Starting phenix.real_space_refine on Thu May 15 15:45:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.map" model { file = "/net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8om5_16969/05_2025/8om5_16969.cif" } resolution = 3.52 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= 0.025 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 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8366 2.51 5 N 2239 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6551 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 802} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6531 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 26, 'TRANS': 785} Chain breaks: 9 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: 7.78, per 1000 atoms: 0.59 Number of scatterers: 13138 At special positions: 0 Unit cell: (94.1626, 162.728, 119.76, 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 4 15.00 Mg 2 11.99 O 2465 8.00 N 2239 7.00 C 8366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS B 274 " distance=2.50 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: 3.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 54.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.740A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.605A 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 236 through 242 removed outlier: 3.606A pdb=" N ASP A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.867A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 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 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.685A pdb=" N ARG A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 421 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 429 through 457 removed outlier: 5.015A pdb=" N VAL A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Proline residue: A 439 - end of helix removed outlier: 4.628A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 504 removed outlier: 3.675A pdb=" N SER A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 553 through 588 removed outlier: 5.410A pdb=" N ALA A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 614 Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 876 through 891 Processing helix chain 'A' and resid 909 through 919 Processing helix chain 'B' and resid 232 through 243 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 411 through 421 Processing helix chain 'B' and resid 433 through 446 removed outlier: 4.089A pdb=" N VAL B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 467 through 476 Processing helix chain 'B' and resid 491 through 495 removed outlier: 4.194A pdb=" N ASN B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 545 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 602 Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 660 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 665 through 679 Proline residue: B 676 - end of helix removed outlier: 3.790A pdb=" N LEU B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 4.009A pdb=" N HIS B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 688 " --> pdb=" O HIS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 697 Processing helix chain 'B' and resid 709 through 737 removed outlier: 4.224A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 817 Processing helix chain 'B' and resid 817 through 843 removed outlier: 4.112A pdb=" N LEU B 821 " --> pdb=" O HIS B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 871 removed outlier: 3.879A pdb=" N VAL B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 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 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1067 through 1076 Processing helix chain 'B' and resid 1079 through 1113 removed outlier: 3.691A pdb=" N THR B1112 " --> pdb=" O ALA B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1125 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.865A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 103 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 38 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 104 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 119 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.143A pdb=" N CYS A 199 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.007A pdb=" N LEU A 173 " --> pdb=" O THR A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.719A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 803 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 516 removed outlier: 3.794A pdb=" N LYS A 512 " --> pdb=" O ARG A 524 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 543 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 552 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N THR A 541 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 308 removed outlier: 3.921A pdb=" N ALA B 332 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 6.951A pdb=" N LEU B 369 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 386 through 390 Processing sheet with id=AB2, first strand: chain 'B' and resid 745 through 747 removed outlier: 6.507A pdb=" N VAL B 745 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 752 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 747 " --> pdb=" O GLN B 750 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 754 " --> pdb=" O PHE B 780 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 777 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER B 773 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 779 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 880 through 885 removed outlier: 5.063A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 934 through 937 removed outlier: 6.432A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER B 970 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU B1006 " --> pdb=" O SER B 970 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET B 892 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B1030 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B1031 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN B1058 " --> pdb=" O GLY B1031 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3907 1.34 - 1.46: 3260 1.46 - 1.58: 6088 1.58 - 1.70: 5 1.70 - 1.82: 100 Bond restraints: 13360 Sorted by residual: bond pdb=" C4 ADP B1201 " pdb=" C5 ADP B1201 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C5 ADP A2000 " pdb=" C6 ADP A2000 " ideal model delta sigma weight residual 1.490 1.419 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 ADP B1201 " pdb=" C6 ADP B1201 " ideal model delta sigma weight residual 1.490 1.422 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CE1 HIS A 801 " pdb=" NE2 HIS A 801 " ideal model delta sigma weight residual 1.321 1.347 -0.026 1.00e-02 1.00e+04 6.52e+00 ... (remaining 13355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 16547 1.76 - 3.52: 1278 3.52 - 5.28: 150 5.28 - 7.04: 37 7.04 - 8.80: 9 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C HIS B 817 " pdb=" N TYR B 818 " pdb=" CA TYR B 818 " ideal model delta sigma weight residual 120.28 126.60 -6.32 1.44e+00 4.82e-01 1.93e+01 angle pdb=" CA ASP A 446 " pdb=" CB ASP A 446 " pdb=" CG ASP A 446 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " pdb=" CD GLU B 496 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.70e+00 3.46e-01 1.62e+01 angle pdb=" N ILE B 656 " pdb=" CA ILE B 656 " pdb=" CB ILE B 656 " ideal model delta sigma weight residual 110.52 113.18 -2.66 6.70e-01 2.23e+00 1.58e+01 angle pdb=" CB GLU B 415 " pdb=" CG GLU B 415 " pdb=" CD GLU B 415 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.70e+00 3.46e-01 1.53e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 7802 33.06 - 66.12: 303 66.12 - 99.17: 34 99.17 - 132.23: 2 132.23 - 165.29: 1 Dihedral angle restraints: 8142 sinusoidal: 3355 harmonic: 4787 Sorted by residual: dihedral pdb=" C5' ADP B1201 " pdb=" O5' ADP B1201 " pdb=" PA ADP B1201 " pdb=" O2A ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 105.29 -165.29 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O2A ADP B1201 " pdb=" O3A ADP B1201 " pdb=" PA ADP B1201 " pdb=" PB ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 71.59 -131.59 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP B1201 " pdb=" O3A ADP B1201 " pdb=" PB ADP B1201 " pdb=" PA ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 -166.12 106.12 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 8139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1403 0.077 - 0.154: 577 0.154 - 0.230: 72 0.230 - 0.307: 8 0.307 - 0.384: 3 Chirality restraints: 2063 Sorted by residual: chirality pdb=" CA LEU A 833 " pdb=" N LEU A 833 " pdb=" C LEU A 833 " pdb=" CB LEU A 833 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CG LEU B 828 " pdb=" CB LEU B 828 " pdb=" CD1 LEU B 828 " pdb=" CD2 LEU B 828 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU B 811 " pdb=" CB LEU B 811 " pdb=" CD1 LEU B 811 " pdb=" CD2 LEU B 811 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 2060 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 815 " 0.021 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR A 815 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 815 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 815 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 815 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1068 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR B1068 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B1068 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B1068 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B1068 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1068 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B1068 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1068 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 818 " 0.024 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR B 818 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 818 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 818 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 818 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 818 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 818 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 818 " 0.003 2.00e-02 2.50e+03 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 139 2.56 - 3.14: 11298 3.14 - 3.73: 22064 3.73 - 4.31: 29661 4.31 - 4.90: 46663 Nonbonded interactions: 109825 Sorted by model distance: nonbonded pdb=" O2B ADP B1201 " pdb="MG MG B1202 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 1.996 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B1202 " model vdw 2.011 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 2.022 2.170 nonbonded pdb=" OE2 GLU A 749 " pdb="MG MG A2001 " model vdw 2.113 2.170 ... (remaining 109820 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.990 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.466 13361 Z= 0.485 Angle : 1.082 12.465 18023 Z= 0.667 Chirality : 0.078 0.384 2063 Planarity : 0.004 0.047 2286 Dihedral : 17.612 165.291 5025 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 1.93 % Allowed : 24.72 % Favored : 73.34 % Cbeta Deviations : 0.06 % 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: -1.45 (0.21), residues: 1602 helix: 0.12 (0.18), residues: 783 sheet: -2.07 (0.38), residues: 162 loop : -1.96 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 807 HIS 0.015 0.003 HIS B 614 PHE 0.015 0.003 PHE B 402 TYR 0.037 0.004 TYR A 815 ARG 0.010 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.14208 ( 676) hydrogen bonds : angle 6.42712 ( 1908) SS BOND : bond 0.46556 ( 1) SS BOND : angle 9.38362 ( 2) covalent geometry : bond 0.00686 (13360) covalent geometry : angle 1.07742 (18021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 404 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8738 (t) cc_final: 0.8520 (p) REVERT: A 198 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 245 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 261 MET cc_start: 0.7552 (mmp) cc_final: 0.7338 (mmp) REVERT: A 274 ILE cc_start: 0.8501 (mm) cc_final: 0.8272 (mt) REVERT: A 275 LYS cc_start: 0.8902 (tppt) cc_final: 0.8588 (mmmm) REVERT: A 298 GLN cc_start: 0.8948 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 359 ARG cc_start: 0.8150 (mtt90) cc_final: 0.6830 (mtt180) REVERT: A 396 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8395 (ptp90) REVERT: A 460 MET cc_start: 0.8416 (mmt) cc_final: 0.8170 (mmt) REVERT: A 483 GLU cc_start: 0.8442 (tp30) cc_final: 0.8196 (mt-10) REVERT: A 562 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8786 (tp30) REVERT: A 569 GLU cc_start: 0.8755 (tt0) cc_final: 0.8279 (tp30) REVERT: A 579 LYS cc_start: 0.9042 (mttt) cc_final: 0.8687 (mmmm) REVERT: A 621 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8333 (ttt-90) REVERT: A 681 GLN cc_start: 0.8273 (tt0) cc_final: 0.8041 (tt0) REVERT: A 688 MET cc_start: 0.8742 (mtt) cc_final: 0.8493 (mtp) REVERT: A 728 GLU cc_start: 0.8006 (tp30) cc_final: 0.7757 (tp30) REVERT: A 838 LYS cc_start: 0.8693 (mttt) cc_final: 0.8402 (mmmm) REVERT: B 235 GLN cc_start: 0.8617 (tp40) cc_final: 0.8362 (tp40) REVERT: B 296 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8556 (tmm-80) REVERT: B 375 LYS cc_start: 0.9215 (mttt) cc_final: 0.8998 (mtpp) REVERT: B 476 TYR cc_start: 0.8278 (m-10) cc_final: 0.8076 (m-10) REVERT: B 577 LYS cc_start: 0.8816 (tttt) cc_final: 0.8594 (tppp) REVERT: B 674 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 906 ILE cc_start: 0.8996 (pt) cc_final: 0.8679 (tt) REVERT: B 1070 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 1081 GLU cc_start: 0.8717 (pm20) cc_final: 0.8320 (pm20) REVERT: B 1084 LYS cc_start: 0.8829 (mttt) cc_final: 0.8452 (mmmm) outliers start: 28 outliers final: 19 residues processed: 416 average time/residue: 0.3119 time to fit residues: 176.5963 Evaluate side-chains 400 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 379 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1070 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 127 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 0.0770 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS B 345 ASN B 394 GLN B 544 ASN B 898 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.167774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137564 restraints weight = 22745.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141897 restraints weight = 10205.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144584 restraints weight = 5719.875| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13361 Z= 0.165 Angle : 0.703 12.587 18023 Z= 0.356 Chirality : 0.044 0.241 2063 Planarity : 0.005 0.048 2286 Dihedral : 8.431 176.398 1810 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.45 % Allowed : 24.59 % Favored : 71.96 % 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: -1.00 (0.21), residues: 1602 helix: 0.38 (0.18), residues: 807 sheet: -1.82 (0.37), residues: 188 loop : -1.63 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.020 0.001 PHE B 463 TYR 0.018 0.002 TYR A 815 ARG 0.012 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 676) hydrogen bonds : angle 5.40932 ( 1908) SS BOND : bond 0.01142 ( 1) SS BOND : angle 1.10060 ( 2) covalent geometry : bond 0.00355 (13360) covalent geometry : angle 0.70297 (18021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 381 time to evaluate : 1.340 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 150 VAL cc_start: 0.8302 (t) cc_final: 0.8002 (p) REVERT: A 172 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7333 (mmtt) REVERT: A 192 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 198 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5841 (mm-30) REVERT: A 226 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6588 (mm-30) REVERT: A 245 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7012 (mp) REVERT: A 261 MET cc_start: 0.6313 (mmp) cc_final: 0.5975 (mmp) REVERT: A 298 GLN cc_start: 0.8045 (tt0) cc_final: 0.7544 (tm-30) REVERT: A 339 GLN cc_start: 0.7496 (tt0) cc_final: 0.7267 (tt0) REVERT: A 345 TRP cc_start: 0.8203 (m-10) cc_final: 0.7330 (m-10) REVERT: A 382 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7686 (ptt90) REVERT: A 386 ASP cc_start: 0.7633 (t0) cc_final: 0.7393 (t0) REVERT: A 389 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7422 (tpp80) REVERT: A 393 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7852 (ttpt) REVERT: A 395 GLN cc_start: 0.7651 (tp40) cc_final: 0.7414 (tp40) REVERT: A 466 HIS cc_start: 0.8039 (t-90) cc_final: 0.7835 (t70) REVERT: A 482 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7701 (mmm-85) REVERT: A 569 GLU cc_start: 0.7700 (tt0) cc_final: 0.7396 (tp30) REVERT: A 579 LYS cc_start: 0.8487 (mttt) cc_final: 0.8035 (mmmm) REVERT: A 595 LEU cc_start: 0.8727 (tp) cc_final: 0.8409 (tt) REVERT: A 603 ASP cc_start: 0.7429 (t0) cc_final: 0.7134 (t0) REVERT: A 688 MET cc_start: 0.7798 (mtt) cc_final: 0.7583 (mtp) REVERT: A 736 LEU cc_start: 0.8291 (mp) cc_final: 0.8006 (mp) REVERT: A 779 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7361 (mtp) REVERT: B 296 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7485 (tmm-80) REVERT: B 297 LEU cc_start: 0.8197 (mp) cc_final: 0.7939 (mm) REVERT: B 303 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8114 (ttpt) REVERT: B 544 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7627 (t0) REVERT: B 577 LYS cc_start: 0.8171 (tttt) cc_final: 0.7802 (ttmm) REVERT: B 614 HIS cc_start: 0.6392 (m170) cc_final: 0.6183 (m170) REVERT: B 653 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 674 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6612 (mt-10) REVERT: B 699 LYS cc_start: 0.8709 (tppt) cc_final: 0.8407 (tppt) REVERT: B 933 ASP cc_start: 0.7934 (p0) cc_final: 0.7729 (p0) REVERT: B 961 GLU cc_start: 0.7420 (pp20) cc_final: 0.7217 (pp20) REVERT: B 1084 LYS cc_start: 0.8274 (mttt) cc_final: 0.7769 (mmmm) outliers start: 50 outliers final: 24 residues processed: 411 average time/residue: 0.2830 time to fit residues: 161.3992 Evaluate side-chains 395 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 108 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 361 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B 969 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.165837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135327 restraints weight = 23105.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139653 restraints weight = 10286.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142369 restraints weight = 5727.331| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13361 Z= 0.222 Angle : 0.699 12.161 18023 Z= 0.355 Chirality : 0.045 0.243 2063 Planarity : 0.005 0.073 2286 Dihedral : 7.400 155.821 1773 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 5.04 % Allowed : 24.31 % Favored : 70.65 % 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: -0.97 (0.21), residues: 1602 helix: 0.42 (0.18), residues: 807 sheet: -1.86 (0.36), residues: 189 loop : -1.61 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.022 0.001 PHE B 638 TYR 0.024 0.002 TYR B 476 ARG 0.011 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 676) hydrogen bonds : angle 5.24874 ( 1908) SS BOND : bond 0.01287 ( 1) SS BOND : angle 1.76077 ( 2) covalent geometry : bond 0.00462 (13360) covalent geometry : angle 0.69832 (18021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 372 time to evaluate : 1.324 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 150 VAL cc_start: 0.8297 (t) cc_final: 0.7963 (p) REVERT: A 172 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7186 (mmtm) REVERT: A 192 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7494 (mp) REVERT: A 198 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5762 (mm-30) REVERT: A 226 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6665 (mm-30) REVERT: A 245 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7032 (mp) REVERT: A 261 MET cc_start: 0.6403 (mmp) cc_final: 0.5953 (mmp) REVERT: A 270 LEU cc_start: 0.8258 (tp) cc_final: 0.8037 (mt) REVERT: A 271 SER cc_start: 0.8464 (t) cc_final: 0.8185 (p) REVERT: A 339 GLN cc_start: 0.7540 (tt0) cc_final: 0.7332 (tt0) REVERT: A 361 ASN cc_start: 0.7596 (m-40) cc_final: 0.7219 (m110) REVERT: A 386 ASP cc_start: 0.7809 (t0) cc_final: 0.7458 (t0) REVERT: A 389 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7397 (tpp80) REVERT: A 393 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7801 (ttpt) REVERT: A 395 GLN cc_start: 0.7699 (tp40) cc_final: 0.7395 (tp40) REVERT: A 449 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8042 (mmmm) REVERT: A 458 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6667 (tt) REVERT: A 466 HIS cc_start: 0.8074 (t-90) cc_final: 0.7870 (t70) REVERT: A 482 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7634 (mmm-85) REVERT: A 569 GLU cc_start: 0.7726 (tt0) cc_final: 0.7405 (tp30) REVERT: A 579 LYS cc_start: 0.8487 (mttt) cc_final: 0.8047 (mmmm) REVERT: A 593 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: A 603 ASP cc_start: 0.7436 (t0) cc_final: 0.7028 (t0) REVERT: A 729 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6920 (mpp) REVERT: A 736 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 737 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7106 (ttp80) REVERT: A 742 ASP cc_start: 0.6921 (t0) cc_final: 0.6439 (t0) REVERT: A 778 CYS cc_start: 0.7731 (t) cc_final: 0.7375 (t) REVERT: A 850 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: B 303 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8144 (ttpt) REVERT: B 454 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7674 (ttp80) REVERT: B 508 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7990 (tttt) REVERT: B 577 LYS cc_start: 0.8229 (tttt) cc_final: 0.7806 (ttmm) REVERT: B 653 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 674 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6573 (mt-10) REVERT: B 677 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 699 LYS cc_start: 0.8695 (tppt) cc_final: 0.8366 (tppt) REVERT: B 1018 GLU cc_start: 0.7337 (pp20) cc_final: 0.7027 (pp20) REVERT: B 1084 LYS cc_start: 0.8297 (mttt) cc_final: 0.7799 (mmmm) outliers start: 73 outliers final: 42 residues processed: 414 average time/residue: 0.2874 time to fit residues: 166.1745 Evaluate side-chains 416 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 969 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 377 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135892 restraints weight = 22865.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140204 restraints weight = 10250.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.142829 restraints weight = 5771.530| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13361 Z= 0.195 Angle : 0.687 12.892 18023 Z= 0.346 Chirality : 0.044 0.268 2063 Planarity : 0.005 0.053 2286 Dihedral : 6.995 136.851 1773 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 5.18 % Allowed : 24.86 % Favored : 69.96 % 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 (0.21), residues: 1602 helix: 0.49 (0.18), residues: 808 sheet: -1.90 (0.36), residues: 195 loop : -1.57 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.020 0.001 PHE A 313 TYR 0.029 0.002 TYR A 619 ARG 0.010 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 676) hydrogen bonds : angle 5.12913 ( 1908) SS BOND : bond 0.01187 ( 1) SS BOND : angle 1.84345 ( 2) covalent geometry : bond 0.00414 (13360) covalent geometry : angle 0.68696 (18021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 388 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8290 (t) cc_final: 0.7968 (p) REVERT: A 172 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7292 (mmtt) REVERT: A 198 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5772 (mm-30) REVERT: A 226 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 270 LEU cc_start: 0.8258 (tp) cc_final: 0.7803 (mp) REVERT: A 271 SER cc_start: 0.8449 (t) cc_final: 0.8167 (p) REVERT: A 299 TYR cc_start: 0.7827 (m-80) cc_final: 0.7547 (m-80) REVERT: A 345 TRP cc_start: 0.8321 (m-10) cc_final: 0.7397 (m-10) REVERT: A 361 ASN cc_start: 0.7519 (m-40) cc_final: 0.7184 (m110) REVERT: A 386 ASP cc_start: 0.7817 (t0) cc_final: 0.7394 (t0) REVERT: A 389 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7305 (tpp80) REVERT: A 393 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7795 (ttpt) REVERT: A 395 GLN cc_start: 0.7699 (tp40) cc_final: 0.7180 (mm-40) REVERT: A 449 LYS cc_start: 0.8316 (mmmm) cc_final: 0.7984 (mmmm) REVERT: A 458 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6840 (tt) REVERT: A 482 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7714 (mmm-85) REVERT: A 569 GLU cc_start: 0.7716 (tt0) cc_final: 0.7402 (tp30) REVERT: A 579 LYS cc_start: 0.8466 (mttt) cc_final: 0.7928 (mmmm) REVERT: A 603 ASP cc_start: 0.7427 (t0) cc_final: 0.6866 (t0) REVERT: A 619 TYR cc_start: 0.7616 (m-80) cc_final: 0.7109 (m-80) REVERT: A 681 GLN cc_start: 0.7577 (tt0) cc_final: 0.7211 (tt0) REVERT: A 682 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8507 (t) REVERT: A 698 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 729 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6918 (mpp) REVERT: A 737 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7059 (ttp80) REVERT: A 742 ASP cc_start: 0.7084 (t0) cc_final: 0.6517 (t0) REVERT: A 778 CYS cc_start: 0.7701 (t) cc_final: 0.7320 (t) REVERT: B 290 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4472 (tt) REVERT: B 303 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8182 (ttpt) REVERT: B 425 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6032 (mt-10) REVERT: B 454 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7818 (ttp80) REVERT: B 508 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8043 (tttt) REVERT: B 541 THR cc_start: 0.8414 (m) cc_final: 0.8179 (t) REVERT: B 577 LYS cc_start: 0.8246 (tttt) cc_final: 0.7800 (ttmm) REVERT: B 582 GLN cc_start: 0.7724 (mt0) cc_final: 0.7519 (mt0) REVERT: B 614 HIS cc_start: 0.6398 (m170) cc_final: 0.6186 (m170) REVERT: B 653 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 674 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6502 (mt-10) REVERT: B 683 GLU cc_start: 0.6489 (tp30) cc_final: 0.6206 (tp30) REVERT: B 699 LYS cc_start: 0.8663 (tppt) cc_final: 0.8174 (ttpt) REVERT: B 869 VAL cc_start: 0.8776 (t) cc_final: 0.8524 (m) REVERT: B 885 SER cc_start: 0.7833 (t) cc_final: 0.7563 (t) REVERT: B 886 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: B 933 ASP cc_start: 0.7967 (p0) cc_final: 0.7766 (p0) REVERT: B 969 GLN cc_start: 0.8076 (mp10) cc_final: 0.7724 (mp10) REVERT: B 1018 GLU cc_start: 0.7328 (pp20) cc_final: 0.6942 (pp20) REVERT: B 1084 LYS cc_start: 0.8293 (mttt) cc_final: 0.7771 (mmmm) REVERT: B 1091 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7681 (mmmm) outliers start: 75 outliers final: 43 residues processed: 432 average time/residue: 0.2835 time to fit residues: 170.2897 Evaluate side-chains 426 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 376 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 886 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 339 GLN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 467 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136970 restraints weight = 23165.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141331 restraints weight = 10450.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144020 restraints weight = 5877.618| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13361 Z= 0.170 Angle : 0.689 13.196 18023 Z= 0.342 Chirality : 0.045 0.309 2063 Planarity : 0.005 0.055 2286 Dihedral : 6.561 125.674 1771 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 5.25 % Allowed : 25.76 % Favored : 68.99 % 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: -0.89 (0.22), residues: 1602 helix: 0.52 (0.18), residues: 817 sheet: -1.93 (0.35), residues: 201 loop : -1.58 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.017 0.001 PHE A 551 TYR 0.024 0.002 TYR A 619 ARG 0.009 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 676) hydrogen bonds : angle 5.02172 ( 1908) SS BOND : bond 0.01064 ( 1) SS BOND : angle 1.91581 ( 2) covalent geometry : bond 0.00371 (13360) covalent geometry : angle 0.68904 (18021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 390 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8278 (t) cc_final: 0.7940 (p) REVERT: A 172 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7286 (mmtt) REVERT: A 192 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 198 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5726 (mm-30) REVERT: A 226 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6635 (mm-30) REVERT: A 245 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6844 (tp) REVERT: A 270 LEU cc_start: 0.8281 (tp) cc_final: 0.8042 (mt) REVERT: A 271 SER cc_start: 0.8428 (t) cc_final: 0.8153 (p) REVERT: A 313 PHE cc_start: 0.7952 (m-80) cc_final: 0.7585 (m-80) REVERT: A 345 TRP cc_start: 0.8310 (m-10) cc_final: 0.7505 (m-10) REVERT: A 359 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7128 (ttm-80) REVERT: A 386 ASP cc_start: 0.7845 (t0) cc_final: 0.7385 (t0) REVERT: A 389 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7337 (tpp80) REVERT: A 393 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7743 (ttpt) REVERT: A 449 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7940 (mmmm) REVERT: A 569 GLU cc_start: 0.7693 (tt0) cc_final: 0.7375 (tp30) REVERT: A 579 LYS cc_start: 0.8425 (mttt) cc_final: 0.7883 (mmmm) REVERT: A 603 ASP cc_start: 0.7398 (t0) cc_final: 0.6817 (t0) REVERT: A 682 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8502 (t) REVERT: A 698 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 709 LEU cc_start: 0.8021 (mt) cc_final: 0.7809 (mt) REVERT: A 728 GLU cc_start: 0.6693 (tp30) cc_final: 0.6363 (tp30) REVERT: A 729 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6953 (mpp) REVERT: A 737 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7189 (mtp-110) REVERT: A 742 ASP cc_start: 0.7179 (t0) cc_final: 0.6430 (t0) REVERT: A 778 CYS cc_start: 0.7686 (t) cc_final: 0.7338 (t) REVERT: B 290 LEU cc_start: 0.4739 (OUTLIER) cc_final: 0.4532 (tt) REVERT: B 303 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8159 (ttpt) REVERT: B 425 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6153 (mt-10) REVERT: B 454 ARG cc_start: 0.8104 (ttt180) cc_final: 0.6448 (ttp80) REVERT: B 508 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8017 (tttm) REVERT: B 541 THR cc_start: 0.8405 (m) cc_final: 0.8177 (t) REVERT: B 577 LYS cc_start: 0.8240 (tttt) cc_final: 0.7758 (ttmm) REVERT: B 614 HIS cc_start: 0.6349 (m170) cc_final: 0.6116 (m170) REVERT: B 647 HIS cc_start: 0.7587 (t70) cc_final: 0.7125 (t-90) REVERT: B 653 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 674 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6560 (mt-10) REVERT: B 699 LYS cc_start: 0.8649 (tppt) cc_final: 0.8187 (ttpt) REVERT: B 869 VAL cc_start: 0.8771 (t) cc_final: 0.8537 (m) REVERT: B 885 SER cc_start: 0.7799 (t) cc_final: 0.7532 (t) REVERT: B 933 ASP cc_start: 0.7934 (p0) cc_final: 0.7730 (p0) REVERT: B 955 GLU cc_start: 0.7159 (mp0) cc_final: 0.6439 (mp0) REVERT: B 1018 GLU cc_start: 0.7316 (pp20) cc_final: 0.6865 (pp20) REVERT: B 1084 LYS cc_start: 0.8294 (mttt) cc_final: 0.7762 (mmmm) REVERT: B 1091 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7716 (mmmm) outliers start: 76 outliers final: 50 residues processed: 432 average time/residue: 0.2911 time to fit residues: 173.7025 Evaluate side-chains 435 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 377 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137323 restraints weight = 23388.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141757 restraints weight = 10416.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144480 restraints weight = 5813.338| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13361 Z= 0.164 Angle : 0.698 13.364 18023 Z= 0.345 Chirality : 0.045 0.333 2063 Planarity : 0.005 0.053 2286 Dihedral : 6.363 121.985 1771 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 5.52 % Allowed : 26.10 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1602 helix: 0.54 (0.18), residues: 819 sheet: -1.85 (0.35), residues: 201 loop : -1.64 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 807 HIS 0.009 0.001 HIS B 817 PHE 0.017 0.001 PHE A 551 TYR 0.019 0.002 TYR A 619 ARG 0.009 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 676) hydrogen bonds : angle 5.00626 ( 1908) SS BOND : bond 0.00949 ( 1) SS BOND : angle 1.78417 ( 2) covalent geometry : bond 0.00358 (13360) covalent geometry : angle 0.69783 (18021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 384 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8274 (t) cc_final: 0.7941 (p) REVERT: A 172 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7271 (mmtt) REVERT: A 192 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 198 GLU cc_start: 0.6464 (mm-30) cc_final: 0.5705 (mm-30) REVERT: A 226 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6622 (mm-30) REVERT: A 245 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6811 (tp) REVERT: A 270 LEU cc_start: 0.8282 (tp) cc_final: 0.7969 (mt) REVERT: A 345 TRP cc_start: 0.8303 (m-10) cc_final: 0.7320 (m-10) REVERT: A 357 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: A 361 ASN cc_start: 0.7741 (m-40) cc_final: 0.7265 (m110) REVERT: A 382 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7701 (ptt90) REVERT: A 386 ASP cc_start: 0.7846 (t0) cc_final: 0.7383 (t0) REVERT: A 389 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7256 (tpp80) REVERT: A 393 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: A 449 LYS cc_start: 0.8308 (mmmm) cc_final: 0.7905 (mmmm) REVERT: A 482 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7668 (mmm-85) REVERT: A 569 GLU cc_start: 0.7691 (tt0) cc_final: 0.7375 (tp30) REVERT: A 579 LYS cc_start: 0.8426 (mttt) cc_final: 0.7876 (mmmm) REVERT: A 595 LEU cc_start: 0.8675 (tp) cc_final: 0.8353 (tt) REVERT: A 603 ASP cc_start: 0.7413 (t0) cc_final: 0.6840 (t0) REVERT: A 619 TYR cc_start: 0.7492 (m-10) cc_final: 0.7192 (m-10) REVERT: A 682 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8484 (t) REVERT: A 698 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 728 GLU cc_start: 0.6690 (tp30) cc_final: 0.6337 (tp30) REVERT: A 729 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6937 (mpp) REVERT: A 737 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7361 (ttm110) REVERT: A 742 ASP cc_start: 0.7199 (t0) cc_final: 0.6400 (t0) REVERT: A 850 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: B 259 PHE cc_start: 0.7556 (m-10) cc_final: 0.7323 (m-10) REVERT: B 290 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4667 (tt) REVERT: B 303 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8163 (ttpt) REVERT: B 307 VAL cc_start: 0.8517 (t) cc_final: 0.8062 (p) REVERT: B 425 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5892 (mt-10) REVERT: B 508 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8017 (tttt) REVERT: B 512 GLU cc_start: 0.7662 (tp30) cc_final: 0.7165 (tp30) REVERT: B 577 LYS cc_start: 0.8247 (tttt) cc_final: 0.7747 (ttmm) REVERT: B 614 HIS cc_start: 0.6398 (m170) cc_final: 0.6198 (m170) REVERT: B 647 HIS cc_start: 0.7586 (t70) cc_final: 0.7064 (t-90) REVERT: B 653 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 674 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6560 (mt-10) REVERT: B 699 LYS cc_start: 0.8647 (tppt) cc_final: 0.8208 (ttpt) REVERT: B 812 GLU cc_start: 0.7192 (tp30) cc_final: 0.6526 (tp30) REVERT: B 823 LYS cc_start: 0.8062 (tptm) cc_final: 0.7715 (tptp) REVERT: B 855 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: B 869 VAL cc_start: 0.8761 (t) cc_final: 0.8530 (m) REVERT: B 873 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: B 885 SER cc_start: 0.7769 (t) cc_final: 0.7513 (t) REVERT: B 955 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: B 956 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7967 (mm) REVERT: B 969 GLN cc_start: 0.7951 (mp10) cc_final: 0.7669 (mm-40) REVERT: B 1018 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6858 (pp20) REVERT: B 1084 LYS cc_start: 0.8281 (mttt) cc_final: 0.7874 (mmmm) REVERT: B 1091 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7713 (mmmm) outliers start: 80 outliers final: 53 residues processed: 432 average time/residue: 0.2781 time to fit residues: 167.8529 Evaluate side-chains 444 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 378 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.0000 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** 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 = 0.4171 r_free = 0.4171 target = 0.168181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138008 restraints weight = 23019.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142481 restraints weight = 10336.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145144 restraints weight = 5749.696| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13361 Z= 0.155 Angle : 0.690 13.488 18023 Z= 0.339 Chirality : 0.044 0.305 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.115 120.862 1771 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 5.52 % Allowed : 26.45 % Favored : 68.02 % 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: -0.83 (0.21), residues: 1602 helix: 0.60 (0.18), residues: 815 sheet: -1.85 (0.35), residues: 201 loop : -1.63 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.017 0.001 PHE A 551 TYR 0.032 0.002 TYR B 236 ARG 0.009 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 676) hydrogen bonds : angle 4.93570 ( 1908) SS BOND : bond 0.00903 ( 1) SS BOND : angle 1.71197 ( 2) covalent geometry : bond 0.00342 (13360) covalent geometry : angle 0.68952 (18021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 382 time to evaluate : 1.429 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 150 VAL cc_start: 0.8272 (t) cc_final: 0.7925 (p) REVERT: A 172 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7113 (mmtm) REVERT: A 192 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 198 GLU cc_start: 0.6453 (mm-30) cc_final: 0.5645 (mm-30) REVERT: A 226 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6575 (mm-30) REVERT: A 245 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6791 (tp) REVERT: A 270 LEU cc_start: 0.8280 (tp) cc_final: 0.7969 (mt) REVERT: A 345 TRP cc_start: 0.8296 (m-10) cc_final: 0.7300 (m-10) REVERT: A 357 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: A 361 ASN cc_start: 0.7728 (m-40) cc_final: 0.7245 (m110) REVERT: A 386 ASP cc_start: 0.7863 (t0) cc_final: 0.7383 (t0) REVERT: A 389 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7293 (tpp80) REVERT: A 393 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7713 (ttpt) REVERT: A 449 LYS cc_start: 0.8323 (mmmm) cc_final: 0.7915 (mmmm) REVERT: A 482 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7550 (mmm-85) REVERT: A 569 GLU cc_start: 0.7631 (tt0) cc_final: 0.7310 (tp30) REVERT: A 579 LYS cc_start: 0.8404 (mttt) cc_final: 0.7855 (mmmm) REVERT: A 603 ASP cc_start: 0.7402 (t0) cc_final: 0.6804 (t0) REVERT: A 681 GLN cc_start: 0.7583 (tt0) cc_final: 0.7322 (tt0) REVERT: A 682 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8502 (t) REVERT: A 698 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 728 GLU cc_start: 0.6658 (tp30) cc_final: 0.6314 (tp30) REVERT: A 729 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6938 (mpp) REVERT: A 737 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7336 (ttm110) REVERT: A 742 ASP cc_start: 0.7174 (t0) cc_final: 0.6486 (t0) REVERT: A 850 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: B 303 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8171 (ttpt) REVERT: B 307 VAL cc_start: 0.8502 (t) cc_final: 0.8038 (p) REVERT: B 425 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6158 (mt-10) REVERT: B 508 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8037 (tttt) REVERT: B 577 LYS cc_start: 0.8244 (tttt) cc_final: 0.7731 (ttmm) REVERT: B 586 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8040 (mmtt) REVERT: B 614 HIS cc_start: 0.6403 (m170) cc_final: 0.6186 (m170) REVERT: B 647 HIS cc_start: 0.7545 (t70) cc_final: 0.7053 (t70) REVERT: B 653 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 659 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7852 (t) REVERT: B 674 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6517 (mt-10) REVERT: B 699 LYS cc_start: 0.8648 (tppt) cc_final: 0.8218 (ttpt) REVERT: B 823 LYS cc_start: 0.8055 (tptm) cc_final: 0.7725 (tptp) REVERT: B 855 ARG cc_start: 0.7220 (mtm-85) cc_final: 0.6941 (mtm-85) REVERT: B 869 VAL cc_start: 0.8755 (t) cc_final: 0.8521 (m) REVERT: B 873 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: B 885 SER cc_start: 0.7754 (t) cc_final: 0.7501 (t) REVERT: B 955 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: B 969 GLN cc_start: 0.7982 (mp10) cc_final: 0.7632 (mm-40) REVERT: B 1018 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6843 (pp20) REVERT: B 1084 LYS cc_start: 0.8278 (mttt) cc_final: 0.7855 (mmmm) REVERT: B 1091 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7727 (mmmm) outliers start: 80 outliers final: 46 residues processed: 430 average time/residue: 0.2833 time to fit residues: 169.4900 Evaluate side-chains 433 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 375 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 64 optimal weight: 0.6980 chunk 144 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137697 restraints weight = 23007.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142118 restraints weight = 10306.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144776 restraints weight = 5751.626| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13361 Z= 0.166 Angle : 0.705 13.416 18023 Z= 0.348 Chirality : 0.045 0.276 2063 Planarity : 0.005 0.063 2286 Dihedral : 6.088 124.510 1771 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 4.70 % Allowed : 28.25 % Favored : 67.06 % 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: -0.82 (0.21), residues: 1602 helix: 0.61 (0.18), residues: 820 sheet: -1.80 (0.35), residues: 201 loop : -1.68 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 807 HIS 0.009 0.001 HIS A 839 PHE 0.023 0.001 PHE A 313 TYR 0.025 0.002 TYR B 236 ARG 0.007 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 676) hydrogen bonds : angle 4.92501 ( 1908) SS BOND : bond 0.00926 ( 1) SS BOND : angle 1.74107 ( 2) covalent geometry : bond 0.00362 (13360) covalent geometry : angle 0.70465 (18021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 1.396 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 150 VAL cc_start: 0.8252 (t) cc_final: 0.7878 (p) REVERT: A 172 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7195 (mmtm) REVERT: A 192 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7490 (mp) REVERT: A 198 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5684 (mm-30) REVERT: A 226 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6583 (mm-30) REVERT: A 245 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6771 (tp) REVERT: A 270 LEU cc_start: 0.8286 (tp) cc_final: 0.8018 (mt) REVERT: A 271 SER cc_start: 0.8446 (t) cc_final: 0.8158 (p) REVERT: A 357 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: A 361 ASN cc_start: 0.7722 (m-40) cc_final: 0.7277 (m110) REVERT: A 382 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7606 (ttp80) REVERT: A 386 ASP cc_start: 0.7871 (t0) cc_final: 0.7380 (t0) REVERT: A 389 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7281 (tpp80) REVERT: A 393 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7633 (ttpt) REVERT: A 449 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7909 (mmmm) REVERT: A 482 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7776 (mmm-85) REVERT: A 493 GLN cc_start: 0.7956 (mt0) cc_final: 0.7588 (mp10) REVERT: A 569 GLU cc_start: 0.7634 (tt0) cc_final: 0.7325 (tp30) REVERT: A 579 LYS cc_start: 0.8395 (mttt) cc_final: 0.7837 (mmmm) REVERT: A 592 MET cc_start: 0.7627 (ptm) cc_final: 0.7338 (ptp) REVERT: A 603 ASP cc_start: 0.7398 (t0) cc_final: 0.6792 (t0) REVERT: A 682 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 698 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 726 MET cc_start: 0.8200 (tpp) cc_final: 0.7602 (tpp) REVERT: A 728 GLU cc_start: 0.6680 (tp30) cc_final: 0.6271 (tp30) REVERT: A 729 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7095 (mmm) REVERT: A 742 ASP cc_start: 0.7096 (t0) cc_final: 0.6406 (t0) REVERT: A 749 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6519 (mt-10) REVERT: A 850 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: B 303 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8184 (ttpt) REVERT: B 307 VAL cc_start: 0.8501 (t) cc_final: 0.8031 (p) REVERT: B 425 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6153 (mt-10) REVERT: B 508 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8059 (tttt) REVERT: B 512 GLU cc_start: 0.7664 (tp30) cc_final: 0.7094 (tp30) REVERT: B 577 LYS cc_start: 0.8245 (tttt) cc_final: 0.7724 (ttmm) REVERT: B 582 GLN cc_start: 0.7746 (mt0) cc_final: 0.7541 (mt0) REVERT: B 614 HIS cc_start: 0.6407 (m170) cc_final: 0.6180 (m170) REVERT: B 647 HIS cc_start: 0.7498 (t70) cc_final: 0.7066 (t-170) REVERT: B 653 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7476 (tm-30) REVERT: B 659 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7846 (t) REVERT: B 674 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6545 (mt-10) REVERT: B 699 LYS cc_start: 0.8656 (tppt) cc_final: 0.8346 (tppt) REVERT: B 823 LYS cc_start: 0.8062 (tptm) cc_final: 0.7671 (tptp) REVERT: B 869 VAL cc_start: 0.8754 (t) cc_final: 0.8520 (m) REVERT: B 873 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.5791 (tm-30) REVERT: B 885 SER cc_start: 0.7759 (t) cc_final: 0.7498 (t) REVERT: B 886 GLU cc_start: 0.7590 (tp30) cc_final: 0.7176 (tp30) REVERT: B 933 ASP cc_start: 0.7764 (p0) cc_final: 0.7557 (p0) REVERT: B 955 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: B 956 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7971 (mm) REVERT: B 969 GLN cc_start: 0.7987 (mp10) cc_final: 0.7654 (mm110) REVERT: B 1018 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6891 (pp20) REVERT: B 1084 LYS cc_start: 0.8281 (mttt) cc_final: 0.7862 (mmmm) REVERT: B 1091 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7735 (mmmm) outliers start: 68 outliers final: 45 residues processed: 422 average time/residue: 0.2885 time to fit residues: 169.3012 Evaluate side-chains 432 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 374 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138315 restraints weight = 22897.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142670 restraints weight = 10401.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145212 restraints weight = 5851.773| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13361 Z= 0.169 Angle : 0.704 13.441 18023 Z= 0.352 Chirality : 0.045 0.265 2063 Planarity : 0.005 0.065 2286 Dihedral : 6.082 126.366 1771 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 4.63 % Allowed : 28.18 % Favored : 67.20 % 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: -0.82 (0.21), residues: 1602 helix: 0.62 (0.18), residues: 812 sheet: -1.82 (0.35), residues: 201 loop : -1.65 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 807 HIS 0.013 0.001 HIS B 817 PHE 0.017 0.001 PHE A 551 TYR 0.022 0.002 TYR B 236 ARG 0.010 0.001 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 676) hydrogen bonds : angle 4.89903 ( 1908) SS BOND : bond 0.00926 ( 1) SS BOND : angle 1.73710 ( 2) covalent geometry : bond 0.00373 (13360) covalent geometry : angle 0.70426 (18021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 1.303 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 150 VAL cc_start: 0.8211 (t) cc_final: 0.7830 (p) REVERT: A 172 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7178 (mmtt) REVERT: A 192 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 226 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 245 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6788 (tp) REVERT: A 270 LEU cc_start: 0.8282 (tp) cc_final: 0.8021 (mt) REVERT: A 271 SER cc_start: 0.8463 (t) cc_final: 0.8169 (p) REVERT: A 357 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: A 361 ASN cc_start: 0.7739 (m-40) cc_final: 0.7301 (m110) REVERT: A 382 ARG cc_start: 0.7994 (ptm-80) cc_final: 0.7664 (ttp80) REVERT: A 386 ASP cc_start: 0.7874 (t0) cc_final: 0.7378 (t0) REVERT: A 388 ASN cc_start: 0.8443 (t0) cc_final: 0.8120 (t0) REVERT: A 389 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7295 (tpp80) REVERT: A 393 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7623 (ttpt) REVERT: A 449 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7884 (mmmm) REVERT: A 482 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7847 (mmm-85) REVERT: A 493 GLN cc_start: 0.7940 (mt0) cc_final: 0.7587 (mp10) REVERT: A 569 GLU cc_start: 0.7645 (tt0) cc_final: 0.7322 (tp30) REVERT: A 579 LYS cc_start: 0.8411 (mttt) cc_final: 0.7873 (mmmm) REVERT: A 592 MET cc_start: 0.7665 (ptm) cc_final: 0.7396 (ptp) REVERT: A 603 ASP cc_start: 0.7401 (t0) cc_final: 0.6783 (t0) REVERT: A 682 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8512 (t) REVERT: A 726 MET cc_start: 0.8182 (tpp) cc_final: 0.7641 (tpp) REVERT: A 728 GLU cc_start: 0.6756 (tp30) cc_final: 0.6313 (tp30) REVERT: A 729 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7083 (mmm) REVERT: A 737 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7402 (ttp80) REVERT: A 742 ASP cc_start: 0.7139 (t0) cc_final: 0.6415 (t0) REVERT: A 749 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6513 (mt-10) REVERT: A 850 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: B 342 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6835 (mm-30) REVERT: B 425 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6104 (mt-10) REVERT: B 508 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (tttt) REVERT: B 512 GLU cc_start: 0.7688 (tp30) cc_final: 0.7043 (tp30) REVERT: B 577 LYS cc_start: 0.8247 (tttt) cc_final: 0.7724 (ttmm) REVERT: B 582 GLN cc_start: 0.7687 (mt0) cc_final: 0.7482 (mt0) REVERT: B 614 HIS cc_start: 0.6428 (m170) cc_final: 0.6201 (m170) REVERT: B 647 HIS cc_start: 0.7507 (t70) cc_final: 0.7070 (t-170) REVERT: B 653 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 659 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7857 (t) REVERT: B 674 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6476 (mt-10) REVERT: B 699 LYS cc_start: 0.8636 (tppt) cc_final: 0.8231 (ttpt) REVERT: B 823 LYS cc_start: 0.8049 (tptm) cc_final: 0.7671 (tptp) REVERT: B 869 VAL cc_start: 0.8748 (t) cc_final: 0.8512 (m) REVERT: B 873 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: B 885 SER cc_start: 0.7772 (t) cc_final: 0.7505 (t) REVERT: B 955 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: B 956 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 1018 GLU cc_start: 0.7321 (pp20) cc_final: 0.6890 (pp20) REVERT: B 1084 LYS cc_start: 0.8283 (mttt) cc_final: 0.7847 (mmmm) REVERT: B 1088 HIS cc_start: 0.8040 (t70) cc_final: 0.7787 (t-90) REVERT: B 1091 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7743 (mmmm) outliers start: 67 outliers final: 47 residues processed: 419 average time/residue: 0.2760 time to fit residues: 161.6604 Evaluate side-chains 436 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 377 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 145 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138484 restraints weight = 23017.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142880 restraints weight = 10321.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145539 restraints weight = 5790.866| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13361 Z= 0.160 Angle : 0.723 13.556 18023 Z= 0.358 Chirality : 0.045 0.260 2063 Planarity : 0.005 0.065 2286 Dihedral : 6.071 126.209 1771 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 4.28 % Allowed : 28.31 % Favored : 67.40 % 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: -0.83 (0.21), residues: 1602 helix: 0.63 (0.18), residues: 812 sheet: -1.86 (0.35), residues: 210 loop : -1.65 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 807 HIS 0.014 0.001 HIS B 817 PHE 0.024 0.001 PHE A 313 TYR 0.021 0.002 TYR B 236 ARG 0.010 0.001 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 676) hydrogen bonds : angle 4.90569 ( 1908) SS BOND : bond 0.00868 ( 1) SS BOND : angle 1.67656 ( 2) covalent geometry : bond 0.00362 (13360) covalent geometry : angle 0.72312 (18021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 377 time to evaluate : 1.407 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 150 VAL cc_start: 0.8211 (t) cc_final: 0.7817 (p) REVERT: A 172 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7164 (mmtm) REVERT: A 192 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 226 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 245 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6781 (tp) REVERT: A 270 LEU cc_start: 0.8271 (tp) cc_final: 0.8021 (mt) REVERT: A 271 SER cc_start: 0.8444 (t) cc_final: 0.8142 (p) REVERT: A 313 PHE cc_start: 0.7935 (m-80) cc_final: 0.7619 (m-80) REVERT: A 357 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: A 361 ASN cc_start: 0.7712 (m-40) cc_final: 0.7273 (m110) REVERT: A 382 ARG cc_start: 0.7989 (ptm-80) cc_final: 0.7643 (ttp80) REVERT: A 386 ASP cc_start: 0.7879 (t0) cc_final: 0.7371 (t0) REVERT: A 388 ASN cc_start: 0.8442 (t0) cc_final: 0.8119 (t0) REVERT: A 389 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7291 (tpp80) REVERT: A 393 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7676 (ttpt) REVERT: A 449 LYS cc_start: 0.8295 (mmmm) cc_final: 0.7861 (mmmm) REVERT: A 469 LEU cc_start: 0.7983 (pt) cc_final: 0.7695 (pt) REVERT: A 482 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7809 (mmm-85) REVERT: A 493 GLN cc_start: 0.7962 (mt0) cc_final: 0.7688 (mp10) REVERT: A 569 GLU cc_start: 0.7631 (tt0) cc_final: 0.7293 (tp30) REVERT: A 579 LYS cc_start: 0.8410 (mttt) cc_final: 0.7869 (mmmm) REVERT: A 592 MET cc_start: 0.7633 (ptm) cc_final: 0.7354 (ptp) REVERT: A 603 ASP cc_start: 0.7382 (t0) cc_final: 0.6768 (t0) REVERT: A 682 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (t) REVERT: A 726 MET cc_start: 0.8171 (tpp) cc_final: 0.7591 (tpp) REVERT: A 729 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7040 (mmm) REVERT: A 737 ARG cc_start: 0.7668 (ttm110) cc_final: 0.6930 (ttp80) REVERT: A 742 ASP cc_start: 0.7109 (t0) cc_final: 0.6379 (t0) REVERT: A 749 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6481 (mt-10) REVERT: A 768 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6982 (pp20) REVERT: A 850 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: B 236 TYR cc_start: 0.6511 (t80) cc_final: 0.6293 (t80) REVERT: B 259 PHE cc_start: 0.7577 (m-10) cc_final: 0.7237 (m-10) REVERT: B 307 VAL cc_start: 0.8543 (t) cc_final: 0.8111 (p) REVERT: B 425 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6043 (mt-10) REVERT: B 508 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8056 (tttt) REVERT: B 512 GLU cc_start: 0.7658 (tp30) cc_final: 0.7023 (tp30) REVERT: B 577 LYS cc_start: 0.8241 (tttt) cc_final: 0.7720 (ttmm) REVERT: B 582 GLN cc_start: 0.7690 (mt0) cc_final: 0.7477 (mt0) REVERT: B 614 HIS cc_start: 0.6449 (m170) cc_final: 0.6217 (m170) REVERT: B 647 HIS cc_start: 0.7466 (t70) cc_final: 0.7065 (t-170) REVERT: B 653 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 659 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7849 (t) REVERT: B 674 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6374 (mt-10) REVERT: B 699 LYS cc_start: 0.8644 (tppt) cc_final: 0.8216 (ttpt) REVERT: B 735 LYS cc_start: 0.8292 (tmtt) cc_final: 0.8070 (tmtt) REVERT: B 823 LYS cc_start: 0.8027 (tptm) cc_final: 0.7723 (tptp) REVERT: B 869 VAL cc_start: 0.8747 (t) cc_final: 0.8510 (m) REVERT: B 873 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.5820 (tm-30) REVERT: B 885 SER cc_start: 0.7737 (t) cc_final: 0.7478 (t) REVERT: B 955 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 956 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7946 (mm) REVERT: B 969 GLN cc_start: 0.7963 (mp10) cc_final: 0.7671 (mm-40) REVERT: B 1018 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: B 1084 LYS cc_start: 0.8277 (mttt) cc_final: 0.7824 (mmmm) REVERT: B 1091 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7714 (mmmm) outliers start: 62 outliers final: 47 residues processed: 413 average time/residue: 0.2827 time to fit residues: 163.4116 Evaluate side-chains 436 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 376 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 137 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138016 restraints weight = 23121.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142386 restraints weight = 10386.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145061 restraints weight = 5843.580| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13361 Z= 0.170 Angle : 0.726 13.349 18023 Z= 0.359 Chirality : 0.045 0.234 2063 Planarity : 0.005 0.062 2286 Dihedral : 6.057 124.698 1771 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 4.42 % Allowed : 27.90 % Favored : 67.68 % 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: -0.83 (0.21), residues: 1602 helix: 0.62 (0.18), residues: 812 sheet: -1.85 (0.35), residues: 210 loop : -1.65 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 807 HIS 0.013 0.001 HIS B 630 PHE 0.022 0.001 PHE A 313 TYR 0.025 0.002 TYR B 302 ARG 0.009 0.001 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 676) hydrogen bonds : angle 4.90553 ( 1908) SS BOND : bond 0.00896 ( 1) SS BOND : angle 1.69683 ( 2) covalent geometry : bond 0.00373 (13360) covalent geometry : angle 0.72555 (18021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.84 seconds wall clock time: 93 minutes 28.20 seconds (5608.20 seconds total)