Starting phenix.real_space_refine on Sun Jul 21 06:07:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/07_2024/8om9_16971_neut.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8317 2.51 5 N 2286 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 976": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5783 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 22, 'TRANS': 709} Chain breaks: 7 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6566 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.87, per 1000 atoms: 0.59 Number of scatterers: 13314 At special positions: 0 Unit cell: (95.0768, 170.041, 134.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 48 15.00 Mg 2 11.99 O 2599 8.00 N 2286 7.00 C 8317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 56.5% alpha, 9.6% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.012A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.593A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.564A pdb=" N ASN A 285 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.914A pdb=" N GLN A 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.543A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.875A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 436 through 456 removed outlier: 4.704A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 475 through 503 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.869A pdb=" N GLU A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 553 through 615 removed outlier: 3.780A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.438A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 785 through 788 Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.676A pdb=" N ALA A 831 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 877 through 894 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.881A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.907A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.933A pdb=" N GLU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.550A pdb=" N PHE B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 546 removed outlier: 3.673A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.612A pdb=" N GLY B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 663 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 667 through 680 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 688 removed outlier: 3.557A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 688 " --> pdb=" O HIS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 709 through 737 removed outlier: 4.216A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 762 Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 843 Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 918 Processing helix chain 'B' and resid 951 through 964 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.986A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1076 removed outlier: 3.504A pdb=" N ASN B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1112 removed outlier: 3.827A pdb=" N THR B1112 " --> pdb=" O ALA B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.662A pdb=" N THR B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.804A pdb=" N VAL A 148 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.519A pdb=" N LEU A 173 " --> pdb=" O THR A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.832A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.508A pdb=" N CYS A 697 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 637 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 708 through 711 removed outlier: 3.716A pdb=" N ILE A 747 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LEU A 805 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 814 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.164A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.526A pdb=" N THR B 282 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 454 through 458 removed outlier: 6.507A pdb=" N LEU B 369 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE B 371 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 370 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 372 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 880 through 884 removed outlier: 6.972A pdb=" N THR B 882 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS B 860 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 884 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 858 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 858 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 934 through 937 removed outlier: 6.740A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 970 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU B1006 " --> pdb=" O SER B 970 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 892 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2681 1.33 - 1.46: 4196 1.46 - 1.58: 6562 1.58 - 1.71: 91 1.71 - 1.83: 99 Bond restraints: 13629 Sorted by residual: bond pdb=" C LEU A 414 " pdb=" N PRO A 415 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.64e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B2000 " pdb=" C5 ADP B2000 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 1.470 1.417 0.053 1.01e-02 9.80e+03 2.77e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 67.52 - 82.19: 3 82.19 - 96.86: 1 96.86 - 111.53: 5423 111.53 - 126.20: 12902 126.20 - 140.87: 249 Bond angle restraints: 18578 Sorted by residual: angle pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 110.00 140.87 -30.87 1.12e+00 7.97e-01 7.60e+02 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 102.17 75.57 26.60 1.05e+00 9.07e-01 6.42e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 74.69 28.51 1.50e+00 4.44e-01 3.61e+02 angle pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 106.10 67.52 38.58 3.20e+00 9.77e-02 1.45e+02 angle pdb=" C LEU A 414 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 121.00 109.91 11.09 1.16e+00 7.43e-01 9.14e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 7694 33.71 - 67.43: 476 67.43 - 101.14: 15 101.14 - 134.85: 2 134.85 - 168.56: 1 Dihedral angle restraints: 8188 sinusoidal: 3661 harmonic: 4527 Sorted by residual: dihedral pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual 115.10 86.80 28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C PRO A 415 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual -120.70 -139.41 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" O1B ADP B2000 " pdb=" O3A ADP B2000 " pdb=" PB ADP B2000 " pdb=" PA ADP B2000 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.56 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1966 0.146 - 0.293: 162 0.293 - 0.439: 4 0.439 - 0.585: 0 0.585 - 0.731: 1 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C3' DG C 36 " pdb=" C4' DG C 36 " pdb=" O3' DG C 36 " pdb=" C2' DG C 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2130 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 415 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO A 415 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO A 415 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 416 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " -0.039 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 415 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2000 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.62e+00 pdb=" C2 ADP B2000 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP B2000 " 0.006 2.00e-02 2.50e+03 pdb=" C5 ADP B2000 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP B2000 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP B2000 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP B2000 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ADP B2000 " -0.008 2.00e-02 2.50e+03 pdb=" N7 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ADP B2000 " 0.022 2.00e-02 2.50e+03 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 178 2.60 - 3.18: 11938 3.18 - 3.75: 23146 3.75 - 4.33: 31652 4.33 - 4.90: 48445 Nonbonded interactions: 115359 Sorted by model distance: nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 2.025 2.170 nonbonded pdb=" OH TYR A 757 " pdb=" CD1 ILE B1097 " model vdw 2.056 3.460 nonbonded pdb=" O2B ADP B2000 " pdb="MG MG B2001 " model vdw 2.073 2.170 nonbonded pdb=" OG SER B 903 " pdb=" OD2 ASP B 975 " model vdw 2.079 2.440 nonbonded pdb=" O HIS A 785 " pdb=" OG1 THR A 788 " model vdw 2.118 2.440 ... (remaining 115354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.790 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.188 13629 Z= 0.474 Angle : 1.286 38.579 18578 Z= 0.843 Chirality : 0.088 0.731 2133 Planarity : 0.005 0.057 2201 Dihedral : 18.878 168.563 5240 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.76 % Allowed : 22.53 % Favored : 74.71 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1518 helix: 0.15 (0.18), residues: 766 sheet: -2.38 (0.36), residues: 172 loop : -1.92 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A 764 HIS 0.011 0.003 HIS A 829 PHE 0.027 0.004 PHE B 784 TYR 0.027 0.004 TYR B1021 ARG 0.013 0.002 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.6585 (mp10) cc_final: 0.6260 (mp10) REVERT: A 347 LYS cc_start: 0.8169 (pttp) cc_final: 0.7923 (pttp) REVERT: A 364 GLU cc_start: 0.7710 (tp30) cc_final: 0.7506 (tp30) REVERT: A 429 GLN cc_start: 0.7845 (mt0) cc_final: 0.7541 (mt0) REVERT: A 480 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 482 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8484 (tpm170) REVERT: A 626 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 647 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7987 (tm-30) REVERT: A 817 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 818 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7361 (mttp) REVERT: A 846 GLN cc_start: 0.7773 (mt0) cc_final: 0.7514 (mm110) REVERT: A 850 GLU cc_start: 0.7825 (mp0) cc_final: 0.7509 (mp0) REVERT: B 434 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8543 (pm20) REVERT: B 526 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 626 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 860 LYS cc_start: 0.8413 (mttt) cc_final: 0.8185 (mmmt) REVERT: B 883 ASP cc_start: 0.7686 (t0) cc_final: 0.7395 (t0) REVERT: B 1015 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (t) REVERT: B 1085 LYS cc_start: 0.8252 (tttt) cc_final: 0.8014 (tttt) REVERT: B 1091 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7994 (mmmm) outliers start: 38 outliers final: 16 residues processed: 298 average time/residue: 0.2865 time to fit residues: 119.2629 Evaluate side-chains 279 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN B1098 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13629 Z= 0.226 Angle : 0.625 6.728 18578 Z= 0.328 Chirality : 0.042 0.159 2133 Planarity : 0.004 0.048 2201 Dihedral : 17.969 172.234 2176 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.51 % Allowed : 21.95 % Favored : 73.55 % 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: -0.96 (0.22), residues: 1518 helix: 0.56 (0.18), residues: 789 sheet: -2.39 (0.34), residues: 193 loop : -1.66 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.008 0.001 HIS B 984 PHE 0.020 0.002 PHE A 468 TYR 0.016 0.002 TYR B 846 ARG 0.005 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 279 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5912 (mp) REVERT: A 347 LYS cc_start: 0.8375 (pttp) cc_final: 0.8087 (pttp) REVERT: A 364 GLU cc_start: 0.7670 (tp30) cc_final: 0.7397 (tp30) REVERT: A 377 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6888 (tp-100) REVERT: A 480 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 482 ARG cc_start: 0.8672 (tpm170) cc_final: 0.8383 (tpm170) REVERT: A 625 LEU cc_start: 0.7764 (mp) cc_final: 0.7464 (mp) REVERT: A 647 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7895 (tm-30) REVERT: A 846 GLN cc_start: 0.7749 (mt0) cc_final: 0.7440 (mm-40) REVERT: A 850 GLU cc_start: 0.8034 (mp0) cc_final: 0.7823 (mp0) REVERT: B 264 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: B 407 ASP cc_start: 0.7713 (m-30) cc_final: 0.7512 (m-30) REVERT: B 434 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8430 (pm20) REVERT: B 526 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7744 (mmmm) REVERT: B 626 CYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8163 (t) REVERT: B 630 HIS cc_start: 0.7383 (m90) cc_final: 0.6972 (m90) REVERT: B 636 GLN cc_start: 0.8603 (tp40) cc_final: 0.8326 (tp40) REVERT: B 674 GLU cc_start: 0.7895 (tp30) cc_final: 0.7644 (mm-30) REVERT: B 713 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7702 (mmtt) REVERT: B 732 GLU cc_start: 0.8241 (mp0) cc_final: 0.7920 (tm-30) REVERT: B 812 GLU cc_start: 0.7806 (tp30) cc_final: 0.7345 (tp30) REVERT: B 902 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7230 (mtpm) REVERT: B 938 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6466 (tpm-80) REVERT: B 1030 MET cc_start: 0.4301 (mmm) cc_final: 0.3858 (mmm) REVERT: B 1085 LYS cc_start: 0.8226 (tttt) cc_final: 0.7942 (tttt) REVERT: B 1091 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7848 (mmmm) REVERT: B 1093 LEU cc_start: 0.7671 (tp) cc_final: 0.7348 (tp) REVERT: B 1094 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 62 outliers final: 29 residues processed: 316 average time/residue: 0.2902 time to fit residues: 129.0456 Evaluate side-chains 296 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 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 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN B 544 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13629 Z= 0.237 Angle : 0.604 8.703 18578 Z= 0.318 Chirality : 0.041 0.174 2133 Planarity : 0.004 0.055 2201 Dihedral : 17.902 167.091 2155 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.87 % Allowed : 22.09 % Favored : 73.04 % 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: -0.78 (0.22), residues: 1518 helix: 0.62 (0.18), residues: 789 sheet: -2.05 (0.37), residues: 183 loop : -1.56 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.005 0.001 HIS B 984 PHE 0.016 0.002 PHE A 725 TYR 0.019 0.001 TYR B 846 ARG 0.006 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 276 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.5827 (mp) REVERT: A 337 GLN cc_start: 0.6849 (mm110) cc_final: 0.6462 (mm-40) REVERT: A 347 LYS cc_start: 0.8387 (pttp) cc_final: 0.8081 (pttp) REVERT: A 364 GLU cc_start: 0.7682 (tp30) cc_final: 0.7310 (tp30) REVERT: A 372 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8602 (pt) REVERT: A 452 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8144 (tp30) REVERT: A 647 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7879 (tm-30) REVERT: A 698 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 711 ARG cc_start: 0.6829 (tpt170) cc_final: 0.6592 (tpt90) REVERT: A 728 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: A 849 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 850 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7885 (mp0) REVERT: B 264 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: B 367 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 383 LYS cc_start: 0.8250 (tppt) cc_final: 0.7879 (mptt) REVERT: B 434 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8438 (pm20) REVERT: B 526 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7740 (mmmm) REVERT: B 580 VAL cc_start: 0.7339 (OUTLIER) cc_final: 0.7010 (t) REVERT: B 626 CYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8149 (t) REVERT: B 630 HIS cc_start: 0.7448 (m90) cc_final: 0.6981 (m90) REVERT: B 636 GLN cc_start: 0.8632 (tp40) cc_final: 0.8316 (tp-100) REVERT: B 674 GLU cc_start: 0.7897 (tp30) cc_final: 0.7612 (mm-30) REVERT: B 713 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7703 (mmtt) REVERT: B 729 HIS cc_start: 0.8147 (t-90) cc_final: 0.7866 (t-90) REVERT: B 732 GLU cc_start: 0.8335 (mp0) cc_final: 0.7910 (tm-30) REVERT: B 812 GLU cc_start: 0.7841 (tp30) cc_final: 0.7368 (tp30) REVERT: B 902 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7102 (mtpm) REVERT: B 908 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 1030 MET cc_start: 0.4419 (mmm) cc_final: 0.3974 (mmm) outliers start: 67 outliers final: 38 residues processed: 313 average time/residue: 0.2784 time to fit residues: 122.5885 Evaluate side-chains 313 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 266 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 144 optimal weight: 0.0980 chunk 152 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13629 Z= 0.200 Angle : 0.593 8.207 18578 Z= 0.310 Chirality : 0.041 0.307 2133 Planarity : 0.004 0.060 2201 Dihedral : 17.786 162.402 2155 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.89 % Allowed : 21.95 % Favored : 72.17 % 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: -0.61 (0.22), residues: 1518 helix: 0.80 (0.19), residues: 785 sheet: -2.06 (0.36), residues: 190 loop : -1.48 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1122 HIS 0.007 0.001 HIS B 729 PHE 0.019 0.001 PHE A 468 TYR 0.015 0.001 TYR B1011 ARG 0.009 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 267 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.6847 (mm110) cc_final: 0.6564 (mm-40) REVERT: A 357 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 358 GLU cc_start: 0.7983 (pt0) cc_final: 0.7528 (pp20) REVERT: A 452 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8126 (tp30) REVERT: A 503 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.3958 (tp) REVERT: A 647 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7877 (tm-30) REVERT: A 685 ILE cc_start: 0.8614 (mm) cc_final: 0.8038 (tt) REVERT: A 698 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 728 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: A 817 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8042 (p) REVERT: A 850 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7797 (mp0) REVERT: B 264 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: B 290 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6589 (pp) REVERT: B 367 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 383 LYS cc_start: 0.8232 (tppt) cc_final: 0.7845 (mptt) REVERT: B 434 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8377 (pm20) REVERT: B 514 ASN cc_start: 0.8163 (t0) cc_final: 0.7955 (t0) REVERT: B 526 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7732 (mmmm) REVERT: B 626 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8072 (t) REVERT: B 630 HIS cc_start: 0.7387 (m90) cc_final: 0.6876 (m90) REVERT: B 636 GLN cc_start: 0.8553 (tp40) cc_final: 0.8161 (tp40) REVERT: B 687 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7507 (mmmt) REVERT: B 713 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7657 (mmtt) REVERT: B 714 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8737 (tmmt) REVERT: B 729 HIS cc_start: 0.8166 (t-90) cc_final: 0.7900 (t-90) REVERT: B 732 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: B 737 LEU cc_start: 0.8079 (tp) cc_final: 0.7860 (mm) REVERT: B 812 GLU cc_start: 0.7842 (tp30) cc_final: 0.7358 (tp30) REVERT: B 902 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7160 (mtpm) REVERT: B 1030 MET cc_start: 0.4350 (mmm) cc_final: 0.3955 (mmm) outliers start: 81 outliers final: 44 residues processed: 316 average time/residue: 0.2829 time to fit residues: 125.8517 Evaluate side-chains 320 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 538 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13629 Z= 0.394 Angle : 0.700 8.323 18578 Z= 0.368 Chirality : 0.045 0.220 2133 Planarity : 0.005 0.060 2201 Dihedral : 17.889 164.339 2153 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.10 % Allowed : 22.89 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.08 (0.22), residues: 1518 helix: 0.32 (0.18), residues: 787 sheet: -1.95 (0.39), residues: 180 loop : -1.72 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 764 HIS 0.009 0.002 HIS B 864 PHE 0.018 0.002 PHE A 468 TYR 0.039 0.002 TYR B1011 ARG 0.016 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 267 time to evaluate : 1.359 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 357 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 372 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8665 (pt) REVERT: A 402 GLN cc_start: 0.8643 (mm110) cc_final: 0.8408 (mm-40) REVERT: A 452 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7997 (pt0) REVERT: A 503 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4220 (tp) REVERT: A 647 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7898 (tm-30) REVERT: A 685 ILE cc_start: 0.8679 (mm) cc_final: 0.8313 (tt) REVERT: A 698 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 728 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: A 838 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8166 (mmmm) REVERT: A 850 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7844 (mp0) REVERT: B 264 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: B 290 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6395 (pp) REVERT: B 367 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7626 (t80) REVERT: B 434 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8537 (pm20) REVERT: B 457 ARG cc_start: 0.8426 (mmt90) cc_final: 0.7523 (mmt90) REVERT: B 514 ASN cc_start: 0.8296 (t0) cc_final: 0.8092 (t0) REVERT: B 526 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7780 (mmmm) REVERT: B 562 TRP cc_start: 0.8350 (t60) cc_final: 0.8087 (t60) REVERT: B 580 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7074 (t) REVERT: B 626 CYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8371 (m) REVERT: B 636 GLN cc_start: 0.8656 (tp40) cc_final: 0.8437 (tp-100) REVERT: B 647 HIS cc_start: 0.7748 (t-90) cc_final: 0.7542 (t-90) REVERT: B 673 LEU cc_start: 0.7494 (mt) cc_final: 0.7291 (mp) REVERT: B 674 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7520 (tp30) REVERT: B 720 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8184 (tp-100) REVERT: B 729 HIS cc_start: 0.8178 (t-90) cc_final: 0.7880 (t-90) REVERT: B 732 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: B 812 GLU cc_start: 0.8045 (tp30) cc_final: 0.7540 (tp30) REVERT: B 860 LYS cc_start: 0.8450 (mttt) cc_final: 0.8203 (mmmm) REVERT: B 883 ASP cc_start: 0.7908 (t70) cc_final: 0.7364 (t0) REVERT: B 1030 MET cc_start: 0.4892 (mmm) cc_final: 0.4428 (mmm) REVERT: B 1094 GLU cc_start: 0.8188 (tt0) cc_final: 0.7897 (tt0) outliers start: 84 outliers final: 51 residues processed: 318 average time/residue: 0.2800 time to fit residues: 124.7049 Evaluate side-chains 320 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 260 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13629 Z= 0.232 Angle : 0.629 8.495 18578 Z= 0.325 Chirality : 0.043 0.432 2133 Planarity : 0.004 0.063 2201 Dihedral : 17.729 153.967 2153 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.31 % Allowed : 24.71 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1518 helix: 0.58 (0.18), residues: 786 sheet: -1.95 (0.38), residues: 185 loop : -1.58 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 768 HIS 0.007 0.001 HIS A 829 PHE 0.021 0.002 PHE A 286 TYR 0.017 0.001 TYR B1011 ARG 0.015 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8561 (pt) REVERT: A 402 GLN cc_start: 0.8543 (mm110) cc_final: 0.8310 (mm-40) REVERT: A 452 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7972 (pt0) REVERT: A 647 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7895 (tm-30) REVERT: A 685 ILE cc_start: 0.8633 (mm) cc_final: 0.8150 (tt) REVERT: A 691 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 698 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 724 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7108 (t) REVERT: A 728 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6109 (pm20) REVERT: A 784 PHE cc_start: 0.7361 (m-80) cc_final: 0.7008 (m-80) REVERT: A 838 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8230 (mmtm) REVERT: A 850 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7815 (mp0) REVERT: B 264 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: B 290 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6460 (pp) REVERT: B 367 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 383 LYS cc_start: 0.8181 (tppt) cc_final: 0.7793 (mptt) REVERT: B 434 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8456 (pm20) REVERT: B 457 ARG cc_start: 0.8379 (mmt90) cc_final: 0.6360 (mmt90) REVERT: B 562 TRP cc_start: 0.8283 (t60) cc_final: 0.8004 (t60) REVERT: B 580 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.6979 (t) REVERT: B 626 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8458 (m) REVERT: B 647 HIS cc_start: 0.7652 (t-90) cc_final: 0.7432 (t-90) REVERT: B 687 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7660 (mmmt) REVERT: B 713 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7807 (mmtt) REVERT: B 729 HIS cc_start: 0.8143 (t-90) cc_final: 0.7811 (t-90) REVERT: B 732 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: B 812 GLU cc_start: 0.7923 (tp30) cc_final: 0.7430 (tp30) REVERT: B 839 LYS cc_start: 0.7509 (mmtp) cc_final: 0.7304 (mppt) REVERT: B 883 ASP cc_start: 0.7986 (t70) cc_final: 0.7449 (t0) REVERT: B 1030 MET cc_start: 0.4639 (mmm) cc_final: 0.4261 (mmm) REVERT: B 1094 GLU cc_start: 0.8175 (tt0) cc_final: 0.7903 (tt0) outliers start: 73 outliers final: 46 residues processed: 309 average time/residue: 0.2823 time to fit residues: 122.6007 Evaluate side-chains 316 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13629 Z= 0.225 Angle : 0.629 9.909 18578 Z= 0.325 Chirality : 0.042 0.390 2133 Planarity : 0.004 0.066 2201 Dihedral : 17.664 145.898 2153 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.38 % Allowed : 24.93 % Favored : 69.69 % 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: -0.78 (0.22), residues: 1518 helix: 0.66 (0.18), residues: 786 sheet: -1.88 (0.38), residues: 190 loop : -1.68 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 768 HIS 0.007 0.001 HIS B 729 PHE 0.013 0.002 PHE A 836 TYR 0.020 0.001 TYR B1011 ARG 0.008 0.001 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8297 (pttp) REVERT: A 364 GLU cc_start: 0.7704 (tp30) cc_final: 0.7252 (tp30) REVERT: A 372 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8624 (pt) REVERT: A 402 GLN cc_start: 0.8537 (mm110) cc_final: 0.8272 (mm-40) REVERT: A 430 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8364 (ptpp) REVERT: A 452 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7975 (pt0) REVERT: A 647 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7909 (tm-30) REVERT: A 681 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: A 691 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 698 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 711 ARG cc_start: 0.6817 (tpt170) cc_final: 0.6569 (tpt90) REVERT: A 724 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.6900 (t) REVERT: A 728 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: A 784 PHE cc_start: 0.7364 (m-80) cc_final: 0.6962 (m-80) REVERT: A 850 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7807 (mp0) REVERT: B 264 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: B 290 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6537 (pp) REVERT: B 367 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 383 LYS cc_start: 0.8229 (tppt) cc_final: 0.7845 (mptt) REVERT: B 434 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8456 (pm20) REVERT: B 562 TRP cc_start: 0.8269 (t60) cc_final: 0.8005 (t60) REVERT: B 580 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7016 (t) REVERT: B 636 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8292 (tp40) REVERT: B 647 HIS cc_start: 0.7638 (t-90) cc_final: 0.7403 (t-90) REVERT: B 674 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7504 (tp30) REVERT: B 687 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7661 (mmmt) REVERT: B 713 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7732 (mmtt) REVERT: B 729 HIS cc_start: 0.8137 (t-90) cc_final: 0.7837 (t-90) REVERT: B 732 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: B 812 GLU cc_start: 0.7885 (tp30) cc_final: 0.7407 (tp30) REVERT: B 839 LYS cc_start: 0.7469 (mmtp) cc_final: 0.7239 (mppt) REVERT: B 848 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6676 (ttt90) REVERT: B 860 LYS cc_start: 0.8459 (mttt) cc_final: 0.8205 (mmmm) REVERT: B 883 ASP cc_start: 0.7999 (t70) cc_final: 0.7490 (t0) REVERT: B 1093 LEU cc_start: 0.7754 (tp) cc_final: 0.7434 (tp) REVERT: B 1094 GLU cc_start: 0.8139 (tt0) cc_final: 0.7865 (tt0) outliers start: 74 outliers final: 46 residues processed: 321 average time/residue: 0.2913 time to fit residues: 129.9522 Evaluate side-chains 315 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13629 Z= 0.270 Angle : 0.662 8.189 18578 Z= 0.341 Chirality : 0.043 0.408 2133 Planarity : 0.005 0.066 2201 Dihedral : 17.661 142.432 2152 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.31 % Allowed : 25.80 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1518 helix: 0.51 (0.18), residues: 788 sheet: -1.87 (0.38), residues: 189 loop : -1.66 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 768 HIS 0.007 0.001 HIS B 729 PHE 0.039 0.002 PHE A 760 TYR 0.027 0.002 TYR B1011 ARG 0.010 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 267 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8086 (tppt) REVERT: A 347 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8249 (pttp) REVERT: A 372 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8792 (pt) REVERT: A 430 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8386 (ptpp) REVERT: A 452 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7980 (pt0) REVERT: A 643 GLU cc_start: 0.8470 (tp30) cc_final: 0.8244 (tp30) REVERT: A 647 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7926 (tm-30) REVERT: A 681 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 691 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7679 (tt) REVERT: A 698 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 711 ARG cc_start: 0.6853 (tpt170) cc_final: 0.6584 (tpt90) REVERT: A 724 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7180 (t) REVERT: A 728 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6114 (pm20) REVERT: A 850 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7800 (mp0) REVERT: B 264 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: B 290 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6410 (pp) REVERT: B 367 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 434 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8494 (pm20) REVERT: B 457 ARG cc_start: 0.8386 (mmt90) cc_final: 0.6406 (mmt90) REVERT: B 562 TRP cc_start: 0.8297 (t60) cc_final: 0.8025 (t60) REVERT: B 594 LEU cc_start: 0.7942 (mt) cc_final: 0.7626 (mt) REVERT: B 647 HIS cc_start: 0.7653 (t-90) cc_final: 0.7376 (t-90) REVERT: B 674 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7523 (tp30) REVERT: B 687 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7687 (mmmt) REVERT: B 713 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7729 (mmtt) REVERT: B 729 HIS cc_start: 0.8142 (t-90) cc_final: 0.7800 (t-90) REVERT: B 732 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: B 812 GLU cc_start: 0.7900 (tp30) cc_final: 0.7409 (tp30) REVERT: B 839 LYS cc_start: 0.7502 (mmtp) cc_final: 0.7265 (mppt) REVERT: B 848 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6697 (ttt90) REVERT: B 860 LYS cc_start: 0.8486 (mttt) cc_final: 0.8238 (mmmm) REVERT: B 883 ASP cc_start: 0.7992 (t70) cc_final: 0.7484 (t0) REVERT: B 1094 GLU cc_start: 0.8174 (tt0) cc_final: 0.7943 (tt0) outliers start: 73 outliers final: 52 residues processed: 315 average time/residue: 0.2930 time to fit residues: 127.6479 Evaluate side-chains 326 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 263 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13629 Z= 0.208 Angle : 0.633 9.197 18578 Z= 0.325 Chirality : 0.042 0.425 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.565 140.704 2152 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.01 % Allowed : 26.09 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1518 helix: 0.66 (0.19), residues: 793 sheet: -1.78 (0.39), residues: 189 loop : -1.71 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 768 HIS 0.007 0.001 HIS B 729 PHE 0.020 0.002 PHE A 760 TYR 0.017 0.001 TYR B1011 ARG 0.014 0.001 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8058 (tppt) REVERT: A 312 LEU cc_start: 0.7811 (mt) cc_final: 0.7586 (mt) REVERT: A 347 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8244 (pttp) REVERT: A 372 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8437 (pt) REVERT: A 430 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8386 (ptpp) REVERT: A 446 ASP cc_start: 0.8442 (m-30) cc_final: 0.8190 (m-30) REVERT: A 452 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7959 (pt0) REVERT: A 647 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7912 (tm-30) REVERT: A 658 GLU cc_start: 0.8248 (tp30) cc_final: 0.7945 (tp30) REVERT: A 681 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 691 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 698 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 711 ARG cc_start: 0.6770 (tpt170) cc_final: 0.6560 (tpt90) REVERT: A 728 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6036 (pm20) REVERT: A 817 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 850 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7731 (mp0) REVERT: B 264 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: B 290 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6450 (pp) REVERT: B 367 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7601 (t80) REVERT: B 434 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8474 (pm20) REVERT: B 647 HIS cc_start: 0.7596 (t-90) cc_final: 0.7332 (t-90) REVERT: B 674 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7489 (tp30) REVERT: B 713 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7750 (mmtt) REVERT: B 729 HIS cc_start: 0.8118 (t-90) cc_final: 0.7770 (t-90) REVERT: B 732 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: B 737 LEU cc_start: 0.8097 (tp) cc_final: 0.7877 (mm) REVERT: B 812 GLU cc_start: 0.7802 (tp30) cc_final: 0.7323 (tp30) REVERT: B 839 LYS cc_start: 0.7465 (mmtp) cc_final: 0.7233 (mppt) REVERT: B 860 LYS cc_start: 0.8447 (mttt) cc_final: 0.8198 (mmmm) REVERT: B 883 ASP cc_start: 0.7978 (t70) cc_final: 0.7488 (t0) REVERT: B 902 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7117 (mtpm) REVERT: B 1094 GLU cc_start: 0.8152 (tt0) cc_final: 0.7911 (tt0) outliers start: 69 outliers final: 48 residues processed: 311 average time/residue: 0.3031 time to fit residues: 132.2682 Evaluate side-chains 316 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 257 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 133 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13629 Z= 0.234 Angle : 0.658 9.769 18578 Z= 0.339 Chirality : 0.043 0.392 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.559 141.397 2152 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.36 % Allowed : 26.45 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1518 helix: 0.65 (0.19), residues: 793 sheet: -1.88 (0.38), residues: 191 loop : -1.74 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 768 HIS 0.006 0.001 HIS B 729 PHE 0.036 0.002 PHE A 760 TYR 0.021 0.001 TYR B1011 ARG 0.012 0.001 ARG B 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 261 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (tppt) REVERT: A 347 LYS cc_start: 0.8723 (ptpt) cc_final: 0.8251 (pttp) REVERT: A 372 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8683 (pp) REVERT: A 430 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8370 (ptpp) REVERT: A 446 ASP cc_start: 0.8420 (m-30) cc_final: 0.8147 (m-30) REVERT: A 452 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7893 (pt0) REVERT: A 647 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7936 (tm-30) REVERT: A 681 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: A 691 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 698 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 711 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6568 (tpt90) REVERT: A 728 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6016 (pm20) REVERT: A 817 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 850 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7753 (mp0) REVERT: B 264 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: B 290 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6452 (pp) REVERT: B 367 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7597 (t80) REVERT: B 434 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8483 (pm20) REVERT: B 562 TRP cc_start: 0.8231 (t60) cc_final: 0.7917 (t60) REVERT: B 636 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8168 (tp40) REVERT: B 647 HIS cc_start: 0.7587 (t-90) cc_final: 0.7304 (t-90) REVERT: B 713 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7726 (mmtt) REVERT: B 729 HIS cc_start: 0.8126 (t-90) cc_final: 0.7775 (t-90) REVERT: B 732 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: B 737 LEU cc_start: 0.8159 (tp) cc_final: 0.7903 (mm) REVERT: B 812 GLU cc_start: 0.7792 (tp30) cc_final: 0.7376 (tm-30) REVERT: B 839 LYS cc_start: 0.7480 (mmtp) cc_final: 0.7253 (mppt) REVERT: B 860 LYS cc_start: 0.8462 (mttt) cc_final: 0.8207 (mmmm) REVERT: B 883 ASP cc_start: 0.7977 (t70) cc_final: 0.7508 (t0) REVERT: B 1094 GLU cc_start: 0.8162 (tt0) cc_final: 0.7927 (tt0) outliers start: 60 outliers final: 47 residues processed: 298 average time/residue: 0.2831 time to fit residues: 118.2213 Evaluate side-chains 315 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 258 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.203811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.165142 restraints weight = 20520.471| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.10 r_work: 0.4046 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13629 Z= 0.217 Angle : 0.650 9.325 18578 Z= 0.334 Chirality : 0.042 0.396 2133 Planarity : 0.005 0.067 2201 Dihedral : 17.527 141.585 2152 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.29 % Allowed : 26.74 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1518 helix: 0.71 (0.19), residues: 793 sheet: -1.90 (0.37), residues: 197 loop : -1.69 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 768 HIS 0.006 0.001 HIS B 729 PHE 0.022 0.002 PHE A 650 TYR 0.019 0.001 TYR B1011 ARG 0.012 0.000 ARG B 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.30 seconds wall clock time: 64 minutes 38.30 seconds (3878.30 seconds total)