 0.7276 (mppt) REVERT: B 848 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6781 (ttt90) REVERT: B 938 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6216 (tpm-80) REVERT: B 1030 MET cc_start: 0.4793 (mmm) cc_final: 0.3893 (mmm) REVERT: B 1085 LYS cc_start: 0.8250 (tttt) cc_final: 0.8023 (tttt) REVERT: B 1094 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7846 (mt-10) outliers start: 62 outliers final: 46 residues processed: 300 average time/residue: 0.3111 time to fit residues: 128.6773 Evaluate side-chains 315 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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 497 ILE 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 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 726 MET 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 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 415 GLU 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 580 VAL 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 732 GLU 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 847 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 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.202933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.164420 restraints weight = 20660.924| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.08 r_work: 0.4050 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13629 Z= 0.212 Angle : 0.647 10.883 18578 Z= 0.332 Chirality : 0.042 0.410 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.671 174.337 2153 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.36 % Allowed : 25.00 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1518 helix: 0.74 (0.19), residues: 776 sheet: -2.15 (0.36), residues: 187 loop : -1.53 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 768 HIS 0.007 0.001 HIS B 817 PHE 0.013 0.002 PHE A 725 TYR 0.028 0.001 TYR A 678 ARG 0.011 0.000 ARG B 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.18 seconds wall clock time: 66 minutes 19.81 seconds (3979.81 seconds total)