Starting phenix.real_space_refine on Sun Nov 17 08:45:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_16969.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_16969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_16969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_16969.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/11_2024/8om5_16969.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8366 2.51 5 N 2239 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6551 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 802} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6531 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 26, 'TRANS': 785} Chain breaks: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.03, per 1000 atoms: 0.61 Number of scatterers: 13138 At special positions: 0 Unit cell: (94.1626, 162.728, 119.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 4 15.00 Mg 2 11.99 O 2465 8.00 N 2239 7.00 C 8366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS B 274 " distance=2.50 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 54.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 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: 4.66 Time building geometry restraints manager: 3.86 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.710 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 : 0.007 0.105 13360 Z= 0.441 Angle : 1.077 8.802 18021 Z= 0.665 Chirality : 0.078 0.384 2063 Planarity : 0.004 0.047 2286 Dihedral : 17.612 165.291 5025 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 1.93 % Allowed : 24.72 % Favored : 73.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1602 helix: 0.12 (0.18), residues: 783 sheet: -2.07 (0.38), residues: 162 loop : -1.96 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 807 HIS 0.015 0.003 HIS B 614 PHE 0.015 0.003 PHE B 402 TYR 0.037 0.004 TYR A 815 ARG 0.010 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 404 time to evaluate : 1.327 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: 0.3148 time to fit residues: 179.0409 Evaluate side-chains 400 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 379 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1070 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 127 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 0.0770 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS B 345 ASN B 394 GLN B 544 ASN B 898 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13360 Z= 0.231 Angle : 0.703 12.587 18021 Z= 0.356 Chirality : 0.044 0.241 2063 Planarity : 0.005 0.048 2286 Dihedral : 8.431 176.398 1810 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.45 % Allowed : 24.59 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1602 helix: 0.38 (0.18), residues: 807 sheet: -1.82 (0.37), residues: 188 loop : -1.63 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.020 0.001 PHE B 463 TYR 0.018 0.002 TYR A 815 ARG 0.012 0.001 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 381 time to evaluate : 1.439 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: 0.8664 (t) cc_final: 0.8432 (p) REVERT: A 192 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 198 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 226 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 245 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 261 MET cc_start: 0.7479 (mmp) cc_final: 0.7141 (mmp) REVERT: A 298 GLN cc_start: 0.8969 (tt0) cc_final: 0.8499 (tm-30) REVERT: A 345 TRP cc_start: 0.8535 (m-10) cc_final: 0.7725 (m-10) REVERT: A 386 ASP cc_start: 0.8650 (t0) cc_final: 0.8409 (t0) REVERT: A 389 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8788 (tpp80) REVERT: A 425 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8227 (tp30) REVERT: A 482 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8546 (mmm-85) REVERT: A 562 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8739 (tp30) REVERT: A 569 GLU cc_start: 0.8718 (tt0) cc_final: 0.8214 (tp30) REVERT: A 579 LYS cc_start: 0.8991 (mttt) cc_final: 0.8606 (mmmm) REVERT: A 593 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8777 (mt0) REVERT: A 595 LEU cc_start: 0.9114 (tp) cc_final: 0.8850 (tt) REVERT: A 603 ASP cc_start: 0.8277 (t0) cc_final: 0.8062 (t0) REVERT: A 779 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (mtp) REVERT: A 809 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8522 (mp0) REVERT: A 838 LYS cc_start: 0.8517 (mttt) cc_final: 0.8161 (mmmm) REVERT: B 296 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8524 (tmm-80) REVERT: B 297 LEU cc_start: 0.8741 (mp) cc_final: 0.8527 (mm) REVERT: B 375 LYS cc_start: 0.9192 (mttt) cc_final: 0.8990 (mtpp) REVERT: B 544 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (t0) REVERT: B 577 LYS cc_start: 0.8780 (tttt) cc_final: 0.8485 (ttmm) REVERT: B 653 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 674 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 1081 GLU cc_start: 0.8656 (pm20) cc_final: 0.8421 (pm20) REVERT: B 1084 LYS cc_start: 0.8794 (mttt) cc_final: 0.8365 (mmmm) REVERT: B 1091 LYS cc_start: 0.8205 (mttt) cc_final: 0.7976 (mtpp) outliers start: 50 outliers final: 24 residues processed: 411 average time/residue: 0.3093 time to fit residues: 177.4959 Evaluate side-chains 393 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 365 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 361 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B 969 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13360 Z= 0.218 Angle : 0.675 12.642 18021 Z= 0.339 Chirality : 0.043 0.230 2063 Planarity : 0.005 0.070 2286 Dihedral : 7.320 157.757 1773 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 4.63 % Allowed : 24.03 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1602 helix: 0.50 (0.18), residues: 815 sheet: -1.87 (0.35), residues: 195 loop : -1.56 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.022 0.001 PHE B 638 TYR 0.022 0.002 TYR A 815 ARG 0.012 0.001 ARG B 938 *********************** 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 441 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 1.467 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: 0.8661 (t) cc_final: 0.8412 (p) REVERT: A 192 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 198 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 226 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 261 MET cc_start: 0.7501 (mmp) cc_final: 0.7077 (mmp) REVERT: A 298 GLN cc_start: 0.8956 (tt0) cc_final: 0.8476 (tm-30) REVERT: A 345 TRP cc_start: 0.8529 (m-10) cc_final: 0.7663 (m-10) REVERT: A 361 ASN cc_start: 0.8139 (m-40) cc_final: 0.7717 (m110) REVERT: A 382 ARG cc_start: 0.8916 (ptt90) cc_final: 0.8586 (ttp80) REVERT: A 386 ASP cc_start: 0.8771 (t0) cc_final: 0.8425 (t0) REVERT: A 389 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8745 (tpp80) REVERT: A 482 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8463 (mmm-85) REVERT: A 562 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8758 (tp30) REVERT: A 569 GLU cc_start: 0.8692 (tt0) cc_final: 0.8159 (tp30) REVERT: A 579 LYS cc_start: 0.8964 (mttt) cc_final: 0.8470 (mmmm) REVERT: A 593 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8762 (mt0) REVERT: A 603 ASP cc_start: 0.8269 (t0) cc_final: 0.7984 (t0) REVERT: A 729 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8051 (mpp) REVERT: A 742 ASP cc_start: 0.8080 (t0) cc_final: 0.7785 (t0) REVERT: A 809 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8583 (mp0) REVERT: A 838 LYS cc_start: 0.8431 (mttt) cc_final: 0.8184 (mmmm) REVERT: A 850 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: B 307 VAL cc_start: 0.8642 (t) cc_final: 0.8234 (p) REVERT: B 375 LYS cc_start: 0.9169 (mttt) cc_final: 0.8964 (mtpp) REVERT: B 508 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8340 (tttm) REVERT: B 577 LYS cc_start: 0.8777 (tttt) cc_final: 0.8473 (ttmm) REVERT: B 653 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 674 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 677 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 885 SER cc_start: 0.8205 (t) cc_final: 0.7972 (t) REVERT: B 886 GLU cc_start: 0.8410 (tp30) cc_final: 0.8015 (tp30) REVERT: B 1084 LYS cc_start: 0.8763 (mttt) cc_final: 0.8326 (mmmm) REVERT: B 1091 LYS cc_start: 0.8202 (mttt) cc_final: 0.7908 (mmmm) outliers start: 67 outliers final: 38 residues processed: 414 average time/residue: 0.2934 time to fit residues: 169.1265 Evaluate side-chains 413 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 387 LEU 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 146 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 377 GLN A 409 GLN ** A 451 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13360 Z= 0.277 Angle : 0.683 12.799 18021 Z= 0.343 Chirality : 0.044 0.260 2063 Planarity : 0.005 0.055 2286 Dihedral : 6.823 137.955 1771 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 4.49 % Allowed : 25.69 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1602 helix: 0.53 (0.18), residues: 815 sheet: -1.87 (0.36), residues: 195 loop : -1.62 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.020 0.001 PHE B 638 TYR 0.027 0.002 TYR A 619 ARG 0.010 0.001 ARG A 711 *********************** 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 456 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 391 time to evaluate : 1.490 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: 0.8659 (t) cc_final: 0.8395 (p) REVERT: A 198 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7368 (mm-30) REVERT: A 226 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 245 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (tp) REVERT: A 261 MET cc_start: 0.7562 (mmp) cc_final: 0.7111 (mmp) REVERT: A 271 SER cc_start: 0.8552 (t) cc_final: 0.8293 (p) REVERT: A 299 TYR cc_start: 0.8494 (m-80) cc_final: 0.8226 (m-80) REVERT: A 345 TRP cc_start: 0.8619 (m-10) cc_final: 0.7765 (m-10) REVERT: A 361 ASN cc_start: 0.8198 (m-40) cc_final: 0.7749 (m110) REVERT: A 382 ARG cc_start: 0.8935 (ptt90) cc_final: 0.8574 (ttp80) REVERT: A 386 ASP cc_start: 0.8777 (t0) cc_final: 0.8367 (t0) REVERT: A 389 ARG cc_start: 0.9101 (tpp80) cc_final: 0.8703 (tpp80) REVERT: A 395 GLN cc_start: 0.9102 (tp40) cc_final: 0.8792 (tt0) REVERT: A 446 ASP cc_start: 0.8782 (t0) cc_final: 0.8581 (t0) REVERT: A 482 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8515 (mmm-85) REVERT: A 562 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8800 (tp30) REVERT: A 569 GLU cc_start: 0.8704 (tt0) cc_final: 0.8161 (tp30) REVERT: A 579 LYS cc_start: 0.8970 (mttt) cc_final: 0.8472 (mmmm) REVERT: A 593 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8781 (mt0) REVERT: A 603 ASP cc_start: 0.8284 (t0) cc_final: 0.7855 (t0) REVERT: A 619 TYR cc_start: 0.8485 (m-80) cc_final: 0.8133 (m-80) REVERT: A 681 GLN cc_start: 0.8311 (tt0) cc_final: 0.8038 (tt0) REVERT: A 729 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8065 (mpp) REVERT: A 737 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8145 (ttp80) REVERT: A 742 ASP cc_start: 0.8332 (t0) cc_final: 0.7954 (t0) REVERT: A 778 CYS cc_start: 0.8545 (t) cc_final: 0.8217 (t) REVERT: A 779 MET cc_start: 0.8128 (mtp) cc_final: 0.7923 (mtp) REVERT: A 809 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8655 (mp0) REVERT: A 838 LYS cc_start: 0.8494 (mttt) cc_final: 0.8192 (mmmm) REVERT: B 269 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: B 454 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8240 (ttp80) REVERT: B 508 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8409 (tttm) REVERT: B 541 THR cc_start: 0.8724 (m) cc_final: 0.8333 (t) REVERT: B 577 LYS cc_start: 0.8846 (tttt) cc_final: 0.8547 (ttmm) REVERT: B 653 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 674 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 683 GLU cc_start: 0.7441 (tp30) cc_final: 0.7101 (tp30) REVERT: B 698 ASP cc_start: 0.8475 (t0) cc_final: 0.8096 (t0) REVERT: B 853 GLU cc_start: 0.8861 (pm20) cc_final: 0.8574 (pm20) REVERT: B 869 VAL cc_start: 0.9124 (t) cc_final: 0.8889 (m) REVERT: B 885 SER cc_start: 0.8175 (t) cc_final: 0.7932 (t) REVERT: B 886 GLU cc_start: 0.8433 (tp30) cc_final: 0.8125 (tp30) REVERT: B 933 ASP cc_start: 0.8493 (p0) cc_final: 0.8292 (p0) REVERT: B 1084 LYS cc_start: 0.8784 (mttt) cc_final: 0.8340 (mmmm) REVERT: B 1091 LYS cc_start: 0.8278 (mttt) cc_final: 0.7971 (mmmm) outliers start: 65 outliers final: 41 residues processed: 431 average time/residue: 0.3059 time to fit residues: 184.8783 Evaluate side-chains 424 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 348 GLN Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 387 LEU 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 773 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 269 GLU 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 871 LEU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 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 131 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13360 Z= 0.299 Angle : 0.704 12.840 18021 Z= 0.353 Chirality : 0.046 0.291 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.631 129.523 1771 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 5.11 % Allowed : 26.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1602 helix: 0.49 (0.18), residues: 818 sheet: -1.93 (0.35), residues: 201 loop : -1.57 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 288 PHE 0.020 0.001 PHE A 313 TYR 0.029 0.002 TYR A 619 ARG 0.010 0.001 ARG A 711 *********************** 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 464 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 390 time to evaluate : 1.471 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: 0.8658 (t) cc_final: 0.8386 (p) REVERT: A 192 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 198 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 226 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 245 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7589 (tp) REVERT: A 261 MET cc_start: 0.7585 (mmp) cc_final: 0.7106 (mmp) REVERT: A 345 TRP cc_start: 0.8652 (m-10) cc_final: 0.7966 (m-10) REVERT: A 351 MET cc_start: 0.8611 (ttm) cc_final: 0.8293 (ttm) REVERT: A 359 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7418 (ttm110) REVERT: A 361 ASN cc_start: 0.8164 (m-40) cc_final: 0.7944 (m-40) REVERT: A 386 ASP cc_start: 0.8773 (t0) cc_final: 0.8351 (t0) REVERT: A 389 ARG cc_start: 0.9119 (tpp80) cc_final: 0.8692 (tpp80) REVERT: A 395 GLN cc_start: 0.9117 (tp40) cc_final: 0.8795 (tt0) REVERT: A 460 MET cc_start: 0.8515 (mmt) cc_final: 0.8205 (mmt) REVERT: A 562 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8789 (tp30) REVERT: A 569 GLU cc_start: 0.8718 (tt0) cc_final: 0.8189 (tp30) REVERT: A 579 LYS cc_start: 0.8972 (mttt) cc_final: 0.8504 (mmmm) REVERT: A 593 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8817 (mt0) REVERT: A 603 ASP cc_start: 0.8263 (t0) cc_final: 0.7814 (t0) REVERT: A 619 TYR cc_start: 0.8506 (m-10) cc_final: 0.8246 (m-80) REVERT: A 621 ARG cc_start: 0.8843 (ttm-80) cc_final: 0.8558 (ttt-90) REVERT: A 729 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: A 737 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8496 (mtp-110) REVERT: A 742 ASP cc_start: 0.8483 (t0) cc_final: 0.8010 (t0) REVERT: A 778 CYS cc_start: 0.8523 (t) cc_final: 0.8204 (t) REVERT: A 809 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8647 (mp0) REVERT: A 838 LYS cc_start: 0.8510 (mttt) cc_final: 0.8201 (mmmm) REVERT: A 850 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: B 242 GLN cc_start: 0.8669 (mm110) cc_final: 0.8275 (mt0) REVERT: B 269 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: B 307 VAL cc_start: 0.8733 (t) cc_final: 0.8412 (p) REVERT: B 425 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 508 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8369 (tttt) REVERT: B 512 GLU cc_start: 0.8779 (tp30) cc_final: 0.8363 (tp30) REVERT: B 541 THR cc_start: 0.8732 (m) cc_final: 0.8342 (t) REVERT: B 577 LYS cc_start: 0.8853 (tttt) cc_final: 0.8549 (ttmm) REVERT: B 653 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 674 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8087 (mt-10) REVERT: B 683 GLU cc_start: 0.7423 (tp30) cc_final: 0.7054 (tp30) REVERT: B 698 ASP cc_start: 0.8475 (t0) cc_final: 0.8137 (t0) REVERT: B 853 GLU cc_start: 0.8853 (pm20) cc_final: 0.8555 (pm20) REVERT: B 869 VAL cc_start: 0.9125 (t) cc_final: 0.8888 (m) REVERT: B 885 SER cc_start: 0.8177 (t) cc_final: 0.7928 (t) REVERT: B 886 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: B 955 GLU cc_start: 0.8671 (mp0) cc_final: 0.8208 (mp0) REVERT: B 1084 LYS cc_start: 0.8785 (mttt) cc_final: 0.8343 (mmmm) REVERT: B 1091 LYS cc_start: 0.8308 (mttt) cc_final: 0.7988 (mmmm) outliers start: 74 outliers final: 46 residues processed: 436 average time/residue: 0.2979 time to fit residues: 180.9368 Evaluate side-chains 429 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 376 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 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 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 793 GLN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 269 GLU 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 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 130 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 377 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13360 Z= 0.234 Angle : 0.700 13.393 18021 Z= 0.345 Chirality : 0.044 0.320 2063 Planarity : 0.005 0.055 2286 Dihedral : 6.363 122.574 1771 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 5.52 % Allowed : 26.10 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1602 helix: 0.57 (0.18), residues: 814 sheet: -1.97 (0.35), residues: 201 loop : -1.58 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.009 0.001 HIS B 817 PHE 0.019 0.001 PHE A 551 TYR 0.021 0.002 TYR B 302 ARG 0.005 0.000 ARG A 373 *********************** 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 461 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 381 time to evaluate : 1.355 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: 0.8659 (t) cc_final: 0.8401 (p) REVERT: A 172 LYS cc_start: 0.8014 (mptt) cc_final: 0.7756 (mmtt) REVERT: A 192 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 198 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 226 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 245 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7572 (tp) REVERT: A 261 MET cc_start: 0.7596 (mmp) cc_final: 0.7175 (mmp) REVERT: A 345 TRP cc_start: 0.8607 (m-10) cc_final: 0.7686 (m-10) REVERT: A 351 MET cc_start: 0.8625 (ttm) cc_final: 0.8304 (ttm) REVERT: A 361 ASN cc_start: 0.8229 (m-40) cc_final: 0.7821 (m-40) REVERT: A 382 ARG cc_start: 0.8924 (ptt90) cc_final: 0.8541 (ttp80) REVERT: A 386 ASP cc_start: 0.8773 (t0) cc_final: 0.8341 (t0) REVERT: A 388 ASN cc_start: 0.9063 (t0) cc_final: 0.8857 (t0) REVERT: A 389 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8668 (tpp80) REVERT: A 395 GLN cc_start: 0.9112 (tp40) cc_final: 0.8804 (tt0) REVERT: A 460 MET cc_start: 0.8445 (mmt) cc_final: 0.8132 (mmt) REVERT: A 482 ARG cc_start: 0.8721 (mmm160) cc_final: 0.8451 (mmm-85) REVERT: A 562 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8768 (tp30) REVERT: A 569 GLU cc_start: 0.8676 (tt0) cc_final: 0.8118 (tp30) REVERT: A 579 LYS cc_start: 0.8955 (mttt) cc_final: 0.8483 (mmmm) REVERT: A 593 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8762 (mt0) REVERT: A 603 ASP cc_start: 0.8235 (t0) cc_final: 0.7777 (t0) REVERT: A 737 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8042 (ttp80) REVERT: A 742 ASP cc_start: 0.8518 (t0) cc_final: 0.7998 (t0) REVERT: A 752 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8504 (tpp-160) REVERT: A 778 CYS cc_start: 0.8481 (t) cc_final: 0.8127 (t) REVERT: A 790 LEU cc_start: 0.8797 (tp) cc_final: 0.8551 (tp) REVERT: A 809 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8578 (mp0) REVERT: A 838 LYS cc_start: 0.8488 (mttt) cc_final: 0.8175 (mmmm) REVERT: A 850 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: B 242 GLN cc_start: 0.8694 (mm110) cc_final: 0.8322 (mt0) REVERT: B 269 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: B 296 ARG cc_start: 0.9102 (mmm160) cc_final: 0.8374 (tpt90) REVERT: B 307 VAL cc_start: 0.8730 (t) cc_final: 0.8387 (p) REVERT: B 425 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7270 (mt-10) REVERT: B 434 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8087 (pm20) REVERT: B 508 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8371 (tttm) REVERT: B 577 LYS cc_start: 0.8833 (tttt) cc_final: 0.8531 (ttmm) REVERT: B 653 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 674 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8032 (mt-10) REVERT: B 698 ASP cc_start: 0.8464 (t0) cc_final: 0.8117 (t0) REVERT: B 699 LYS cc_start: 0.8998 (tppt) cc_final: 0.8742 (mppt) REVERT: B 798 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: B 869 VAL cc_start: 0.9118 (t) cc_final: 0.8891 (m) REVERT: B 873 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: B 885 SER cc_start: 0.8184 (t) cc_final: 0.7933 (t) REVERT: B 886 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: B 955 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: B 1084 LYS cc_start: 0.8774 (mttt) cc_final: 0.8320 (mmmm) REVERT: B 1091 LYS cc_start: 0.8298 (mttt) cc_final: 0.8000 (mmmm) outliers start: 80 outliers final: 53 residues processed: 428 average time/residue: 0.2893 time to fit residues: 173.0839 Evaluate side-chains 437 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 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 269 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 798 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 820 SER 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 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 409 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13360 Z= 0.228 Angle : 0.706 13.400 18021 Z= 0.346 Chirality : 0.045 0.314 2063 Planarity : 0.005 0.052 2286 Dihedral : 6.156 121.795 1771 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 5.18 % Allowed : 27.35 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1602 helix: 0.59 (0.18), residues: 819 sheet: -1.95 (0.35), residues: 201 loop : -1.55 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.027 0.001 PHE B 638 TYR 0.034 0.002 TYR B 236 ARG 0.007 0.001 ARG A 711 *********************** 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 447 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.461 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: 0.8655 (t) cc_final: 0.8398 (p) REVERT: A 192 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 198 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 226 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 245 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7548 (tp) REVERT: A 261 MET cc_start: 0.7602 (mmp) cc_final: 0.7124 (mmp) REVERT: A 313 PHE cc_start: 0.8340 (m-80) cc_final: 0.8066 (m-80) REVERT: A 345 TRP cc_start: 0.8605 (m-10) cc_final: 0.7678 (m-10) REVERT: A 351 MET cc_start: 0.8636 (ttm) cc_final: 0.8204 (ttm) REVERT: A 361 ASN cc_start: 0.8237 (m-40) cc_final: 0.7844 (m-40) REVERT: A 382 ARG cc_start: 0.8910 (ptt90) cc_final: 0.8512 (ttp80) REVERT: A 386 ASP cc_start: 0.8782 (t0) cc_final: 0.8346 (t0) REVERT: A 388 ASN cc_start: 0.9079 (t0) cc_final: 0.8858 (t0) REVERT: A 389 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8667 (tpp80) REVERT: A 395 GLN cc_start: 0.9096 (tp40) cc_final: 0.8797 (tt0) REVERT: A 460 MET cc_start: 0.8409 (mmt) cc_final: 0.8126 (mmt) REVERT: A 482 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8384 (mmm-85) REVERT: A 493 GLN cc_start: 0.8760 (mt0) cc_final: 0.8485 (mp10) REVERT: A 562 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8776 (tp30) REVERT: A 569 GLU cc_start: 0.8677 (tt0) cc_final: 0.8107 (tp30) REVERT: A 579 LYS cc_start: 0.8944 (mttt) cc_final: 0.8475 (mmmm) REVERT: A 593 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8769 (mt0) REVERT: A 603 ASP cc_start: 0.8229 (t0) cc_final: 0.7774 (t0) REVERT: A 729 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8104 (mpp) REVERT: A 737 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8018 (ttp-170) REVERT: A 742 ASP cc_start: 0.8536 (t0) cc_final: 0.8020 (t0) REVERT: A 778 CYS cc_start: 0.8447 (t) cc_final: 0.8095 (t) REVERT: A 790 LEU cc_start: 0.8795 (tp) cc_final: 0.8521 (tp) REVERT: A 809 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8648 (mp0) REVERT: A 838 LYS cc_start: 0.8524 (mttt) cc_final: 0.8310 (mmmm) REVERT: A 850 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: B 242 GLN cc_start: 0.8686 (mm110) cc_final: 0.8304 (mt0) REVERT: B 296 ARG cc_start: 0.9100 (mmm160) cc_final: 0.8866 (mmm160) REVERT: B 307 VAL cc_start: 0.8729 (t) cc_final: 0.8376 (p) REVERT: B 456 GLU cc_start: 0.8591 (tp30) cc_final: 0.7812 (mp0) REVERT: B 512 GLU cc_start: 0.8747 (tp30) cc_final: 0.8346 (tp30) REVERT: B 577 LYS cc_start: 0.8819 (tttt) cc_final: 0.8519 (ttmm) REVERT: B 653 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 659 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (t) REVERT: B 666 ASP cc_start: 0.8631 (t0) cc_final: 0.8384 (t0) REVERT: B 674 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 698 ASP cc_start: 0.8500 (t0) cc_final: 0.8216 (t0) REVERT: B 699 LYS cc_start: 0.8975 (tppt) cc_final: 0.8769 (mppt) REVERT: B 798 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: B 869 VAL cc_start: 0.9109 (t) cc_final: 0.8894 (m) REVERT: B 873 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: B 885 SER cc_start: 0.8200 (t) cc_final: 0.7951 (t) REVERT: B 886 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: B 955 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: B 1084 LYS cc_start: 0.8769 (mttt) cc_final: 0.8323 (mmmm) REVERT: B 1091 LYS cc_start: 0.8327 (mttt) cc_final: 0.8008 (mmmm) outliers start: 75 outliers final: 50 residues processed: 417 average time/residue: 0.2929 time to fit residues: 171.0974 Evaluate side-chains 429 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 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 793 GLN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 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 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 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 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 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 969 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1111 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** 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 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS B1027 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13360 Z= 0.244 Angle : 0.709 13.338 18021 Z= 0.350 Chirality : 0.045 0.331 2063 Planarity : 0.005 0.054 2286 Dihedral : 6.106 123.866 1771 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 5.04 % Allowed : 27.07 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1602 helix: 0.61 (0.18), residues: 814 sheet: -1.91 (0.35), residues: 201 loop : -1.55 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 807 HIS 0.011 0.001 HIS B 817 PHE 0.017 0.001 PHE B 638 TYR 0.026 0.002 TYR B 236 ARG 0.007 0.001 ARG B 669 *********************** 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 447 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 374 time to evaluate : 1.718 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: 0.8656 (t) cc_final: 0.8404 (p) REVERT: A 172 LYS cc_start: 0.8015 (mptt) cc_final: 0.7796 (mmtt) REVERT: A 192 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 198 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 226 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8200 (mm-30) REVERT: A 245 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (tp) REVERT: A 261 MET cc_start: 0.7606 (mmp) cc_final: 0.7113 (mmp) REVERT: A 313 PHE cc_start: 0.8353 (m-80) cc_final: 0.8090 (m-80) REVERT: A 345 TRP cc_start: 0.8620 (m-10) cc_final: 0.7695 (m-10) REVERT: A 351 MET cc_start: 0.8641 (ttm) cc_final: 0.8208 (ttm) REVERT: A 361 ASN cc_start: 0.8269 (m-40) cc_final: 0.7861 (m-40) REVERT: A 382 ARG cc_start: 0.8923 (ptt90) cc_final: 0.8507 (ttp80) REVERT: A 386 ASP cc_start: 0.8787 (t0) cc_final: 0.8346 (t0) REVERT: A 388 ASN cc_start: 0.9086 (t0) cc_final: 0.8856 (t0) REVERT: A 389 ARG cc_start: 0.9119 (tpp80) cc_final: 0.8675 (tpp80) REVERT: A 395 GLN cc_start: 0.9100 (tp40) cc_final: 0.8788 (tt0) REVERT: A 460 MET cc_start: 0.8420 (mmt) cc_final: 0.8150 (mmt) REVERT: A 493 GLN cc_start: 0.8741 (mt0) cc_final: 0.8480 (mp10) REVERT: A 562 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8787 (tp30) REVERT: A 569 GLU cc_start: 0.8686 (tt0) cc_final: 0.8117 (tp30) REVERT: A 579 LYS cc_start: 0.8944 (mttt) cc_final: 0.8467 (mmmm) REVERT: A 593 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8774 (mt0) REVERT: A 603 ASP cc_start: 0.8232 (t0) cc_final: 0.7773 (t0) REVERT: A 729 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: A 737 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8013 (ttp-170) REVERT: A 742 ASP cc_start: 0.8551 (t0) cc_final: 0.8058 (t0) REVERT: A 778 CYS cc_start: 0.8440 (t) cc_final: 0.8080 (t) REVERT: A 790 LEU cc_start: 0.8797 (tp) cc_final: 0.8546 (tp) REVERT: A 809 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8544 (mp0) REVERT: A 838 LYS cc_start: 0.8454 (mttt) cc_final: 0.8237 (mmmm) REVERT: A 850 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 242 GLN cc_start: 0.8690 (mm110) cc_final: 0.8306 (mt0) REVERT: B 296 ARG cc_start: 0.9114 (mmm160) cc_final: 0.8428 (tpt90) REVERT: B 307 VAL cc_start: 0.8736 (t) cc_final: 0.8420 (p) REVERT: B 456 GLU cc_start: 0.8580 (tp30) cc_final: 0.7798 (mp0) REVERT: B 508 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8394 (tttm) REVERT: B 512 GLU cc_start: 0.8743 (tp30) cc_final: 0.8333 (tp30) REVERT: B 577 LYS cc_start: 0.8825 (tttt) cc_final: 0.8527 (ttmm) REVERT: B 653 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 659 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8602 (t) REVERT: B 666 ASP cc_start: 0.8627 (t0) cc_final: 0.8384 (t0) REVERT: B 674 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7925 (mt-10) REVERT: B 698 ASP cc_start: 0.8512 (t0) cc_final: 0.8103 (t0) REVERT: B 798 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7392 (mm-40) REVERT: B 869 VAL cc_start: 0.9110 (t) cc_final: 0.8895 (m) REVERT: B 873 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: B 885 SER cc_start: 0.8201 (t) cc_final: 0.7955 (t) REVERT: B 886 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: B 955 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: B 1084 LYS cc_start: 0.8771 (mttt) cc_final: 0.8326 (mmmm) REVERT: B 1091 LYS cc_start: 0.8294 (mttt) cc_final: 0.7987 (mmmm) outliers start: 73 outliers final: 54 residues processed: 415 average time/residue: 0.3060 time to fit residues: 176.6493 Evaluate side-chains 425 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 361 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 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 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 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 797 VAL Chi-restraints excluded: chain A residue 816 GLN 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 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 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 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 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 969 GLN 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 137 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 63 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13360 Z= 0.227 Angle : 0.724 13.418 18021 Z= 0.358 Chirality : 0.045 0.325 2063 Planarity : 0.005 0.059 2286 Dihedral : 6.083 125.943 1771 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 4.70 % Allowed : 27.28 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1602 helix: 0.62 (0.18), residues: 814 sheet: -1.93 (0.35), residues: 204 loop : -1.51 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 807 HIS 0.014 0.001 HIS B 817 PHE 0.017 0.001 PHE B 638 TYR 0.024 0.002 TYR B 302 ARG 0.006 0.001 ARG A 711 *********************** 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 440 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 1.653 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: 0.8651 (t) cc_final: 0.8386 (p) REVERT: A 165 TYR cc_start: 0.8504 (p90) cc_final: 0.8001 (p90) REVERT: A 172 LYS cc_start: 0.8020 (mptt) cc_final: 0.7788 (mmtt) REVERT: A 192 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 226 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 245 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 261 MET cc_start: 0.7614 (mmp) cc_final: 0.7111 (mmp) REVERT: A 313 PHE cc_start: 0.8329 (m-80) cc_final: 0.8067 (m-80) REVERT: A 345 TRP cc_start: 0.8594 (m-10) cc_final: 0.7846 (m-10) REVERT: A 351 MET cc_start: 0.8644 (ttm) cc_final: 0.8209 (ttm) REVERT: A 359 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7430 (ttm-80) REVERT: A 361 ASN cc_start: 0.8258 (m-40) cc_final: 0.7882 (m-40) REVERT: A 382 ARG cc_start: 0.8905 (ptt90) cc_final: 0.8488 (ttp80) REVERT: A 386 ASP cc_start: 0.8788 (t0) cc_final: 0.8341 (t0) REVERT: A 388 ASN cc_start: 0.9086 (t0) cc_final: 0.8859 (t0) REVERT: A 389 ARG cc_start: 0.9099 (tpp80) cc_final: 0.8630 (tpp80) REVERT: A 395 GLN cc_start: 0.9079 (tp40) cc_final: 0.8777 (tt0) REVERT: A 460 MET cc_start: 0.8353 (mmt) cc_final: 0.8110 (mmt) REVERT: A 493 GLN cc_start: 0.8736 (mt0) cc_final: 0.8480 (mp10) REVERT: A 514 ASP cc_start: 0.7872 (t0) cc_final: 0.7620 (t0) REVERT: A 562 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8789 (tp30) REVERT: A 569 GLU cc_start: 0.8668 (tt0) cc_final: 0.8089 (tp30) REVERT: A 579 LYS cc_start: 0.8891 (mttt) cc_final: 0.8412 (mmmm) REVERT: A 593 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8767 (mt0) REVERT: A 603 ASP cc_start: 0.8215 (t0) cc_final: 0.7739 (t0) REVERT: A 638 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8509 (mtm-85) REVERT: A 729 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8079 (mpp) REVERT: A 737 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8373 (mtp-110) REVERT: A 742 ASP cc_start: 0.8533 (t0) cc_final: 0.8069 (t0) REVERT: A 778 CYS cc_start: 0.8417 (t) cc_final: 0.8037 (t) REVERT: A 790 LEU cc_start: 0.8804 (tp) cc_final: 0.8523 (tp) REVERT: A 809 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8534 (mp0) REVERT: A 838 LYS cc_start: 0.8549 (mttt) cc_final: 0.8339 (mmmm) REVERT: B 242 GLN cc_start: 0.8689 (mm110) cc_final: 0.8301 (mt0) REVERT: B 296 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8420 (tpt90) REVERT: B 456 GLU cc_start: 0.8578 (tp30) cc_final: 0.7777 (mp0) REVERT: B 508 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8357 (tttm) REVERT: B 512 GLU cc_start: 0.8700 (tp30) cc_final: 0.8153 (tp30) REVERT: B 577 LYS cc_start: 0.8816 (tttt) cc_final: 0.8517 (ttmm) REVERT: B 653 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 659 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8594 (t) REVERT: B 666 ASP cc_start: 0.8620 (t0) cc_final: 0.8377 (t0) REVERT: B 674 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 698 ASP cc_start: 0.8525 (t0) cc_final: 0.8154 (t0) REVERT: B 798 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: B 869 VAL cc_start: 0.9104 (t) cc_final: 0.8879 (m) REVERT: B 873 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: B 885 SER cc_start: 0.8189 (t) cc_final: 0.7935 (t) REVERT: B 886 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: B 955 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: B 1084 LYS cc_start: 0.8755 (mttt) cc_final: 0.8308 (mmmm) REVERT: B 1091 LYS cc_start: 0.8298 (mttt) cc_final: 0.7997 (mmmm) outliers start: 68 outliers final: 49 residues processed: 409 average time/residue: 0.3028 time to fit residues: 170.6227 Evaluate side-chains 428 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 370 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 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 458 LEU Chi-restraints excluded: chain A residue 521 TYR 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 797 VAL 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 275 HIS 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 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 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 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 969 GLN 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 154 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 129 optimal weight: 0.0060 chunk 13 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** 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 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13360 Z= 0.221 Angle : 0.731 13.564 18021 Z= 0.361 Chirality : 0.045 0.316 2063 Planarity : 0.005 0.055 2286 Dihedral : 6.040 125.902 1771 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 4.56 % Allowed : 27.76 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1602 helix: 0.64 (0.18), residues: 813 sheet: -1.92 (0.35), residues: 204 loop : -1.47 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 807 HIS 0.014 0.001 HIS B 817 PHE 0.015 0.001 PHE B 463 TYR 0.062 0.002 TYR B 236 ARG 0.007 0.001 ARG A 373 ********************** 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 442 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 1.431 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: 0.8632 (t) cc_final: 0.8346 (p) REVERT: A 165 TYR cc_start: 0.8526 (p90) cc_final: 0.8032 (p90) REVERT: A 172 LYS cc_start: 0.8016 (mptt) cc_final: 0.7775 (mmtt) REVERT: A 192 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 198 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7530 (mm-30) REVERT: A 226 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 245 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7503 (tp) REVERT: A 261 MET cc_start: 0.7611 (mmp) cc_final: 0.7099 (mmp) REVERT: A 271 SER cc_start: 0.8466 (t) cc_final: 0.8111 (p) REVERT: A 275 LYS cc_start: 0.8933 (tppt) cc_final: 0.8605 (mmmm) REVERT: A 313 PHE cc_start: 0.8337 (m-80) cc_final: 0.8067 (m-80) REVERT: A 345 TRP cc_start: 0.8577 (m-10) cc_final: 0.7612 (m-10) REVERT: A 351 MET cc_start: 0.8654 (ttm) cc_final: 0.8252 (ttm) REVERT: A 361 ASN cc_start: 0.8251 (m-40) cc_final: 0.7863 (m-40) REVERT: A 382 ARG cc_start: 0.8882 (ptt90) cc_final: 0.8474 (ttp80) REVERT: A 386 ASP cc_start: 0.8792 (t0) cc_final: 0.8349 (t0) REVERT: A 388 ASN cc_start: 0.9091 (t0) cc_final: 0.8866 (t0) REVERT: A 389 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8615 (tpp80) REVERT: A 395 GLN cc_start: 0.9083 (tp40) cc_final: 0.8766 (tt0) REVERT: A 482 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8461 (mmm-85) REVERT: A 514 ASP cc_start: 0.7879 (t0) cc_final: 0.7534 (t0) REVERT: A 562 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8811 (tp30) REVERT: A 569 GLU cc_start: 0.8658 (tt0) cc_final: 0.8074 (tp30) REVERT: A 579 LYS cc_start: 0.8863 (mttt) cc_final: 0.8354 (mmmm) REVERT: A 593 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8751 (mt0) REVERT: A 603 ASP cc_start: 0.8206 (t0) cc_final: 0.7725 (t0) REVERT: A 687 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8364 (tp) REVERT: A 729 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8074 (mpp) REVERT: A 742 ASP cc_start: 0.8520 (t0) cc_final: 0.8029 (t0) REVERT: A 768 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8354 (pp20) REVERT: A 778 CYS cc_start: 0.8412 (t) cc_final: 0.8062 (t) REVERT: A 790 LEU cc_start: 0.8796 (tp) cc_final: 0.8525 (tp) REVERT: A 809 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8517 (mp0) REVERT: B 296 ARG cc_start: 0.9118 (mmm160) cc_final: 0.8422 (tpt90) REVERT: B 512 GLU cc_start: 0.8658 (tp30) cc_final: 0.8111 (tp30) REVERT: B 577 LYS cc_start: 0.8808 (tttt) cc_final: 0.8507 (ttmm) REVERT: B 653 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 659 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8593 (t) REVERT: B 666 ASP cc_start: 0.8622 (t0) cc_final: 0.8368 (t0) REVERT: B 674 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 698 ASP cc_start: 0.8495 (t0) cc_final: 0.8071 (t0) REVERT: B 798 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7379 (mm-40) REVERT: B 869 VAL cc_start: 0.9096 (t) cc_final: 0.8870 (m) REVERT: B 873 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: B 885 SER cc_start: 0.8177 (t) cc_final: 0.7925 (t) REVERT: B 886 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: B 953 MET cc_start: 0.8566 (tmm) cc_final: 0.8332 (tmm) REVERT: B 955 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: B 1084 LYS cc_start: 0.8732 (mttt) cc_final: 0.8251 (mmmm) REVERT: B 1091 LYS cc_start: 0.8286 (mttt) cc_final: 0.7979 (mmmm) outliers start: 66 outliers final: 49 residues processed: 414 average time/residue: 0.2958 time to fit residues: 171.2419 Evaluate side-chains 430 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 372 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN 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 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 797 VAL Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 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 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 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 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 969 GLN 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 137 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 54 optimal weight: 0.0770 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138992 restraints weight = 23077.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143244 restraints weight = 10394.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145826 restraints weight = 5862.144| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13360 Z= 0.230 Angle : 0.745 13.460 18021 Z= 0.368 Chirality : 0.045 0.305 2063 Planarity : 0.005 0.053 2286 Dihedral : 6.015 124.379 1771 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 4.21 % Allowed : 28.59 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1602 helix: 0.65 (0.18), residues: 814 sheet: -1.97 (0.35), residues: 212 loop : -1.56 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 807 HIS 0.012 0.001 HIS B 817 PHE 0.017 0.001 PHE A 551 TYR 0.094 0.002 TYR B 236 ARG 0.007 0.001 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.88 seconds wall clock time: 69 minutes 38.62 seconds (4178.62 seconds total)