Starting phenix.real_space_refine on Sat Aug 23 16:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8om5_16969/08_2025/8om5_16969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8om5_16969/08_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_16969/08_2025/8om5_16969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8om5_16969/08_2025/8om5_16969.map" model { file = "/net/cci-nas-00/data/ceres_data/8om5_16969/08_2025/8om5_16969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8om5_16969/08_2025/8om5_16969.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.61, per 1000 atoms: 0.20 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: 0.99 Conformation dependent library (CDL) restraints added in 541.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.47 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: 1.86 Time building geometry restraints manager: 1.34 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (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 ARG 0.010 0.001 ARG A 631 TYR 0.037 0.004 TYR A 815 PHE 0.015 0.003 PHE B 402 TRP 0.016 0.003 TRP B 807 HIS 0.015 0.003 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00686 (13360) covalent geometry : angle 1.07742 (18021) SS BOND : bond 0.46556 ( 1) SS BOND : angle 9.38362 ( 2) hydrogen bonds : bond 0.14208 ( 676) hydrogen bonds : angle 6.42712 ( 1908) *********************** 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 : 0.391 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: 0.1205 time to fit residues: 68.9914 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 : 0.455 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0010 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 377 GLN ** 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 = 0.4161 r_free = 0.4161 target = 0.167744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137498 restraints weight = 22928.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141830 restraints weight = 10264.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144471 restraints weight = 5739.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146152 restraints weight = 3872.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146918 restraints weight = 2992.078| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13361 Z= 0.164 Angle : 0.702 12.539 18023 Z= 0.355 Chirality : 0.044 0.234 2063 Planarity : 0.005 0.049 2286 Dihedral : 8.440 176.722 1810 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.45 % Allowed : 24.65 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.21), residues: 1602 helix: 0.39 (0.18), residues: 806 sheet: -1.82 (0.37), residues: 188 loop : -1.64 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 711 TYR 0.018 0.002 TYR A 815 PHE 0.021 0.001 PHE B 463 TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00354 (13360) covalent geometry : angle 0.70195 (18021) SS BOND : bond 0.01501 ( 1) SS BOND : angle 1.07048 ( 2) hydrogen bonds : bond 0.04735 ( 676) hydrogen bonds : angle 5.40927 ( 1908) *********************** 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 430 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 380 time to evaluate : 0.367 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: 0.8317 (t) cc_final: 0.8015 (p) REVERT: A 172 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7339 (mmtt) REVERT: A 192 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 198 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5871 (mm-30) REVERT: A 226 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6605 (mm-30) REVERT: A 245 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6984 (mp) REVERT: A 261 MET cc_start: 0.6247 (mmp) cc_final: 0.5904 (mmp) REVERT: A 298 GLN cc_start: 0.8034 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 339 GLN cc_start: 0.7511 (tt0) cc_final: 0.7288 (tt0) REVERT: A 345 TRP cc_start: 0.8188 (m-10) cc_final: 0.7328 (m-10) REVERT: A 382 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7672 (ptt90) REVERT: A 386 ASP cc_start: 0.7630 (t0) cc_final: 0.7388 (t0) REVERT: A 389 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7450 (tpp80) REVERT: A 393 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: A 395 GLN cc_start: 0.7668 (tp40) cc_final: 0.7420 (tp40) REVERT: A 466 HIS cc_start: 0.8040 (t-90) cc_final: 0.7838 (t70) REVERT: A 482 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7674 (mmm-85) REVERT: A 569 GLU cc_start: 0.7661 (tt0) cc_final: 0.7384 (tp30) REVERT: A 579 LYS cc_start: 0.8477 (mttt) cc_final: 0.8026 (mmmm) REVERT: A 595 LEU cc_start: 0.8694 (tp) cc_final: 0.8381 (tt) REVERT: A 603 ASP cc_start: 0.7460 (t0) cc_final: 0.7168 (t0) REVERT: A 627 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8314 (tmmt) REVERT: A 688 MET cc_start: 0.7801 (mtt) cc_final: 0.7594 (mtp) REVERT: A 736 LEU cc_start: 0.8286 (mp) cc_final: 0.8000 (mp) REVERT: A 742 ASP cc_start: 0.6483 (t0) cc_final: 0.6248 (t0) REVERT: A 779 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7359 (mtp) REVERT: B 296 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7488 (tmm-80) REVERT: B 297 LEU cc_start: 0.8201 (mp) cc_final: 0.7942 (mm) REVERT: B 303 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8098 (ttpt) REVERT: B 544 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7627 (t0) REVERT: B 577 LYS cc_start: 0.8157 (tttt) cc_final: 0.7770 (ttmm) REVERT: B 614 HIS cc_start: 0.6346 (m170) cc_final: 0.6143 (m170) REVERT: B 653 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 674 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6625 (mt-10) REVERT: B 699 LYS cc_start: 0.8711 (tppt) cc_final: 0.8403 (tppt) REVERT: B 933 ASP cc_start: 0.7923 (p0) cc_final: 0.7721 (p0) REVERT: B 1084 LYS cc_start: 0.8273 (mttt) cc_final: 0.7768 (mmmm) outliers start: 50 outliers final: 24 residues processed: 410 average time/residue: 0.1120 time to fit residues: 64.5919 Evaluate side-chains 390 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 361 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 871 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 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 544 ASN B 664 GLN B 917 GLN B 969 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138350 restraints weight = 23161.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142723 restraints weight = 10290.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145406 restraints weight = 5763.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146881 restraints weight = 3853.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148030 restraints weight = 3029.175| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13361 Z= 0.144 Angle : 0.673 12.761 18023 Z= 0.337 Chirality : 0.043 0.221 2063 Planarity : 0.005 0.075 2286 Dihedral : 7.293 158.003 1773 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 4.83 % Allowed : 23.96 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.21), residues: 1602 helix: 0.53 (0.18), residues: 814 sheet: -1.86 (0.35), residues: 195 loop : -1.55 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 938 TYR 0.022 0.002 TYR A 815 PHE 0.020 0.001 PHE B 638 TRP 0.011 0.001 TRP B 807 HIS 0.007 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00317 (13360) covalent geometry : angle 0.67242 (18021) SS BOND : bond 0.00920 ( 1) SS BOND : angle 1.26900 ( 2) hydrogen bonds : bond 0.04365 ( 676) hydrogen bonds : angle 5.15141 ( 1908) *********************** 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 449 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 379 time to evaluate : 0.508 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: 0.8337 (t) cc_final: 0.7996 (p) REVERT: A 192 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 198 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5813 (mm-30) REVERT: A 226 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6545 (mm-30) REVERT: A 261 MET cc_start: 0.6291 (mmp) cc_final: 0.5873 (mmp) REVERT: A 298 GLN cc_start: 0.7994 (tt0) cc_final: 0.7516 (tm-30) REVERT: A 339 GLN cc_start: 0.7477 (tt0) cc_final: 0.7255 (tt0) REVERT: A 345 TRP cc_start: 0.8160 (m-10) cc_final: 0.7377 (m-10) REVERT: A 359 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7231 (ttm-80) REVERT: A 361 ASN cc_start: 0.7538 (m-40) cc_final: 0.7184 (m110) REVERT: A 382 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7704 (ptm-80) REVERT: A 386 ASP cc_start: 0.7825 (t0) cc_final: 0.7451 (t0) REVERT: A 389 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7308 (tpp80) REVERT: A 393 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7804 (ttpt) REVERT: A 395 GLN cc_start: 0.7711 (tp40) cc_final: 0.7466 (tp40) REVERT: A 449 LYS cc_start: 0.8343 (mmmm) cc_final: 0.8026 (mmmm) REVERT: A 569 GLU cc_start: 0.7592 (tt0) cc_final: 0.7262 (tp30) REVERT: A 579 LYS cc_start: 0.8424 (mttt) cc_final: 0.7887 (mmmm) REVERT: A 603 ASP cc_start: 0.7458 (t0) cc_final: 0.7051 (t0) REVERT: A 627 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8323 (tmmt) REVERT: A 681 GLN cc_start: 0.7490 (tt0) cc_final: 0.7236 (tt0) REVERT: A 729 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: A 737 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7166 (ttp80) REVERT: A 742 ASP cc_start: 0.6939 (t0) cc_final: 0.6412 (t0) REVERT: A 850 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: B 303 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8051 (ttpt) REVERT: B 307 VAL cc_start: 0.8377 (t) cc_final: 0.7935 (p) REVERT: B 508 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8029 (tttt) REVERT: B 577 LYS cc_start: 0.8157 (tttt) cc_final: 0.7744 (ttmm) REVERT: B 614 HIS cc_start: 0.6320 (m170) cc_final: 0.6110 (m170) REVERT: B 653 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7363 (tm-30) REVERT: B 674 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6466 (mt-10) REVERT: B 677 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 699 LYS cc_start: 0.8676 (tppt) cc_final: 0.8335 (tppt) REVERT: B 813 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8078 (tppp) REVERT: B 842 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8422 (ttmm) REVERT: B 855 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6872 (mtm180) REVERT: B 885 SER cc_start: 0.7841 (t) cc_final: 0.7616 (t) REVERT: B 886 GLU cc_start: 0.7557 (tp30) cc_final: 0.6826 (tp30) REVERT: B 933 ASP cc_start: 0.7888 (p0) cc_final: 0.7668 (p0) REVERT: B 1018 GLU cc_start: 0.7301 (pp20) cc_final: 0.6986 (pp20) REVERT: B 1084 LYS cc_start: 0.8282 (mttt) cc_final: 0.7820 (mmmm) outliers start: 70 outliers final: 37 residues processed: 420 average time/residue: 0.1140 time to fit residues: 67.1500 Evaluate side-chains 416 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 374 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 347 LYS 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 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 818 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 908 GLN Chi-restraints excluded: chain B residue 932 VAL 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 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** 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 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138100 restraints weight = 23150.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142506 restraints weight = 10326.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145211 restraints weight = 5776.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146824 restraints weight = 3858.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147679 restraints weight = 3008.839| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13361 Z= 0.154 Angle : 0.661 13.178 18023 Z= 0.329 Chirality : 0.043 0.254 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.773 141.401 1771 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 4.49 % Allowed : 25.62 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.22), residues: 1602 helix: 0.59 (0.18), residues: 818 sheet: -1.84 (0.36), residues: 195 loop : -1.54 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 711 TYR 0.016 0.002 TYR B 302 PHE 0.029 0.001 PHE B 638 TRP 0.017 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00339 (13360) covalent geometry : angle 0.66093 (18021) SS BOND : bond 0.00977 ( 1) SS BOND : angle 1.49848 ( 2) hydrogen bonds : bond 0.04176 ( 676) hydrogen bonds : angle 5.02140 ( 1908) *********************** 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 442 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 377 time to evaluate : 0.462 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: 0.8309 (t) cc_final: 0.7978 (p) REVERT: A 198 GLU cc_start: 0.6401 (mm-30) cc_final: 0.5846 (mm-30) REVERT: A 226 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6531 (mm-30) REVERT: A 245 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6783 (tp) REVERT: A 261 MET cc_start: 0.6388 (mmp) cc_final: 0.5930 (mmp) REVERT: A 298 GLN cc_start: 0.8003 (tt0) cc_final: 0.7520 (tm-30) REVERT: A 339 GLN cc_start: 0.7472 (tt0) cc_final: 0.7252 (tt0) REVERT: A 345 TRP cc_start: 0.8210 (m-10) cc_final: 0.7395 (m-10) REVERT: A 359 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7205 (ttm-80) REVERT: A 361 ASN cc_start: 0.7487 (m-40) cc_final: 0.7197 (m110) REVERT: A 386 ASP cc_start: 0.7848 (t0) cc_final: 0.7396 (t0) REVERT: A 389 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7287 (tpp80) REVERT: A 393 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7755 (ttpt) REVERT: A 395 GLN cc_start: 0.7713 (tp40) cc_final: 0.7387 (tp40) REVERT: A 449 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7996 (mmmm) REVERT: A 490 LYS cc_start: 0.7410 (tptt) cc_final: 0.7182 (tptt) REVERT: A 569 GLU cc_start: 0.7601 (tt0) cc_final: 0.7289 (tp30) REVERT: A 579 LYS cc_start: 0.8394 (mttt) cc_final: 0.7847 (mmmm) REVERT: A 603 ASP cc_start: 0.7478 (t0) cc_final: 0.6877 (t0) REVERT: A 627 LYS cc_start: 0.8579 (tmmt) cc_final: 0.8334 (tmmt) REVERT: A 728 GLU cc_start: 0.6563 (tp30) cc_final: 0.6254 (tp30) REVERT: A 729 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6921 (mpp) REVERT: A 742 ASP cc_start: 0.7054 (t0) cc_final: 0.6417 (t0) REVERT: A 850 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: B 290 LEU cc_start: 0.4673 (OUTLIER) cc_final: 0.4461 (tt) REVERT: B 303 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8140 (ttpt) REVERT: B 307 VAL cc_start: 0.8364 (t) cc_final: 0.7916 (p) REVERT: B 425 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6162 (mt-10) REVERT: B 454 ARG cc_start: 0.8054 (ttt180) cc_final: 0.6443 (ttp80) REVERT: B 508 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (tttm) REVERT: B 577 LYS cc_start: 0.8158 (tttt) cc_final: 0.7713 (ttmm) REVERT: B 586 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8079 (mmtt) REVERT: B 647 HIS cc_start: 0.7524 (t70) cc_final: 0.7072 (t-90) REVERT: B 653 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 674 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6458 (mt-10) REVERT: B 699 LYS cc_start: 0.8675 (tppt) cc_final: 0.8336 (tppt) REVERT: B 823 LYS cc_start: 0.8015 (tptm) cc_final: 0.7676 (tptp) REVERT: B 885 SER cc_start: 0.7850 (t) cc_final: 0.7606 (t) REVERT: B 886 GLU cc_start: 0.7600 (tp30) cc_final: 0.6960 (tp30) REVERT: B 933 ASP cc_start: 0.7899 (p0) cc_final: 0.7661 (p0) REVERT: B 955 GLU cc_start: 0.7048 (mp0) cc_final: 0.6452 (mp0) REVERT: B 1018 GLU cc_start: 0.7279 (pp20) cc_final: 0.6897 (pp20) REVERT: B 1081 GLU cc_start: 0.7711 (pm20) cc_final: 0.7134 (pm20) REVERT: B 1084 LYS cc_start: 0.8246 (mttt) cc_final: 0.7732 (mmmm) REVERT: B 1091 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7626 (mmmm) outliers start: 65 outliers final: 39 residues processed: 420 average time/residue: 0.1141 time to fit residues: 67.3283 Evaluate side-chains 408 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 260 GLU 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 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET 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 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 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 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 46 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 0.0470 chunk 3 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137881 restraints weight = 23228.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142282 restraints weight = 10411.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144956 restraints weight = 5825.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146625 restraints weight = 3890.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147520 restraints weight = 3012.422| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13361 Z= 0.162 Angle : 0.674 13.134 18023 Z= 0.334 Chirality : 0.044 0.336 2063 Planarity : 0.005 0.052 2286 Dihedral : 6.508 132.318 1771 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 5.25 % Allowed : 25.97 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.22), residues: 1602 helix: 0.58 (0.18), residues: 819 sheet: -1.74 (0.36), residues: 195 loop : -1.53 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 711 TYR 0.027 0.002 TYR B 476 PHE 0.017 0.001 PHE A 551 TRP 0.013 0.001 TRP B 807 HIS 0.008 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00351 (13360) covalent geometry : angle 0.67383 (18021) SS BOND : bond 0.01006 ( 1) SS BOND : angle 1.65331 ( 2) hydrogen bonds : bond 0.04155 ( 676) hydrogen bonds : angle 4.95968 ( 1908) *********************** 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 461 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 385 time to evaluate : 0.400 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: 0.8324 (t) cc_final: 0.7978 (p) REVERT: A 192 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 198 GLU cc_start: 0.6420 (mm-30) cc_final: 0.5808 (mm-30) REVERT: A 226 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6554 (mm-30) REVERT: A 245 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6748 (tp) REVERT: A 261 MET cc_start: 0.6390 (mmp) cc_final: 0.5921 (mmp) REVERT: A 270 LEU cc_start: 0.8286 (tp) cc_final: 0.7997 (mt) REVERT: A 298 GLN cc_start: 0.7962 (tt0) cc_final: 0.7495 (tm-30) REVERT: A 339 GLN cc_start: 0.7477 (tt0) cc_final: 0.7247 (tt0) REVERT: A 345 TRP cc_start: 0.8247 (m-10) cc_final: 0.7262 (m-10) REVERT: A 360 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 361 ASN cc_start: 0.7524 (m-40) cc_final: 0.7236 (m-40) REVERT: A 382 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7709 (ptm-80) REVERT: A 386 ASP cc_start: 0.7868 (t0) cc_final: 0.7398 (t0) REVERT: A 389 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7297 (tpp80) REVERT: A 393 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7665 (ttpt) REVERT: A 395 GLN cc_start: 0.7705 (tp40) cc_final: 0.7192 (mm-40) REVERT: A 449 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8009 (mmmm) REVERT: A 482 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7813 (mmm-85) REVERT: A 490 LYS cc_start: 0.7398 (tptt) cc_final: 0.7139 (tptt) REVERT: A 569 GLU cc_start: 0.7583 (tt0) cc_final: 0.7281 (tp30) REVERT: A 579 LYS cc_start: 0.8381 (mttt) cc_final: 0.7883 (mmmm) REVERT: A 603 ASP cc_start: 0.7481 (t0) cc_final: 0.6844 (t0) REVERT: A 627 LYS cc_start: 0.8565 (tmmt) cc_final: 0.8336 (tmmt) REVERT: A 728 GLU cc_start: 0.6611 (tp30) cc_final: 0.6287 (tp30) REVERT: A 729 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6924 (mpp) REVERT: A 742 ASP cc_start: 0.7147 (t0) cc_final: 0.6386 (t0) REVERT: A 778 CYS cc_start: 0.7599 (t) cc_final: 0.7243 (t) REVERT: B 290 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.4571 (tt) REVERT: B 303 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8090 (ttpt) REVERT: B 307 VAL cc_start: 0.8371 (t) cc_final: 0.7915 (p) REVERT: B 425 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5865 (mt-10) REVERT: B 512 GLU cc_start: 0.7644 (tp30) cc_final: 0.7074 (tp30) REVERT: B 531 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8105 (mmmt) REVERT: B 577 LYS cc_start: 0.8234 (tttt) cc_final: 0.7752 (ttmm) REVERT: B 586 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8118 (mmtt) REVERT: B 653 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 666 ASP cc_start: 0.7829 (t0) cc_final: 0.7490 (t0) REVERT: B 674 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6493 (mt-10) REVERT: B 699 LYS cc_start: 0.8674 (tppt) cc_final: 0.8323 (tppt) REVERT: B 823 LYS cc_start: 0.8047 (tptm) cc_final: 0.7700 (tptp) REVERT: B 869 VAL cc_start: 0.8762 (t) cc_final: 0.8524 (m) REVERT: B 885 SER cc_start: 0.7845 (t) cc_final: 0.7601 (t) REVERT: B 886 GLU cc_start: 0.7626 (tp30) cc_final: 0.7042 (tp30) REVERT: B 955 GLU cc_start: 0.7113 (mp0) cc_final: 0.6423 (mp0) REVERT: B 1018 GLU cc_start: 0.7302 (pp20) cc_final: 0.6855 (pp20) REVERT: B 1084 LYS cc_start: 0.8293 (mttt) cc_final: 0.7841 (mmmm) REVERT: B 1091 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7645 (mmmm) outliers start: 76 outliers final: 46 residues processed: 435 average time/residue: 0.1060 time to fit residues: 65.1025 Evaluate side-chains 427 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 181 ASN 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 260 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 360 LEU 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 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 833 LEU Chi-restraints excluded: chain A residue 849 LEU 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 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 599 GLU 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 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 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 1005 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 162 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 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 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 = 0.4145 r_free = 0.4145 target = 0.165981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135611 restraints weight = 23104.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139938 restraints weight = 10386.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142586 restraints weight = 5839.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144220 restraints weight = 3931.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145048 restraints weight = 3047.040| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13361 Z= 0.228 Angle : 0.705 12.832 18023 Z= 0.352 Chirality : 0.046 0.327 2063 Planarity : 0.005 0.055 2286 Dihedral : 6.417 128.974 1771 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 4.83 % Allowed : 26.93 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.21), residues: 1602 helix: 0.52 (0.18), residues: 819 sheet: -1.70 (0.37), residues: 189 loop : -1.62 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 711 TYR 0.029 0.002 TYR A 678 PHE 0.019 0.001 PHE A 551 TRP 0.008 0.001 TRP B 807 HIS 0.010 0.001 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00478 (13360) covalent geometry : angle 0.70457 (18021) SS BOND : bond 0.01202 ( 1) SS BOND : angle 1.95149 ( 2) hydrogen bonds : bond 0.04298 ( 676) hydrogen bonds : angle 5.00963 ( 1908) *********************** 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 456 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 386 time to evaluate : 0.424 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: A 150 VAL cc_start: 0.8307 (t) cc_final: 0.7937 (p) REVERT: A 172 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7391 (mptt) REVERT: A 192 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7493 (mp) REVERT: A 198 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5771 (mm-30) REVERT: A 226 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6652 (mm-30) REVERT: A 245 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6786 (tp) REVERT: A 261 MET cc_start: 0.6402 (mmp) cc_final: 0.5917 (mmp) REVERT: A 270 LEU cc_start: 0.8254 (tp) cc_final: 0.8018 (mt) REVERT: A 271 SER cc_start: 0.8448 (t) cc_final: 0.8175 (p) REVERT: A 339 GLN cc_start: 0.7540 (tt0) cc_final: 0.7300 (tt0) REVERT: A 386 ASP cc_start: 0.7872 (t0) cc_final: 0.7395 (t0) REVERT: A 389 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7340 (tpp80) REVERT: A 393 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7731 (ttpt) REVERT: A 449 LYS cc_start: 0.8327 (mmmm) cc_final: 0.7932 (mmmm) REVERT: A 482 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7711 (mmm-85) REVERT: A 490 LYS cc_start: 0.7453 (tptt) cc_final: 0.7143 (tptt) REVERT: A 569 GLU cc_start: 0.7655 (tt0) cc_final: 0.7367 (tp30) REVERT: A 579 LYS cc_start: 0.8428 (mttt) cc_final: 0.7896 (mmmm) REVERT: A 603 ASP cc_start: 0.7494 (t0) cc_final: 0.7000 (t0) REVERT: A 627 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8364 (tmmt) REVERT: A 698 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 728 GLU cc_start: 0.6765 (tp30) cc_final: 0.6379 (tp30) REVERT: A 729 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6943 (mpp) REVERT: A 737 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.6893 (ptm-80) REVERT: A 742 ASP cc_start: 0.7211 (t0) cc_final: 0.6442 (t0) REVERT: A 778 CYS cc_start: 0.7613 (t) cc_final: 0.7245 (t) REVERT: A 850 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: B 290 LEU cc_start: 0.4644 (OUTLIER) cc_final: 0.4432 (tt) REVERT: B 303 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8171 (ttpt) REVERT: B 508 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8136 (tttm) REVERT: B 541 THR cc_start: 0.8415 (m) cc_final: 0.8182 (t) REVERT: B 577 LYS cc_start: 0.8262 (tttt) cc_final: 0.7748 (ttmm) REVERT: B 582 GLN cc_start: 0.7728 (mt0) cc_final: 0.7499 (mt0) REVERT: B 614 HIS cc_start: 0.6279 (m170) cc_final: 0.6032 (m170) REVERT: B 653 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 674 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6537 (mt-10) REVERT: B 678 LEU cc_start: 0.8226 (mm) cc_final: 0.8021 (mp) REVERT: B 683 GLU cc_start: 0.6475 (tp30) cc_final: 0.6135 (tp30) REVERT: B 699 LYS cc_start: 0.8647 (tppt) cc_final: 0.8321 (tppt) REVERT: B 798 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6678 (mm-40) REVERT: B 812 GLU cc_start: 0.7203 (tp30) cc_final: 0.6503 (tp30) REVERT: B 823 LYS cc_start: 0.8079 (tptm) cc_final: 0.7678 (tptp) REVERT: B 869 VAL cc_start: 0.8784 (t) cc_final: 0.8534 (m) REVERT: B 873 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.5869 (tm-30) REVERT: B 885 SER cc_start: 0.7911 (t) cc_final: 0.7687 (t) REVERT: B 886 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: B 953 MET cc_start: 0.7680 (tmm) cc_final: 0.7241 (tmm) REVERT: B 955 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: B 963 ILE cc_start: 0.8662 (mt) cc_final: 0.8430 (tp) REVERT: B 1018 GLU cc_start: 0.7311 (pp20) cc_final: 0.6872 (pp20) REVERT: B 1081 GLU cc_start: 0.7698 (pm20) cc_final: 0.7430 (pm20) REVERT: B 1084 LYS cc_start: 0.8290 (mttt) cc_final: 0.7782 (mmmm) REVERT: B 1091 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7661 (mmmm) outliers start: 70 outliers final: 45 residues processed: 432 average time/residue: 0.1137 time to fit residues: 69.0764 Evaluate side-chains 433 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 377 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 260 GLU 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 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 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 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 508 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 686 LEU 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 798 GLN 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 886 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 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 130 optimal weight: 0.2980 chunk 60 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 183 GLN ** 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 A 839 HIS 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138044 restraints weight = 23003.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142447 restraints weight = 10286.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145148 restraints weight = 5751.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146750 restraints weight = 3847.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147576 restraints weight = 2993.090| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13361 Z= 0.150 Angle : 0.691 13.394 18023 Z= 0.339 Chirality : 0.044 0.321 2063 Planarity : 0.005 0.061 2286 Dihedral : 6.124 123.907 1771 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 5.04 % Allowed : 27.83 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.22), residues: 1602 helix: 0.61 (0.18), residues: 815 sheet: -1.72 (0.36), residues: 195 loop : -1.57 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 711 TYR 0.027 0.002 TYR A 678 PHE 0.020 0.001 PHE B 638 TRP 0.007 0.001 TRP B 807 HIS 0.008 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00334 (13360) covalent geometry : angle 0.69065 (18021) SS BOND : bond 0.00912 ( 1) SS BOND : angle 1.69462 ( 2) hydrogen bonds : bond 0.04049 ( 676) hydrogen bonds : angle 4.90768 ( 1908) *********************** 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 440 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 0.524 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: 0.8294 (t) cc_final: 0.7945 (p) REVERT: A 172 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7369 (mmtt) REVERT: A 192 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 198 GLU cc_start: 0.6462 (mm-30) cc_final: 0.5695 (mm-30) REVERT: A 226 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 245 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6728 (tp) REVERT: A 261 MET cc_start: 0.6385 (mmp) cc_final: 0.5932 (mmp) REVERT: A 270 LEU cc_start: 0.8252 (tp) cc_final: 0.7938 (mt) REVERT: A 313 PHE cc_start: 0.7946 (m-80) cc_final: 0.7593 (m-80) REVERT: A 339 GLN cc_start: 0.7480 (tt0) cc_final: 0.7241 (tt0) REVERT: A 345 TRP cc_start: 0.8268 (m-10) cc_final: 0.7798 (m-10) REVERT: A 361 ASN cc_start: 0.7652 (m-40) cc_final: 0.7249 (m110) REVERT: A 382 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7712 (ptm-80) REVERT: A 386 ASP cc_start: 0.7876 (t0) cc_final: 0.7379 (t0) REVERT: A 389 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7309 (tpp80) REVERT: A 393 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7687 (ttpt) REVERT: A 449 LYS cc_start: 0.8312 (mmmm) cc_final: 0.7901 (mmmm) REVERT: A 560 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: A 569 GLU cc_start: 0.7602 (tt0) cc_final: 0.7281 (tp30) REVERT: A 579 LYS cc_start: 0.8380 (mttt) cc_final: 0.7842 (mmmm) REVERT: A 603 ASP cc_start: 0.7459 (t0) cc_final: 0.6850 (t0) REVERT: A 627 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8329 (tmmt) REVERT: A 698 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 728 GLU cc_start: 0.6710 (tp30) cc_final: 0.6308 (tp30) REVERT: A 729 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6920 (mpp) REVERT: A 737 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7365 (ttp80) REVERT: A 742 ASP cc_start: 0.7142 (t0) cc_final: 0.6427 (t0) REVERT: A 778 CYS cc_start: 0.7521 (t) cc_final: 0.7102 (t) REVERT: A 790 LEU cc_start: 0.8623 (tp) cc_final: 0.8305 (tp) REVERT: A 814 LEU cc_start: 0.8722 (mt) cc_final: 0.8476 (tt) REVERT: A 850 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: B 259 PHE cc_start: 0.7538 (m-10) cc_final: 0.7281 (m-10) REVERT: B 290 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4618 (tt) REVERT: B 307 VAL cc_start: 0.8553 (t) cc_final: 0.8137 (p) REVERT: B 425 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6113 (mt-10) REVERT: B 508 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8060 (tttt) REVERT: B 577 LYS cc_start: 0.8234 (tttt) cc_final: 0.7714 (ttmm) REVERT: B 582 GLN cc_start: 0.7700 (mt0) cc_final: 0.7477 (mt0) REVERT: B 614 HIS cc_start: 0.6238 (m170) cc_final: 0.6038 (m170) REVERT: B 642 VAL cc_start: 0.8756 (t) cc_final: 0.8539 (m) REVERT: B 653 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 659 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 666 ASP cc_start: 0.7827 (t0) cc_final: 0.7500 (t0) REVERT: B 674 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6507 (mt-10) REVERT: B 699 LYS cc_start: 0.8637 (tppt) cc_final: 0.8327 (tppt) REVERT: B 823 LYS cc_start: 0.8041 (tptm) cc_final: 0.7653 (tptp) REVERT: B 869 VAL cc_start: 0.8770 (t) cc_final: 0.8521 (m) REVERT: B 885 SER cc_start: 0.7835 (t) cc_final: 0.7595 (t) REVERT: B 886 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: B 953 MET cc_start: 0.7617 (tmm) cc_final: 0.7287 (tmm) REVERT: B 955 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: B 1018 GLU cc_start: 0.7305 (pp20) cc_final: 0.6880 (pp20) REVERT: B 1084 LYS cc_start: 0.8280 (mttt) cc_final: 0.7861 (mmmm) REVERT: B 1091 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7665 (mmmm) outliers start: 73 outliers final: 51 residues processed: 415 average time/residue: 0.1375 time to fit residues: 79.7934 Evaluate side-chains 434 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 372 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 181 ASN 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 260 GLU 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 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 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 816 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 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 275 HIS 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 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR 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 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 886 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 1052 PHE 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 87 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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 ** 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 = 0.4166 r_free = 0.4166 target = 0.167917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137475 restraints weight = 22978.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141817 restraints weight = 10355.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144496 restraints weight = 5835.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146184 restraints weight = 3891.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147016 restraints weight = 3020.347| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2302 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= 0.175 Angle : 0.711 13.218 18023 Z= 0.351 Chirality : 0.045 0.307 2063 Planarity : 0.005 0.057 2286 Dihedral : 6.115 126.218 1771 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 4.97 % Allowed : 27.69 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.21), residues: 1602 helix: 0.56 (0.18), residues: 820 sheet: -1.71 (0.36), residues: 195 loop : -1.57 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 711 TYR 0.036 0.002 TYR B 236 PHE 0.030 0.001 PHE B 638 TRP 0.006 0.001 TRP B 807 HIS 0.011 0.001 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00387 (13360) covalent geometry : angle 0.71060 (18021) SS BOND : bond 0.00985 ( 1) SS BOND : angle 1.75679 ( 2) hydrogen bonds : bond 0.04112 ( 676) hydrogen bonds : angle 4.92136 ( 1908) *********************** 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 439 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 367 time to evaluate : 0.554 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: 0.8297 (t) cc_final: 0.7950 (p) REVERT: A 172 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7374 (mmtt) REVERT: A 192 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 198 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5714 (mm-30) REVERT: A 226 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6564 (mm-30) REVERT: A 245 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6736 (tp) REVERT: A 261 MET cc_start: 0.6414 (mmp) cc_final: 0.5925 (mmp) REVERT: A 270 LEU cc_start: 0.8258 (tp) cc_final: 0.8015 (mt) REVERT: A 271 SER cc_start: 0.8410 (t) cc_final: 0.8143 (p) REVERT: A 313 PHE cc_start: 0.7924 (m-80) cc_final: 0.7546 (m-80) REVERT: A 339 GLN cc_start: 0.7486 (tt0) cc_final: 0.7244 (tt0) REVERT: A 345 TRP cc_start: 0.8308 (m-10) cc_final: 0.7877 (m-10) REVERT: A 361 ASN cc_start: 0.7707 (m-40) cc_final: 0.7254 (m110) REVERT: A 386 ASP cc_start: 0.7883 (t0) cc_final: 0.7377 (t0) REVERT: A 389 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7321 (tpp80) REVERT: A 393 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7677 (ttpt) REVERT: A 449 LYS cc_start: 0.8315 (mmmm) cc_final: 0.7914 (mmmm) REVERT: A 482 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7692 (mmm-85) REVERT: A 569 GLU cc_start: 0.7599 (tt0) cc_final: 0.7264 (tp30) REVERT: A 579 LYS cc_start: 0.8391 (mttt) cc_final: 0.7858 (mmmm) REVERT: A 603 ASP cc_start: 0.7473 (t0) cc_final: 0.6853 (t0) REVERT: A 627 LYS cc_start: 0.8605 (tmmt) cc_final: 0.8346 (tmmt) REVERT: A 698 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 728 GLU cc_start: 0.6728 (tp30) cc_final: 0.6349 (tp30) REVERT: A 729 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6909 (mpp) REVERT: A 742 ASP cc_start: 0.7181 (t0) cc_final: 0.6458 (t0) REVERT: A 749 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6564 (mt-10) REVERT: A 778 CYS cc_start: 0.7506 (t) cc_final: 0.7096 (t) REVERT: A 790 LEU cc_start: 0.8626 (tp) cc_final: 0.8304 (tp) REVERT: A 814 LEU cc_start: 0.8721 (mt) cc_final: 0.8516 (tt) REVERT: A 850 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: B 290 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4641 (tt) REVERT: B 425 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6090 (mt-10) REVERT: B 512 GLU cc_start: 0.7652 (tp30) cc_final: 0.7114 (tp30) REVERT: B 577 LYS cc_start: 0.8248 (tttt) cc_final: 0.7710 (ttmm) REVERT: B 582 GLN cc_start: 0.7718 (mt0) cc_final: 0.7500 (mt0) REVERT: B 614 HIS cc_start: 0.6261 (m170) cc_final: 0.6019 (m170) REVERT: B 653 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 659 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7856 (t) REVERT: B 666 ASP cc_start: 0.7856 (t0) cc_final: 0.7527 (t0) REVERT: B 674 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6529 (mt-10) REVERT: B 699 LYS cc_start: 0.8658 (tppt) cc_final: 0.8342 (ttpt) REVERT: B 823 LYS cc_start: 0.8048 (tptm) cc_final: 0.7665 (tptp) REVERT: B 869 VAL cc_start: 0.8764 (t) cc_final: 0.8531 (m) REVERT: B 873 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.5667 (tm-30) REVERT: B 885 SER cc_start: 0.7810 (t) cc_final: 0.7542 (t) REVERT: B 886 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: B 953 MET cc_start: 0.7643 (tmm) cc_final: 0.7294 (tmm) REVERT: B 955 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: B 956 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7937 (mm) REVERT: B 1018 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6892 (pp20) REVERT: B 1084 LYS cc_start: 0.8290 (mttt) cc_final: 0.7871 (mmmm) REVERT: B 1091 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7675 (mmmm) outliers start: 72 outliers final: 47 residues processed: 411 average time/residue: 0.1334 time to fit residues: 78.1010 Evaluate side-chains 419 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 260 GLU 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 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 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 816 GLN 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 B residue 239 MET Chi-restraints excluded: chain B residue 275 HIS 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 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 886 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 1060 THR 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** 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 839 HIS A 919 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138357 restraints weight = 23168.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142804 restraints weight = 10413.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145530 restraints weight = 5833.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147158 restraints weight = 3902.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147920 restraints weight = 3032.179| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13361 Z= 0.159 Angle : 0.718 13.422 18023 Z= 0.354 Chirality : 0.045 0.296 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.071 125.605 1771 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 4.56 % Allowed : 28.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.21), residues: 1602 helix: 0.60 (0.18), residues: 815 sheet: -1.75 (0.36), residues: 195 loop : -1.60 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 711 TYR 0.029 0.002 TYR B 236 PHE 0.027 0.001 PHE B1052 TRP 0.010 0.001 TRP B 807 HIS 0.012 0.001 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00351 (13360) covalent geometry : angle 0.71799 (18021) SS BOND : bond 0.00897 ( 1) SS BOND : angle 1.66441 ( 2) hydrogen bonds : bond 0.04059 ( 676) hydrogen bonds : angle 4.88714 ( 1908) *********************** 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 434 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 368 time to evaluate : 0.464 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: 0.8285 (t) cc_final: 0.7925 (p) REVERT: A 172 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7370 (mptt) REVERT: A 192 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 226 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 245 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6733 (tp) REVERT: A 261 MET cc_start: 0.6400 (mmp) cc_final: 0.5927 (mmp) REVERT: A 271 SER cc_start: 0.8412 (t) cc_final: 0.8147 (p) REVERT: A 313 PHE cc_start: 0.7937 (m-80) cc_final: 0.7567 (m-80) REVERT: A 345 TRP cc_start: 0.8272 (m-10) cc_final: 0.7818 (m-10) REVERT: A 361 ASN cc_start: 0.7723 (m-40) cc_final: 0.7342 (m-40) REVERT: A 382 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7588 (ttp80) REVERT: A 386 ASP cc_start: 0.7880 (t0) cc_final: 0.7361 (t0) REVERT: A 388 ASN cc_start: 0.8406 (t0) cc_final: 0.8066 (t0) REVERT: A 389 ARG cc_start: 0.7915 (tpp80) cc_final: 0.7312 (tpp80) REVERT: A 393 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7602 (ttpt) REVERT: A 409 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 449 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7888 (mmmm) REVERT: A 482 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7695 (mmm-85) REVERT: A 493 GLN cc_start: 0.7950 (mt0) cc_final: 0.7591 (mp10) REVERT: A 569 GLU cc_start: 0.7618 (tt0) cc_final: 0.7270 (tp30) REVERT: A 579 LYS cc_start: 0.8391 (mttt) cc_final: 0.7844 (mmmm) REVERT: A 603 ASP cc_start: 0.7451 (t0) cc_final: 0.6809 (t0) REVERT: A 627 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8313 (tmmt) REVERT: A 678 TYR cc_start: 0.8207 (t80) cc_final: 0.7875 (t80) REVERT: A 728 GLU cc_start: 0.6672 (tp30) cc_final: 0.6322 (tp30) REVERT: A 729 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6924 (mpp) REVERT: A 742 ASP cc_start: 0.7165 (t0) cc_final: 0.6440 (t0) REVERT: A 749 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6517 (mt-10) REVERT: A 768 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6918 (pp20) REVERT: A 778 CYS cc_start: 0.7484 (t) cc_final: 0.7056 (t) REVERT: A 790 LEU cc_start: 0.8622 (tp) cc_final: 0.8299 (tp) REVERT: A 814 LEU cc_start: 0.8655 (mt) cc_final: 0.8447 (tt) REVERT: B 259 PHE cc_start: 0.7589 (m-10) cc_final: 0.7322 (m-10) REVERT: B 342 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 425 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6121 (mt-10) REVERT: B 512 GLU cc_start: 0.7652 (tp30) cc_final: 0.7014 (tp30) REVERT: B 544 ASN cc_start: 0.8010 (t0) cc_final: 0.7713 (t0) REVERT: B 577 LYS cc_start: 0.8222 (tttt) cc_final: 0.7689 (ttmm) REVERT: B 582 GLN cc_start: 0.7714 (mt0) cc_final: 0.7500 (mt0) REVERT: B 614 HIS cc_start: 0.6254 (m170) cc_final: 0.6011 (m170) REVERT: B 647 HIS cc_start: 0.7483 (t70) cc_final: 0.7035 (t-90) REVERT: B 653 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 659 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7844 (t) REVERT: B 666 ASP cc_start: 0.7846 (t0) cc_final: 0.7504 (t0) REVERT: B 674 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6437 (mt-10) REVERT: B 699 LYS cc_start: 0.8650 (tppt) cc_final: 0.8336 (ttpt) REVERT: B 823 LYS cc_start: 0.8003 (tptm) cc_final: 0.7702 (tptp) REVERT: B 869 VAL cc_start: 0.8767 (t) cc_final: 0.8524 (m) REVERT: B 873 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.5655 (tm-30) REVERT: B 885 SER cc_start: 0.7773 (t) cc_final: 0.7496 (t) REVERT: B 886 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: B 955 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: B 956 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7944 (mm) REVERT: B 1018 GLU cc_start: 0.7321 (pp20) cc_final: 0.6903 (pp20) REVERT: B 1084 LYS cc_start: 0.8257 (mttt) cc_final: 0.7764 (mmmm) REVERT: B 1091 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7665 (mmmm) outliers start: 66 outliers final: 47 residues processed: 407 average time/residue: 0.1263 time to fit residues: 71.8667 Evaluate side-chains 417 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 360 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 260 GLU 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 458 LEU Chi-restraints excluded: chain A residue 521 TYR 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 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 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 A residue 919 ASN Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 413 GLU 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 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 886 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 130 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 117 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.170163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139875 restraints weight = 23180.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144255 restraints weight = 10372.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146969 restraints weight = 5810.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148681 restraints weight = 3899.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149539 restraints weight = 3006.520| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13361 Z= 0.144 Angle : 0.735 13.305 18023 Z= 0.361 Chirality : 0.045 0.279 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.037 125.148 1771 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 3.87 % Allowed : 28.52 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.22), residues: 1602 helix: 0.61 (0.18), residues: 812 sheet: -1.88 (0.35), residues: 200 loop : -1.50 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 383 TYR 0.064 0.002 TYR B 236 PHE 0.018 0.001 PHE B1052 TRP 0.019 0.001 TRP B 807 HIS 0.013 0.001 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00315 (13360) covalent geometry : angle 0.73449 (18021) SS BOND : bond 0.00761 ( 1) SS BOND : angle 1.47473 ( 2) hydrogen bonds : bond 0.04013 ( 676) hydrogen bonds : angle 4.84501 ( 1908) ********************** 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 423 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8281 (t) cc_final: 0.7892 (p) REVERT: A 165 TYR cc_start: 0.6805 (p90) cc_final: 0.6223 (p90) REVERT: A 172 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7336 (mptt) REVERT: A 226 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6554 (mm-30) REVERT: A 245 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6675 (tp) REVERT: A 261 MET cc_start: 0.6333 (mmp) cc_final: 0.5850 (mmp) REVERT: A 271 SER cc_start: 0.8369 (t) cc_final: 0.8052 (p) REVERT: A 298 GLN cc_start: 0.7865 (tt0) cc_final: 0.7625 (pt0) REVERT: A 308 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7605 (tpp80) REVERT: A 313 PHE cc_start: 0.7975 (m-80) cc_final: 0.7601 (m-80) REVERT: A 345 TRP cc_start: 0.8255 (m-10) cc_final: 0.7775 (m-10) REVERT: A 361 ASN cc_start: 0.7729 (m-40) cc_final: 0.7346 (m-40) REVERT: A 382 ARG cc_start: 0.7946 (ptm-80) cc_final: 0.7631 (ttp80) REVERT: A 386 ASP cc_start: 0.7895 (t0) cc_final: 0.7367 (t0) REVERT: A 388 ASN cc_start: 0.8401 (t0) cc_final: 0.8065 (t0) REVERT: A 389 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7287 (tpp80) REVERT: A 393 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7519 (ttpt) REVERT: A 409 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 449 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7791 (mmmm) REVERT: A 453 MET cc_start: 0.7748 (tmt) cc_final: 0.7463 (tmt) REVERT: A 482 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7687 (mmm-85) REVERT: A 569 GLU cc_start: 0.7595 (tt0) cc_final: 0.7258 (tp30) REVERT: A 579 LYS cc_start: 0.8340 (mttt) cc_final: 0.7813 (mmmm) REVERT: A 582 VAL cc_start: 0.8032 (m) cc_final: 0.7785 (t) REVERT: A 603 ASP cc_start: 0.7445 (t0) cc_final: 0.6794 (t0) REVERT: A 627 LYS cc_start: 0.8533 (tmmt) cc_final: 0.8263 (tmmt) REVERT: A 678 TYR cc_start: 0.8230 (t80) cc_final: 0.7857 (t80) REVERT: A 707 CYS cc_start: 0.7875 (p) cc_final: 0.7514 (p) REVERT: A 728 GLU cc_start: 0.6609 (tp30) cc_final: 0.6329 (tp30) REVERT: A 729 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6940 (mpp) REVERT: A 737 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7214 (ttp80) REVERT: A 742 ASP cc_start: 0.7112 (t0) cc_final: 0.6394 (t0) REVERT: A 752 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.6991 (tpp-160) REVERT: A 768 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6879 (pp20) REVERT: A 790 LEU cc_start: 0.8617 (tp) cc_final: 0.8298 (tp) REVERT: A 814 LEU cc_start: 0.8660 (mt) cc_final: 0.8454 (tt) REVERT: B 236 TYR cc_start: 0.6643 (t80) cc_final: 0.6335 (t80) REVERT: B 259 PHE cc_start: 0.7384 (m-10) cc_final: 0.7081 (m-10) REVERT: B 425 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6036 (mt-10) REVERT: B 476 TYR cc_start: 0.7754 (m-10) cc_final: 0.7408 (m-10) REVERT: B 508 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8049 (tttt) REVERT: B 512 GLU cc_start: 0.7573 (tp30) cc_final: 0.6941 (tp30) REVERT: B 533 GLU cc_start: 0.6868 (pt0) cc_final: 0.6629 (pm20) REVERT: B 543 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7273 (ttp80) REVERT: B 544 ASN cc_start: 0.7942 (t0) cc_final: 0.7244 (t0) REVERT: B 577 LYS cc_start: 0.8171 (tttt) cc_final: 0.7644 (ttmm) REVERT: B 582 GLN cc_start: 0.7722 (mt0) cc_final: 0.7505 (mt0) REVERT: B 614 HIS cc_start: 0.6245 (m170) cc_final: 0.6006 (m170) REVERT: B 641 ILE cc_start: 0.8990 (tp) cc_final: 0.8725 (tp) REVERT: B 647 HIS cc_start: 0.7465 (t70) cc_final: 0.7042 (t-170) REVERT: B 653 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 659 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7824 (t) REVERT: B 666 ASP cc_start: 0.7856 (t0) cc_final: 0.7520 (t0) REVERT: B 674 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6411 (mt-10) REVERT: B 699 LYS cc_start: 0.8649 (tppt) cc_final: 0.8337 (tppt) REVERT: B 735 LYS cc_start: 0.8289 (tmtt) cc_final: 0.8071 (tmtt) REVERT: B 823 LYS cc_start: 0.7974 (tptm) cc_final: 0.7650 (tptp) REVERT: B 869 VAL cc_start: 0.8744 (t) cc_final: 0.8513 (m) REVERT: B 873 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.5947 (tm-30) REVERT: B 885 SER cc_start: 0.7696 (t) cc_final: 0.7429 (t) REVERT: B 955 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: B 956 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (mm) REVERT: B 1018 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: B 1084 LYS cc_start: 0.8245 (mttt) cc_final: 0.7718 (mmmm) REVERT: B 1088 HIS cc_start: 0.8032 (t70) cc_final: 0.7771 (t-90) REVERT: B 1091 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7674 (mmmm) outliers start: 56 outliers final: 34 residues processed: 399 average time/residue: 0.1365 time to fit residues: 76.2586 Evaluate side-chains 406 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 362 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 255 SER 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 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 793 GLN 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 B residue 275 HIS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS 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 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 873 GLU 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 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 8 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 125 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139947 restraints weight = 22981.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144290 restraints weight = 10286.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147008 restraints weight = 5767.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.148513 restraints weight = 3845.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149643 restraints weight = 3002.055| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 13361 Z= 0.256 Angle : 0.949 59.200 18023 Z= 0.518 Chirality : 0.046 0.422 2063 Planarity : 0.005 0.053 2286 Dihedral : 6.029 125.170 1771 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 3.52 % Allowed : 29.49 % Favored : 66.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.21), residues: 1602 helix: 0.60 (0.18), residues: 812 sheet: -1.88 (0.35), residues: 202 loop : -1.53 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 752 TYR 0.055 0.002 TYR B 236 PHE 0.017 0.001 PHE B1052 TRP 0.017 0.001 TRP B 807 HIS 0.035 0.002 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00493 (13360) covalent geometry : angle 0.94875 (18021) SS BOND : bond 0.00898 ( 1) SS BOND : angle 1.50637 ( 2) hydrogen bonds : bond 0.04033 ( 676) hydrogen bonds : angle 4.84328 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.48 seconds wall clock time: 46 minutes 1.27 seconds (2761.27 seconds total)