Starting phenix.real_space_refine on Tue Apr 9 10:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pcz_17596/04_2024/8pcz_17596.pdb" } resolution = 3.21 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= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10574 2.51 5 N 2686 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16176 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8088 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 30, 'TRANS': 992} Chain breaks: 5 Chain: "B" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8088 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 30, 'TRANS': 992} Chain breaks: 5 Time building chain proxies: 9.28, per 1000 atoms: 0.57 Number of scatterers: 16176 At special positions: 0 Unit cell: (112.86, 152.988, 122.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2832 8.00 N 2686 7.00 C 10574 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: 6.60 Conformation dependent library (CDL) restraints added in 2.8 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 78.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.565A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.986A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.644A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.574A pdb=" N GLY A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.564A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.924A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.566A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 317 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.637A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 381 through 412 removed outlier: 3.835A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 3.997A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.242A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.985A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.881A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.964A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.504A pdb=" N LYS A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 703 removed outlier: 3.942A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 4.093A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 3.657A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.063A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 780 Processing helix chain 'A' and resid 797 through 811 removed outlier: 3.676A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 Proline residue: A 819 - end of helix removed outlier: 3.643A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 942 removed outlier: 3.644A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.525A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 Processing helix chain 'A' and resid 1179 through 1183 Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.566A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.986A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.644A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.574A pdb=" N GLY B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.564A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.924A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.566A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 317 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 376 removed outlier: 3.637A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 381 through 412 removed outlier: 3.835A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.997A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 449 through 469 removed outlier: 4.242A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 4.986A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.880A pdb=" N ALA B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.964A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 Processing helix chain 'B' and resid 653 through 657 removed outlier: 4.504A pdb=" N LYS B 656 " --> pdb=" O SER B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 677 through 703 removed outlier: 3.942A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix removed outlier: 4.093A pdb=" N PHE B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 755 removed outlier: 3.657A pdb=" N ALA B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 4.062A pdb=" N ILE B 759 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 780 Processing helix chain 'B' and resid 797 through 811 removed outlier: 3.676A pdb=" N ARG B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 854 Proline residue: B 819 - end of helix removed outlier: 3.643A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 942 removed outlier: 3.643A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.525A pdb=" N ALA B 964 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 977 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1108 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1123 Processing helix chain 'B' and resid 1179 through 1183 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.366A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.718A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.771A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 removed outlier: 3.644A pdb=" N ALA A1152 " --> pdb=" O ILE A1161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.366A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.718A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.770A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1134 through 1136 removed outlier: 3.644A pdb=" N ALA B1152 " --> pdb=" O ILE B1161 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.26 Time building geometry restraints manager: 7.17 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: 4054 1.33 - 1.46: 3362 1.46 - 1.58: 8922 1.58 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 16492 Sorted by residual: bond pdb=" C GLN B 624 " pdb=" O GLN B 624 " ideal model delta sigma weight residual 1.235 1.210 0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" N ALA B 619 " pdb=" CA ALA B 619 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.36e+00 bond pdb=" C GLN A 624 " pdb=" O GLN A 624 " ideal model delta sigma weight residual 1.235 1.211 0.025 1.19e-02 7.06e+03 4.33e+00 bond pdb=" N ALA A 619 " pdb=" CA ALA A 619 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.23e+00 bond pdb=" N ASP A 623 " pdb=" CA ASP A 623 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.80: 260 105.80 - 112.85: 9327 112.85 - 119.90: 5478 119.90 - 126.94: 7107 126.94 - 133.99: 192 Bond angle restraints: 22364 Sorted by residual: angle pdb=" CA GLN A 624 " pdb=" C GLN A 624 " pdb=" O GLN A 624 " ideal model delta sigma weight residual 120.54 116.32 4.22 1.04e+00 9.25e-01 1.65e+01 angle pdb=" CA GLN B 624 " pdb=" C GLN B 624 " pdb=" O GLN B 624 " ideal model delta sigma weight residual 120.54 116.33 4.21 1.04e+00 9.25e-01 1.64e+01 angle pdb=" CA ASP B 620 " pdb=" C ASP B 620 " pdb=" O ASP B 620 " ideal model delta sigma weight residual 121.32 117.13 4.19 1.16e+00 7.43e-01 1.30e+01 angle pdb=" CA ASP A 620 " pdb=" C ASP A 620 " pdb=" O ASP A 620 " ideal model delta sigma weight residual 121.32 117.16 4.16 1.16e+00 7.43e-01 1.28e+01 angle pdb=" CG MET B1073 " pdb=" SD MET B1073 " pdb=" CE MET B1073 " ideal model delta sigma weight residual 100.90 108.24 -7.34 2.20e+00 2.07e-01 1.11e+01 ... (remaining 22359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 8989 16.44 - 32.88: 649 32.88 - 49.31: 168 49.31 - 65.75: 24 65.75 - 82.19: 18 Dihedral angle restraints: 9848 sinusoidal: 3896 harmonic: 5952 Sorted by residual: dihedral pdb=" CA PRO A 210 " pdb=" C PRO A 210 " pdb=" N VAL A 211 " pdb=" CA VAL A 211 " ideal model delta harmonic sigma weight residual 180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO B 210 " pdb=" C PRO B 210 " pdb=" N VAL B 211 " pdb=" CA VAL B 211 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET A 154 " pdb=" C MET A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1649 0.027 - 0.055: 583 0.055 - 0.082: 305 0.082 - 0.109: 121 0.109 - 0.136: 30 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ILE A 948 " pdb=" N ILE A 948 " pdb=" C ILE A 948 " pdb=" CB ILE A 948 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE B 948 " pdb=" N ILE B 948 " pdb=" C ILE B 948 " pdb=" CB ILE B 948 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B1068 " pdb=" N ILE B1068 " pdb=" C ILE B1068 " pdb=" CB ILE B1068 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2685 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 571 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 572 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 572 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 572 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 571 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 572 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 276 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.024 5.00e-02 4.00e+02 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2207 2.75 - 3.29: 17035 3.29 - 3.83: 26404 3.83 - 4.36: 30483 4.36 - 4.90: 54307 Nonbonded interactions: 130436 Sorted by model distance: nonbonded pdb=" OD1 ASP A 923 " pdb=" N GLU A 924 " model vdw 2.216 2.520 nonbonded pdb=" OD1 ASP B 923 " pdb=" N GLU B 924 " model vdw 2.217 2.520 nonbonded pdb=" O ALA A1140 " pdb=" OG1 THR A1141 " model vdw 2.273 2.440 nonbonded pdb=" O ALA B1140 " pdb=" OG1 THR B1141 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASN B 237 " pdb=" N ASP B 238 " model vdw 2.306 2.520 ... (remaining 130431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.740 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: 0.020 Extract box with map and model: 6.430 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 46.740 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.037 16492 Z= 0.209 Angle : 0.559 8.429 22364 Z= 0.314 Chirality : 0.039 0.136 2688 Planarity : 0.004 0.050 2750 Dihedral : 12.911 82.188 5988 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % 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: 1.86 (0.19), residues: 2022 helix: 1.85 (0.14), residues: 1442 sheet: 0.17 (0.61), residues: 76 loop : -0.34 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 419 HIS 0.005 0.001 HIS A1120 PHE 0.012 0.001 PHE A 769 TYR 0.014 0.001 TYR A 737 ARG 0.006 0.001 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 529 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7528 (ttpt) REVERT: A 132 HIS cc_start: 0.7080 (m-70) cc_final: 0.6727 (m-70) REVERT: A 160 MET cc_start: 0.7337 (mmt) cc_final: 0.6957 (mmm) REVERT: A 163 PHE cc_start: 0.7576 (t80) cc_final: 0.7260 (t80) REVERT: A 164 SER cc_start: 0.7963 (m) cc_final: 0.7696 (p) REVERT: A 233 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7098 (tt0) REVERT: A 250 LYS cc_start: 0.7397 (mttt) cc_final: 0.7148 (mttt) REVERT: A 300 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 316 ASP cc_start: 0.7776 (t0) cc_final: 0.7424 (m-30) REVERT: A 319 LEU cc_start: 0.8222 (mt) cc_final: 0.7981 (mp) REVERT: A 320 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 337 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 375 LYS cc_start: 0.7867 (mttt) cc_final: 0.7474 (mttt) REVERT: A 383 MET cc_start: 0.7343 (tpp) cc_final: 0.6656 (mmm) REVERT: A 485 ASP cc_start: 0.7454 (m-30) cc_final: 0.7228 (p0) REVERT: A 511 MET cc_start: 0.7165 (tmm) cc_final: 0.6732 (ttp) REVERT: A 516 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7853 (ptm160) REVERT: A 580 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6456 (tp30) REVERT: A 633 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 640 ILE cc_start: 0.7070 (mt) cc_final: 0.6416 (tt) REVERT: A 644 LEU cc_start: 0.7025 (mt) cc_final: 0.6559 (mp) REVERT: A 648 LEU cc_start: 0.6689 (mt) cc_final: 0.6487 (mp) REVERT: A 777 ASP cc_start: 0.3050 (m-30) cc_final: 0.2629 (t70) REVERT: A 810 MET cc_start: 0.4995 (ptp) cc_final: 0.4572 (ptp) REVERT: A 837 TYR cc_start: 0.7784 (m-80) cc_final: 0.7553 (m-80) REVERT: A 847 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 877 GLN cc_start: 0.7549 (tt0) cc_final: 0.7141 (tt0) REVERT: A 903 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7250 (ttm-80) REVERT: A 925 MET cc_start: 0.6125 (ppp) cc_final: 0.5885 (ppp) REVERT: A 939 LYS cc_start: 0.7799 (tttt) cc_final: 0.7562 (tttt) REVERT: A 966 ASP cc_start: 0.7729 (t0) cc_final: 0.7289 (t0) REVERT: A 994 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 1003 SER cc_start: 0.7831 (t) cc_final: 0.7501 (t) REVERT: A 1007 LYS cc_start: 0.7572 (tttt) cc_final: 0.7055 (tttp) REVERT: A 1033 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 1037 THR cc_start: 0.7705 (t) cc_final: 0.7491 (m) REVERT: A 1044 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5393 (mt-10) REVERT: A 1051 LYS cc_start: 0.8520 (mttm) cc_final: 0.7998 (mttm) REVERT: A 1054 ASN cc_start: 0.8297 (t0) cc_final: 0.7708 (t0) REVERT: A 1073 MET cc_start: 0.7226 (mmp) cc_final: 0.7024 (mmm) REVERT: A 1107 MET cc_start: 0.5770 (mtt) cc_final: 0.5531 (mpp) REVERT: A 1122 GLU cc_start: 0.7528 (tp30) cc_final: 0.7316 (tp30) REVERT: A 1123 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7076 (ttp80) REVERT: A 1125 TYR cc_start: 0.6141 (p90) cc_final: 0.5810 (p90) REVERT: A 1191 ASN cc_start: 0.7343 (t0) cc_final: 0.7137 (p0) REVERT: B 91 SER cc_start: 0.7829 (m) cc_final: 0.7429 (p) REVERT: B 96 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7551 (ttpt) REVERT: B 97 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7673 (ptmt) REVERT: B 149 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 150 SER cc_start: 0.7821 (t) cc_final: 0.7472 (m) REVERT: B 160 MET cc_start: 0.7593 (mmt) cc_final: 0.7257 (mmm) REVERT: B 161 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: B 164 SER cc_start: 0.7832 (m) cc_final: 0.7616 (p) REVERT: B 233 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7028 (tt0) REVERT: B 250 LYS cc_start: 0.7401 (mttt) cc_final: 0.7044 (mttp) REVERT: B 259 SER cc_start: 0.8037 (m) cc_final: 0.7800 (t) REVERT: B 300 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 320 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7393 (mt-10) REVERT: B 337 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 355 MET cc_start: 0.7787 (tmm) cc_final: 0.7451 (ttp) REVERT: B 383 MET cc_start: 0.7264 (tpp) cc_final: 0.6519 (mmm) REVERT: B 387 TYR cc_start: 0.7641 (m-10) cc_final: 0.7426 (m-10) REVERT: B 443 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 475 GLN cc_start: 0.7628 (tp40) cc_final: 0.7419 (tt0) REVERT: B 486 ILE cc_start: 0.8220 (mp) cc_final: 0.7954 (mm) REVERT: B 580 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6296 (tp30) REVERT: B 591 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6969 (mtpp) REVERT: B 621 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6045 (mt-10) REVERT: B 632 LYS cc_start: 0.7338 (ttmm) cc_final: 0.7098 (ttmm) REVERT: B 633 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7547 (mmtm) REVERT: B 634 SER cc_start: 0.8444 (m) cc_final: 0.8001 (t) REVERT: B 635 TRP cc_start: 0.7385 (p90) cc_final: 0.7021 (p90) REVERT: B 678 MET cc_start: 0.7041 (mmm) cc_final: 0.6839 (mmm) REVERT: B 697 MET cc_start: 0.6135 (ttt) cc_final: 0.5865 (ttt) REVERT: B 777 ASP cc_start: 0.3459 (m-30) cc_final: 0.2638 (t70) REVERT: B 810 MET cc_start: 0.5081 (ptp) cc_final: 0.4529 (ptp) REVERT: B 847 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6719 (mm-30) REVERT: B 877 GLN cc_start: 0.7585 (tt0) cc_final: 0.7095 (tt0) REVERT: B 880 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6938 (tttp) REVERT: B 903 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7085 (ttm-80) REVERT: B 966 ASP cc_start: 0.7552 (t0) cc_final: 0.7193 (t0) REVERT: B 990 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6898 (mtp85) REVERT: B 994 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 1003 SER cc_start: 0.7835 (t) cc_final: 0.7448 (t) REVERT: B 1007 LYS cc_start: 0.7545 (tttt) cc_final: 0.7235 (tttp) REVERT: B 1037 THR cc_start: 0.7762 (t) cc_final: 0.7543 (m) REVERT: B 1051 LYS cc_start: 0.8442 (mttm) cc_final: 0.7938 (mttm) REVERT: B 1054 ASN cc_start: 0.8457 (t0) cc_final: 0.7991 (t0) REVERT: B 1064 GLN cc_start: 0.7620 (mt0) cc_final: 0.7362 (mt0) REVERT: B 1115 GLU cc_start: 0.7495 (tt0) cc_final: 0.7236 (tt0) REVERT: B 1123 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7380 (ttp80) REVERT: B 1125 TYR cc_start: 0.6110 (p90) cc_final: 0.5885 (p90) REVERT: B 1191 ASN cc_start: 0.7324 (t0) cc_final: 0.7112 (p0) outliers start: 4 outliers final: 3 residues processed: 533 average time/residue: 0.3425 time to fit residues: 253.7759 Evaluate side-chains 450 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 447 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 624 GLN A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 624 GLN B1156 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16492 Z= 0.262 Angle : 0.552 8.917 22364 Z= 0.295 Chirality : 0.042 0.154 2688 Planarity : 0.004 0.049 2750 Dihedral : 4.315 38.582 2194 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.10 % Allowed : 10.97 % Favored : 86.93 % 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: 2.13 (0.19), residues: 2022 helix: 1.98 (0.13), residues: 1466 sheet: 0.30 (0.56), residues: 92 loop : -0.11 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 962 HIS 0.006 0.001 HIS B1120 PHE 0.024 0.002 PHE B 769 TYR 0.018 0.001 TYR A 984 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 463 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7674 (ttpt) REVERT: A 163 PHE cc_start: 0.7623 (t80) cc_final: 0.7348 (t80) REVERT: A 164 SER cc_start: 0.8001 (m) cc_final: 0.7787 (p) REVERT: A 233 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7079 (tt0) REVERT: A 238 ASP cc_start: 0.6989 (m-30) cc_final: 0.6703 (m-30) REVERT: A 250 LYS cc_start: 0.7510 (mttt) cc_final: 0.7136 (mttm) REVERT: A 289 PHE cc_start: 0.7998 (m-80) cc_final: 0.7682 (m-80) REVERT: A 316 ASP cc_start: 0.7850 (t0) cc_final: 0.7518 (m-30) REVERT: A 320 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 337 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 375 LYS cc_start: 0.7992 (mttt) cc_final: 0.7699 (ptmm) REVERT: A 383 MET cc_start: 0.7378 (tpp) cc_final: 0.6608 (mmm) REVERT: A 443 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 444 ASN cc_start: 0.8055 (t0) cc_final: 0.7824 (t0) REVERT: A 479 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.7274 (ttp80) REVERT: A 580 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6584 (tp30) REVERT: A 591 LYS cc_start: 0.7325 (mtmt) cc_final: 0.7013 (mtpp) REVERT: A 621 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6216 (mt-10) REVERT: A 622 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6539 (mtpm) REVERT: A 628 VAL cc_start: 0.7747 (p) cc_final: 0.7335 (p) REVERT: A 633 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7475 (mtmm) REVERT: A 640 ILE cc_start: 0.7152 (mt) cc_final: 0.6541 (tt) REVERT: A 644 LEU cc_start: 0.7061 (mt) cc_final: 0.6705 (mp) REVERT: A 678 MET cc_start: 0.7471 (mmm) cc_final: 0.6845 (tmm) REVERT: A 777 ASP cc_start: 0.2937 (m-30) cc_final: 0.2599 (t0) REVERT: A 810 MET cc_start: 0.4888 (ptp) cc_final: 0.4441 (ptp) REVERT: A 828 LYS cc_start: 0.7602 (mttt) cc_final: 0.7159 (mmmm) REVERT: A 847 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6586 (mm-30) REVERT: A 877 GLN cc_start: 0.7634 (tt0) cc_final: 0.7145 (tt0) REVERT: A 880 LYS cc_start: 0.7319 (tttm) cc_final: 0.7014 (tttp) REVERT: A 903 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7359 (ttm-80) REVERT: A 966 ASP cc_start: 0.7506 (t0) cc_final: 0.6871 (t0) REVERT: A 994 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 1003 SER cc_start: 0.7967 (t) cc_final: 0.7579 (t) REVERT: A 1007 LYS cc_start: 0.7699 (tttt) cc_final: 0.7367 (tttt) REVERT: A 1033 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 1037 THR cc_start: 0.7884 (t) cc_final: 0.7639 (m) REVERT: A 1044 GLU cc_start: 0.6138 (mt-10) cc_final: 0.5613 (mt-10) REVERT: A 1051 LYS cc_start: 0.8727 (mttm) cc_final: 0.8148 (mttm) REVERT: A 1054 ASN cc_start: 0.8309 (t0) cc_final: 0.7741 (t0) REVERT: A 1123 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7110 (ttp80) REVERT: A 1125 TYR cc_start: 0.6418 (p90) cc_final: 0.6123 (p90) REVERT: A 1134 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6362 (p90) REVERT: A 1191 ASN cc_start: 0.7438 (t0) cc_final: 0.7101 (p0) REVERT: B 96 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7661 (ttpt) REVERT: B 136 HIS cc_start: 0.7457 (m90) cc_final: 0.7129 (m-70) REVERT: B 150 SER cc_start: 0.7830 (t) cc_final: 0.7483 (m) REVERT: B 160 MET cc_start: 0.7452 (mmt) cc_final: 0.7099 (mmm) REVERT: B 161 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7220 (mtm-85) REVERT: B 184 LEU cc_start: 0.7431 (tp) cc_final: 0.7185 (tp) REVERT: B 205 MET cc_start: 0.7555 (mmm) cc_final: 0.7128 (mmm) REVERT: B 250 LYS cc_start: 0.7577 (mttt) cc_final: 0.7211 (mttm) REVERT: B 300 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 320 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 337 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 355 MET cc_start: 0.7976 (tmm) cc_final: 0.7513 (ttp) REVERT: B 383 MET cc_start: 0.7233 (tpp) cc_final: 0.6325 (mmm) REVERT: B 387 TYR cc_start: 0.7671 (m-10) cc_final: 0.7413 (m-10) REVERT: B 443 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 444 ASN cc_start: 0.7991 (t0) cc_final: 0.7748 (t0) REVERT: B 486 ILE cc_start: 0.8161 (mp) cc_final: 0.7893 (mm) REVERT: B 580 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6487 (tp30) REVERT: B 590 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6735 (mt-10) REVERT: B 591 LYS cc_start: 0.7245 (mtmt) cc_final: 0.7018 (mtpp) REVERT: B 608 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6873 (tp) REVERT: B 621 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6307 (mt-10) REVERT: B 628 VAL cc_start: 0.7912 (p) cc_final: 0.7559 (p) REVERT: B 632 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7164 (ttmm) REVERT: B 633 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7649 (mmtm) REVERT: B 634 SER cc_start: 0.8496 (m) cc_final: 0.8005 (t) REVERT: B 635 TRP cc_start: 0.7642 (p90) cc_final: 0.6814 (p90) REVERT: B 640 ILE cc_start: 0.7304 (mt) cc_final: 0.7014 (tt) REVERT: B 678 MET cc_start: 0.7039 (mmm) cc_final: 0.6816 (mmm) REVERT: B 697 MET cc_start: 0.6078 (ttt) cc_final: 0.5811 (ttt) REVERT: B 810 MET cc_start: 0.4941 (ptp) cc_final: 0.4414 (ptp) REVERT: B 847 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 877 GLN cc_start: 0.7669 (tt0) cc_final: 0.7289 (tt0) REVERT: B 880 LYS cc_start: 0.7216 (ttpp) cc_final: 0.6926 (tttp) REVERT: B 881 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 903 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.7185 (ttm-80) REVERT: B 966 ASP cc_start: 0.7273 (t0) cc_final: 0.6770 (t0) REVERT: B 967 MET cc_start: 0.6543 (mmm) cc_final: 0.6219 (mmm) REVERT: B 972 PHE cc_start: 0.7214 (t80) cc_final: 0.6812 (t80) REVERT: B 990 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.7059 (mtp85) REVERT: B 993 ASP cc_start: 0.6885 (t0) cc_final: 0.6605 (t0) REVERT: B 994 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 995 SER cc_start: 0.7587 (p) cc_final: 0.7193 (t) REVERT: B 1003 SER cc_start: 0.7887 (t) cc_final: 0.7473 (t) REVERT: B 1007 LYS cc_start: 0.7699 (tttt) cc_final: 0.7073 (tttm) REVERT: B 1033 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 1037 THR cc_start: 0.7946 (t) cc_final: 0.7682 (m) REVERT: B 1044 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5755 (mt-10) REVERT: B 1051 LYS cc_start: 0.8609 (mttm) cc_final: 0.8123 (mttm) REVERT: B 1054 ASN cc_start: 0.8471 (t0) cc_final: 0.7982 (t0) REVERT: B 1058 THR cc_start: 0.7606 (m) cc_final: 0.7170 (p) REVERT: B 1060 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 1064 GLN cc_start: 0.7829 (mt0) cc_final: 0.7565 (mt0) REVERT: B 1072 ASP cc_start: 0.7342 (m-30) cc_final: 0.6767 (t0) REVERT: B 1122 GLU cc_start: 0.7542 (tp30) cc_final: 0.7316 (tp30) REVERT: B 1123 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7415 (ttp80) REVERT: B 1134 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6131 (p90) REVERT: B 1185 ARG cc_start: 0.7110 (mmt180) cc_final: 0.6736 (mmt90) REVERT: B 1191 ASN cc_start: 0.7444 (t0) cc_final: 0.7131 (p0) outliers start: 37 outliers final: 16 residues processed: 475 average time/residue: 0.3220 time to fit residues: 220.3511 Evaluate side-chains 459 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 439 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 502 HIS B 914 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16492 Z= 0.207 Angle : 0.503 8.139 22364 Z= 0.268 Chirality : 0.040 0.137 2688 Planarity : 0.004 0.050 2750 Dihedral : 4.036 39.595 2190 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.27 % Allowed : 12.56 % Favored : 85.17 % 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: 2.25 (0.19), residues: 2022 helix: 2.06 (0.13), residues: 1464 sheet: 0.82 (0.60), residues: 82 loop : -0.11 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 PHE 0.023 0.001 PHE B 769 TYR 0.015 0.001 TYR B1009 ARG 0.008 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 451 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7692 (ttpt) REVERT: A 163 PHE cc_start: 0.7608 (t80) cc_final: 0.7226 (t80) REVERT: A 164 SER cc_start: 0.7995 (m) cc_final: 0.7772 (p) REVERT: A 205 MET cc_start: 0.7457 (mmm) cc_final: 0.7031 (mmm) REVERT: A 233 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7096 (tt0) REVERT: A 250 LYS cc_start: 0.7566 (mttt) cc_final: 0.7303 (mttt) REVERT: A 289 PHE cc_start: 0.8035 (m-10) cc_final: 0.7745 (m-80) REVERT: A 300 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 316 ASP cc_start: 0.7827 (t0) cc_final: 0.7507 (m-30) REVERT: A 320 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 337 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 351 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7813 (ttm-80) REVERT: A 375 LYS cc_start: 0.7982 (mttt) cc_final: 0.7667 (ptmm) REVERT: A 383 MET cc_start: 0.7295 (tpp) cc_final: 0.6553 (mmm) REVERT: A 419 TRP cc_start: 0.7794 (p-90) cc_final: 0.7582 (p-90) REVERT: A 443 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 444 ASN cc_start: 0.8094 (t0) cc_final: 0.7817 (t0) REVERT: A 485 ASP cc_start: 0.7575 (m-30) cc_final: 0.7224 (p0) REVERT: A 499 ARG cc_start: 0.6995 (ttm170) cc_final: 0.6717 (ttm170) REVERT: A 511 MET cc_start: 0.7077 (tmm) cc_final: 0.6740 (ttp) REVERT: A 580 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6571 (tp30) REVERT: A 590 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6447 (mt-10) REVERT: A 591 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7009 (mtpp) REVERT: A 621 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6318 (mt-10) REVERT: A 628 VAL cc_start: 0.7726 (p) cc_final: 0.7344 (p) REVERT: A 633 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7505 (mtmm) REVERT: A 640 ILE cc_start: 0.7166 (mt) cc_final: 0.6651 (tt) REVERT: A 644 LEU cc_start: 0.7054 (mt) cc_final: 0.6794 (mp) REVERT: A 645 LYS cc_start: 0.7057 (tttm) cc_final: 0.6832 (tttm) REVERT: A 678 MET cc_start: 0.7345 (mmm) cc_final: 0.6762 (tmm) REVERT: A 810 MET cc_start: 0.4837 (ptp) cc_final: 0.4446 (ptp) REVERT: A 828 LYS cc_start: 0.7605 (mttt) cc_final: 0.7169 (mmmm) REVERT: A 847 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6522 (mm-30) REVERT: A 877 GLN cc_start: 0.7706 (tt0) cc_final: 0.7218 (tt0) REVERT: A 880 LYS cc_start: 0.7335 (tttm) cc_final: 0.7027 (tttp) REVERT: A 903 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7328 (ttm-80) REVERT: A 966 ASP cc_start: 0.7541 (t0) cc_final: 0.7156 (t0) REVERT: A 994 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 1003 SER cc_start: 0.7968 (t) cc_final: 0.7387 (m) REVERT: A 1007 LYS cc_start: 0.7678 (tttt) cc_final: 0.7008 (tttp) REVERT: A 1033 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 1037 THR cc_start: 0.7849 (t) cc_final: 0.7624 (m) REVERT: A 1044 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5674 (mt-10) REVERT: A 1051 LYS cc_start: 0.8749 (mttm) cc_final: 0.8168 (mttm) REVERT: A 1054 ASN cc_start: 0.8290 (t0) cc_final: 0.7738 (t0) REVERT: A 1104 MET cc_start: 0.6341 (mtp) cc_final: 0.6141 (mtp) REVERT: A 1123 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7182 (ttp80) REVERT: A 1125 TYR cc_start: 0.6364 (p90) cc_final: 0.6033 (p90) REVERT: A 1134 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6292 (p90) REVERT: A 1191 ASN cc_start: 0.7421 (t0) cc_final: 0.7062 (p0) REVERT: B 96 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7682 (ttpt) REVERT: B 136 HIS cc_start: 0.7447 (m90) cc_final: 0.7089 (m-70) REVERT: B 150 SER cc_start: 0.7845 (t) cc_final: 0.7512 (m) REVERT: B 160 MET cc_start: 0.7438 (mmt) cc_final: 0.7062 (mmm) REVERT: B 184 LEU cc_start: 0.7458 (tp) cc_final: 0.7211 (tp) REVERT: B 250 LYS cc_start: 0.7584 (mttt) cc_final: 0.7189 (mttm) REVERT: B 300 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 316 ASP cc_start: 0.8126 (t0) cc_final: 0.7805 (m-30) REVERT: B 320 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 337 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 355 MET cc_start: 0.8022 (tmm) cc_final: 0.7537 (ttp) REVERT: B 383 MET cc_start: 0.7188 (tpp) cc_final: 0.6492 (mmm) REVERT: B 387 TYR cc_start: 0.7660 (m-10) cc_final: 0.7406 (m-10) REVERT: B 443 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 444 ASN cc_start: 0.7992 (t0) cc_final: 0.7699 (t0) REVERT: B 486 ILE cc_start: 0.8155 (mp) cc_final: 0.7889 (mm) REVERT: B 580 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6520 (tp30) REVERT: B 591 LYS cc_start: 0.7271 (mtmt) cc_final: 0.7006 (mtpp) REVERT: B 608 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6850 (tp) REVERT: B 621 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6253 (mt-10) REVERT: B 628 VAL cc_start: 0.7940 (p) cc_final: 0.7499 (p) REVERT: B 632 LYS cc_start: 0.7399 (ttmm) cc_final: 0.6792 (ttmm) REVERT: B 633 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7643 (mmtp) REVERT: B 640 ILE cc_start: 0.7307 (mt) cc_final: 0.7059 (tt) REVERT: B 678 MET cc_start: 0.6865 (mmm) cc_final: 0.6653 (mmm) REVERT: B 697 MET cc_start: 0.6044 (ttt) cc_final: 0.5780 (ttt) REVERT: B 810 MET cc_start: 0.4872 (ptp) cc_final: 0.4375 (ptp) REVERT: B 847 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6700 (mm-30) REVERT: B 849 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 877 GLN cc_start: 0.7740 (tt0) cc_final: 0.7027 (tt0) REVERT: B 880 LYS cc_start: 0.7249 (ttpp) cc_final: 0.6955 (tttp) REVERT: B 903 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7214 (ttm-80) REVERT: B 966 ASP cc_start: 0.7332 (t0) cc_final: 0.6731 (t0) REVERT: B 967 MET cc_start: 0.6350 (mmm) cc_final: 0.6040 (mmm) REVERT: B 972 PHE cc_start: 0.7230 (t80) cc_final: 0.6842 (t80) REVERT: B 990 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7131 (mtp85) REVERT: B 993 ASP cc_start: 0.6961 (t0) cc_final: 0.6668 (t0) REVERT: B 994 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 995 SER cc_start: 0.7567 (p) cc_final: 0.7223 (t) REVERT: B 1003 SER cc_start: 0.7917 (t) cc_final: 0.7538 (t) REVERT: B 1007 LYS cc_start: 0.7668 (tttt) cc_final: 0.6950 (tttm) REVERT: B 1033 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 1044 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5908 (mt-10) REVERT: B 1051 LYS cc_start: 0.8626 (mttm) cc_final: 0.8132 (mttm) REVERT: B 1054 ASN cc_start: 0.8438 (t0) cc_final: 0.7914 (t0) REVERT: B 1058 THR cc_start: 0.7627 (m) cc_final: 0.7202 (p) REVERT: B 1060 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 1061 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 1064 GLN cc_start: 0.7851 (mt0) cc_final: 0.7595 (mt0) REVERT: B 1072 ASP cc_start: 0.7318 (m-30) cc_final: 0.6759 (t0) REVERT: B 1123 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7418 (ttp80) REVERT: B 1134 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6089 (p90) REVERT: B 1191 ASN cc_start: 0.7349 (t0) cc_final: 0.7043 (p0) outliers start: 40 outliers final: 25 residues processed: 465 average time/residue: 0.3369 time to fit residues: 221.7081 Evaluate side-chains 459 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 430 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16492 Z= 0.271 Angle : 0.518 8.915 22364 Z= 0.274 Chirality : 0.042 0.158 2688 Planarity : 0.004 0.048 2750 Dihedral : 3.928 39.402 2186 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 13.75 % Favored : 83.30 % 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: 2.16 (0.19), residues: 2022 helix: 2.01 (0.13), residues: 1468 sheet: 1.02 (0.62), residues: 82 loop : -0.30 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.007 0.001 HIS B1120 PHE 0.024 0.002 PHE B 769 TYR 0.015 0.001 TYR B1009 ARG 0.008 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 441 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7693 (t80) cc_final: 0.7432 (t80) REVERT: A 164 SER cc_start: 0.7949 (m) cc_final: 0.7718 (p) REVERT: A 233 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7113 (tt0) REVERT: A 289 PHE cc_start: 0.8137 (m-10) cc_final: 0.7846 (m-80) REVERT: A 300 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 316 ASP cc_start: 0.7850 (t0) cc_final: 0.7541 (m-30) REVERT: A 319 LEU cc_start: 0.8285 (mt) cc_final: 0.8079 (mp) REVERT: A 320 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 337 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 375 LYS cc_start: 0.8002 (mttt) cc_final: 0.7666 (ttpt) REVERT: A 383 MET cc_start: 0.7317 (tpp) cc_final: 0.6567 (mmm) REVERT: A 443 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 444 ASN cc_start: 0.8079 (t0) cc_final: 0.7763 (t0) REVERT: A 475 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7396 (mm-40) REVERT: A 479 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.7318 (ttp80) REVERT: A 485 ASP cc_start: 0.7620 (m-30) cc_final: 0.7203 (p0) REVERT: A 499 ARG cc_start: 0.6999 (ttm170) cc_final: 0.6721 (ttm170) REVERT: A 511 MET cc_start: 0.7126 (tmm) cc_final: 0.6808 (ttp) REVERT: A 580 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6547 (tp30) REVERT: A 591 LYS cc_start: 0.7330 (mtmt) cc_final: 0.7021 (mtpp) REVERT: A 621 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6346 (mt-10) REVERT: A 628 VAL cc_start: 0.7678 (p) cc_final: 0.7207 (p) REVERT: A 633 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7503 (mtmm) REVERT: A 640 ILE cc_start: 0.7216 (mt) cc_final: 0.6734 (tt) REVERT: A 644 LEU cc_start: 0.7053 (mt) cc_final: 0.6850 (mp) REVERT: A 678 MET cc_start: 0.7324 (mmm) cc_final: 0.6970 (tmm) REVERT: A 810 MET cc_start: 0.4792 (ptp) cc_final: 0.4384 (ptp) REVERT: A 828 LYS cc_start: 0.7554 (mttt) cc_final: 0.7140 (mmmm) REVERT: A 847 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6588 (mm-30) REVERT: A 877 GLN cc_start: 0.7771 (tt0) cc_final: 0.7196 (tt0) REVERT: A 880 LYS cc_start: 0.7342 (tttm) cc_final: 0.7033 (tttp) REVERT: A 903 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7416 (ttm-80) REVERT: A 938 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7408 (mtp) REVERT: A 966 ASP cc_start: 0.7576 (t0) cc_final: 0.6982 (t0) REVERT: A 994 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 1003 SER cc_start: 0.7988 (t) cc_final: 0.7392 (m) REVERT: A 1007 LYS cc_start: 0.7684 (tttt) cc_final: 0.6991 (tttp) REVERT: A 1033 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 1037 THR cc_start: 0.7893 (t) cc_final: 0.7658 (m) REVERT: A 1044 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5693 (mt-10) REVERT: A 1051 LYS cc_start: 0.8752 (mttm) cc_final: 0.8174 (mttm) REVERT: A 1054 ASN cc_start: 0.8288 (t0) cc_final: 0.7775 (t0) REVERT: A 1072 ASP cc_start: 0.7173 (m-30) cc_final: 0.6680 (t0) REVERT: A 1123 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7173 (ttp80) REVERT: A 1125 TYR cc_start: 0.6361 (p90) cc_final: 0.6065 (p90) REVERT: A 1134 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6306 (p90) REVERT: A 1191 ASN cc_start: 0.7506 (t0) cc_final: 0.7030 (p0) REVERT: B 96 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7733 (ttpt) REVERT: B 136 HIS cc_start: 0.7454 (m90) cc_final: 0.7087 (m-70) REVERT: B 150 SER cc_start: 0.7885 (t) cc_final: 0.7582 (m) REVERT: B 160 MET cc_start: 0.7481 (mmt) cc_final: 0.7112 (mmm) REVERT: B 184 LEU cc_start: 0.7495 (tp) cc_final: 0.7241 (tp) REVERT: B 205 MET cc_start: 0.7535 (mmm) cc_final: 0.7305 (mmt) REVERT: B 209 ASP cc_start: 0.7210 (t0) cc_final: 0.6983 (t0) REVERT: B 250 LYS cc_start: 0.7610 (mttt) cc_final: 0.7237 (mttp) REVERT: B 300 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 316 ASP cc_start: 0.8136 (t0) cc_final: 0.7811 (m-30) REVERT: B 320 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 337 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 339 THR cc_start: 0.8205 (m) cc_final: 0.7997 (p) REVERT: B 355 MET cc_start: 0.8082 (tmm) cc_final: 0.7596 (ttp) REVERT: B 383 MET cc_start: 0.7252 (tpp) cc_final: 0.6400 (mmm) REVERT: B 444 ASN cc_start: 0.8123 (t0) cc_final: 0.7771 (t0) REVERT: B 486 ILE cc_start: 0.8124 (mp) cc_final: 0.7867 (mm) REVERT: B 580 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6505 (tp30) REVERT: B 591 LYS cc_start: 0.7288 (mtmt) cc_final: 0.7007 (mtpp) REVERT: B 608 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6891 (tp) REVERT: B 621 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6296 (mt-10) REVERT: B 628 VAL cc_start: 0.7919 (p) cc_final: 0.7589 (p) REVERT: B 632 LYS cc_start: 0.7488 (ttmm) cc_final: 0.7207 (ttmm) REVERT: B 633 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7629 (mmtm) REVERT: B 640 ILE cc_start: 0.7333 (mt) cc_final: 0.7089 (tt) REVERT: B 697 MET cc_start: 0.6023 (ttt) cc_final: 0.5762 (ttt) REVERT: B 847 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6804 (mm-30) REVERT: B 849 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7056 (mt-10) REVERT: B 877 GLN cc_start: 0.7772 (tt0) cc_final: 0.7339 (tt0) REVERT: B 880 LYS cc_start: 0.7258 (ttpp) cc_final: 0.6925 (tttp) REVERT: B 881 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 903 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7257 (ttm-80) REVERT: B 938 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7463 (mtp) REVERT: B 966 ASP cc_start: 0.7383 (t0) cc_final: 0.6748 (t0) REVERT: B 967 MET cc_start: 0.6422 (mmm) cc_final: 0.6165 (mmm) REVERT: B 972 PHE cc_start: 0.7205 (t80) cc_final: 0.6846 (t80) REVERT: B 990 ARG cc_start: 0.7497 (mtt-85) cc_final: 0.7137 (mtp85) REVERT: B 995 SER cc_start: 0.7616 (p) cc_final: 0.7231 (t) REVERT: B 1007 LYS cc_start: 0.7688 (tttt) cc_final: 0.6972 (tttp) REVERT: B 1033 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7147 (mt-10) REVERT: B 1044 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6087 (mt-10) REVERT: B 1051 LYS cc_start: 0.8636 (mttm) cc_final: 0.8151 (mttm) REVERT: B 1054 ASN cc_start: 0.8446 (t0) cc_final: 0.7925 (t0) REVERT: B 1058 THR cc_start: 0.7642 (m) cc_final: 0.7197 (p) REVERT: B 1060 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7038 (mt-10) REVERT: B 1064 GLN cc_start: 0.7890 (mt0) cc_final: 0.7661 (mt0) REVERT: B 1072 ASP cc_start: 0.7315 (m-30) cc_final: 0.6741 (t0) REVERT: B 1104 MET cc_start: 0.6302 (mtp) cc_final: 0.6036 (ttp) REVERT: B 1123 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7447 (ttp80) REVERT: B 1134 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6059 (p90) REVERT: B 1191 ASN cc_start: 0.7435 (t0) cc_final: 0.7070 (p0) outliers start: 52 outliers final: 34 residues processed: 466 average time/residue: 0.3167 time to fit residues: 212.2259 Evaluate side-chains 469 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 430 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN A1114 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16492 Z= 0.244 Angle : 0.504 9.125 22364 Z= 0.264 Chirality : 0.041 0.167 2688 Planarity : 0.004 0.047 2750 Dihedral : 3.851 39.875 2186 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.78 % Allowed : 15.57 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 2022 helix: 2.05 (0.13), residues: 1468 sheet: 1.11 (0.63), residues: 82 loop : -0.31 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.007 0.001 HIS B1120 PHE 0.027 0.001 PHE B 769 TYR 0.017 0.001 TYR B 313 ARG 0.008 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 440 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7683 (t80) cc_final: 0.7320 (t80) REVERT: A 164 SER cc_start: 0.7933 (m) cc_final: 0.7692 (p) REVERT: A 205 MET cc_start: 0.7622 (mmt) cc_final: 0.7348 (mmt) REVERT: A 250 LYS cc_start: 0.7572 (mttt) cc_final: 0.7330 (mttp) REVERT: A 289 PHE cc_start: 0.8142 (m-10) cc_final: 0.7855 (m-80) REVERT: A 300 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 319 LEU cc_start: 0.8274 (mt) cc_final: 0.8044 (mp) REVERT: A 320 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 337 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 375 LYS cc_start: 0.7979 (mttt) cc_final: 0.7609 (ptmm) REVERT: A 383 MET cc_start: 0.7293 (tpp) cc_final: 0.6600 (mmm) REVERT: A 443 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 444 ASN cc_start: 0.8054 (t0) cc_final: 0.7708 (t0) REVERT: A 475 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 479 ARG cc_start: 0.7520 (ttp-170) cc_final: 0.7293 (ttp80) REVERT: A 499 ARG cc_start: 0.6981 (ttm170) cc_final: 0.6703 (ttm170) REVERT: A 511 MET cc_start: 0.7122 (tmm) cc_final: 0.6809 (ttp) REVERT: A 580 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6626 (tp30) REVERT: A 591 LYS cc_start: 0.7340 (mtmt) cc_final: 0.7027 (mtpp) REVERT: A 628 VAL cc_start: 0.7776 (p) cc_final: 0.7244 (p) REVERT: A 633 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7496 (mtmm) REVERT: A 640 ILE cc_start: 0.7210 (mt) cc_final: 0.6761 (tt) REVERT: A 678 MET cc_start: 0.7260 (mmm) cc_final: 0.6926 (tmm) REVERT: A 740 PHE cc_start: 0.3969 (t80) cc_final: 0.3616 (t80) REVERT: A 810 MET cc_start: 0.4774 (ptp) cc_final: 0.4359 (ptp) REVERT: A 828 LYS cc_start: 0.7544 (mttt) cc_final: 0.7136 (mmmm) REVERT: A 847 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6559 (mm-30) REVERT: A 877 GLN cc_start: 0.7798 (tt0) cc_final: 0.7189 (tt0) REVERT: A 880 LYS cc_start: 0.7332 (tttm) cc_final: 0.7024 (tttp) REVERT: A 903 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7402 (ttm-80) REVERT: A 938 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7379 (mtp) REVERT: A 966 ASP cc_start: 0.7556 (t0) cc_final: 0.6943 (t0) REVERT: A 989 VAL cc_start: 0.7744 (p) cc_final: 0.7495 (m) REVERT: A 994 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 1003 SER cc_start: 0.7969 (t) cc_final: 0.7360 (m) REVERT: A 1007 LYS cc_start: 0.7657 (tttt) cc_final: 0.6933 (tttp) REVERT: A 1033 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 1037 THR cc_start: 0.7906 (t) cc_final: 0.7687 (m) REVERT: A 1044 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5838 (mt-10) REVERT: A 1051 LYS cc_start: 0.8773 (mttm) cc_final: 0.8210 (mttm) REVERT: A 1054 ASN cc_start: 0.8285 (t0) cc_final: 0.7794 (t0) REVERT: A 1072 ASP cc_start: 0.7378 (m-30) cc_final: 0.6871 (t0) REVERT: A 1104 MET cc_start: 0.6420 (mtp) cc_final: 0.6197 (ttp) REVERT: A 1123 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7198 (ttp80) REVERT: A 1125 TYR cc_start: 0.6386 (p90) cc_final: 0.6091 (p90) REVERT: A 1134 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6280 (p90) REVERT: A 1191 ASN cc_start: 0.7499 (t0) cc_final: 0.7013 (p0) REVERT: B 96 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7750 (ttpt) REVERT: B 136 HIS cc_start: 0.7474 (m90) cc_final: 0.7123 (m-70) REVERT: B 150 SER cc_start: 0.7906 (t) cc_final: 0.7590 (m) REVERT: B 160 MET cc_start: 0.7421 (mmt) cc_final: 0.7056 (mmm) REVERT: B 184 LEU cc_start: 0.7478 (tp) cc_final: 0.7221 (tp) REVERT: B 205 MET cc_start: 0.7525 (mmm) cc_final: 0.7308 (mmt) REVERT: B 209 ASP cc_start: 0.7266 (t0) cc_final: 0.6948 (t0) REVERT: B 250 LYS cc_start: 0.7620 (mttt) cc_final: 0.7227 (mttp) REVERT: B 296 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: B 300 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 316 ASP cc_start: 0.8122 (t0) cc_final: 0.7814 (m-30) REVERT: B 320 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 322 SER cc_start: 0.8130 (t) cc_final: 0.7349 (p) REVERT: B 337 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 339 THR cc_start: 0.8230 (m) cc_final: 0.8004 (p) REVERT: B 355 MET cc_start: 0.8068 (tmm) cc_final: 0.7603 (ttp) REVERT: B 383 MET cc_start: 0.7259 (tpp) cc_final: 0.6363 (mmm) REVERT: B 420 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7230 (mtt-85) REVERT: B 444 ASN cc_start: 0.8006 (t0) cc_final: 0.7657 (t0) REVERT: B 486 ILE cc_start: 0.8123 (mp) cc_final: 0.7871 (mm) REVERT: B 580 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6530 (tp30) REVERT: B 591 LYS cc_start: 0.7304 (mtmt) cc_final: 0.7022 (mtpp) REVERT: B 608 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6869 (tp) REVERT: B 609 ARG cc_start: 0.7265 (mtp180) cc_final: 0.7015 (mtp180) REVERT: B 621 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6240 (mt-10) REVERT: B 628 VAL cc_start: 0.7961 (p) cc_final: 0.7604 (p) REVERT: B 632 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7223 (ttmm) REVERT: B 633 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7666 (mmtm) REVERT: B 640 ILE cc_start: 0.7331 (mt) cc_final: 0.7098 (tt) REVERT: B 697 MET cc_start: 0.6008 (ttt) cc_final: 0.5730 (ttt) REVERT: B 810 MET cc_start: 0.4799 (ptp) cc_final: 0.4425 (ptt) REVERT: B 847 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 849 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7079 (mt-10) REVERT: B 877 GLN cc_start: 0.7787 (tt0) cc_final: 0.7338 (tt0) REVERT: B 880 LYS cc_start: 0.7272 (ttpp) cc_final: 0.6941 (tttp) REVERT: B 881 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6998 (mt-10) REVERT: B 887 ARG cc_start: 0.7626 (ttt90) cc_final: 0.7402 (ttt90) REVERT: B 903 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7256 (ttm-80) REVERT: B 938 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7462 (mtp) REVERT: B 966 ASP cc_start: 0.7379 (t0) cc_final: 0.6707 (t0) REVERT: B 967 MET cc_start: 0.6443 (mmm) cc_final: 0.6197 (mmm) REVERT: B 972 PHE cc_start: 0.7236 (t80) cc_final: 0.6812 (t80) REVERT: B 990 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.6918 (mtt-85) REVERT: B 994 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7201 (mp0) REVERT: B 995 SER cc_start: 0.7654 (p) cc_final: 0.7255 (t) REVERT: B 999 PHE cc_start: 0.7386 (m-80) cc_final: 0.6725 (m-80) REVERT: B 1007 LYS cc_start: 0.7683 (tttt) cc_final: 0.6981 (tttp) REVERT: B 1033 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 1044 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6106 (mt-10) REVERT: B 1051 LYS cc_start: 0.8659 (mttm) cc_final: 0.8162 (mttm) REVERT: B 1054 ASN cc_start: 0.8438 (t0) cc_final: 0.7919 (t0) REVERT: B 1058 THR cc_start: 0.7628 (m) cc_final: 0.7182 (p) REVERT: B 1060 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7036 (mt-10) REVERT: B 1061 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7773 (p) REVERT: B 1064 GLN cc_start: 0.7921 (mt0) cc_final: 0.7686 (mt0) REVERT: B 1072 ASP cc_start: 0.7320 (m-30) cc_final: 0.6737 (t0) REVERT: B 1104 MET cc_start: 0.6307 (mtp) cc_final: 0.6089 (ttp) REVERT: B 1123 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7442 (ttp80) REVERT: B 1134 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6038 (p90) REVERT: B 1191 ASN cc_start: 0.7481 (t0) cc_final: 0.7091 (p0) outliers start: 49 outliers final: 34 residues processed: 466 average time/residue: 0.3095 time to fit residues: 206.9519 Evaluate side-chains 472 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 431 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS B1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16492 Z= 0.216 Angle : 0.506 10.212 22364 Z= 0.263 Chirality : 0.041 0.144 2688 Planarity : 0.004 0.046 2750 Dihedral : 3.822 39.810 2186 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.73 % Allowed : 16.31 % Favored : 80.97 % 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: 2.27 (0.19), residues: 2022 helix: 2.11 (0.13), residues: 1466 sheet: 1.17 (0.62), residues: 82 loop : -0.34 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.006 0.001 HIS B1120 PHE 0.027 0.001 PHE B 769 TYR 0.018 0.001 TYR B 313 ARG 0.009 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 437 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7651 (t80) cc_final: 0.7278 (t80) REVERT: A 164 SER cc_start: 0.7931 (m) cc_final: 0.7686 (p) REVERT: A 205 MET cc_start: 0.7606 (mmt) cc_final: 0.7345 (mmt) REVERT: A 250 LYS cc_start: 0.7570 (mttt) cc_final: 0.7328 (mttp) REVERT: A 289 PHE cc_start: 0.8150 (m-10) cc_final: 0.7844 (m-80) REVERT: A 300 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 316 ASP cc_start: 0.8016 (t0) cc_final: 0.7690 (m-30) REVERT: A 319 LEU cc_start: 0.8270 (mt) cc_final: 0.8024 (mp) REVERT: A 320 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 337 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 375 LYS cc_start: 0.7999 (mttt) cc_final: 0.7632 (ptmm) REVERT: A 383 MET cc_start: 0.7230 (tpp) cc_final: 0.6561 (mmm) REVERT: A 443 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 444 ASN cc_start: 0.8050 (t0) cc_final: 0.7697 (t0) REVERT: A 475 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 479 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.7290 (ttp80) REVERT: A 499 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6699 (ttm170) REVERT: A 511 MET cc_start: 0.7125 (tmm) cc_final: 0.6805 (ttp) REVERT: A 580 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6615 (tp30) REVERT: A 591 LYS cc_start: 0.7335 (mtmt) cc_final: 0.7024 (mtpp) REVERT: A 628 VAL cc_start: 0.7727 (p) cc_final: 0.7177 (p) REVERT: A 633 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7463 (mmtm) REVERT: A 640 ILE cc_start: 0.7227 (mt) cc_final: 0.6990 (tt) REVERT: A 678 MET cc_start: 0.7196 (mmm) cc_final: 0.6858 (tmm) REVERT: A 740 PHE cc_start: 0.3966 (t80) cc_final: 0.3628 (t80) REVERT: A 810 MET cc_start: 0.4752 (ptp) cc_final: 0.4336 (ptp) REVERT: A 828 LYS cc_start: 0.7573 (mttt) cc_final: 0.7152 (mmmm) REVERT: A 847 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 877 GLN cc_start: 0.7808 (tt0) cc_final: 0.7166 (tt0) REVERT: A 880 LYS cc_start: 0.7342 (tttm) cc_final: 0.7029 (tttp) REVERT: A 903 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7386 (ttm-80) REVERT: A 938 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7388 (mtp) REVERT: A 966 ASP cc_start: 0.7587 (t0) cc_final: 0.6951 (t0) REVERT: A 989 VAL cc_start: 0.7722 (p) cc_final: 0.7475 (m) REVERT: A 994 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 1003 SER cc_start: 0.7948 (t) cc_final: 0.7360 (m) REVERT: A 1007 LYS cc_start: 0.7656 (tttt) cc_final: 0.6940 (tttp) REVERT: A 1033 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 1037 THR cc_start: 0.7919 (t) cc_final: 0.7707 (m) REVERT: A 1044 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5893 (mt-10) REVERT: A 1051 LYS cc_start: 0.8761 (mttm) cc_final: 0.8211 (mttm) REVERT: A 1054 ASN cc_start: 0.8281 (t0) cc_final: 0.7804 (t0) REVERT: A 1072 ASP cc_start: 0.7276 (m-30) cc_final: 0.6774 (t0) REVERT: A 1104 MET cc_start: 0.6406 (mtp) cc_final: 0.6181 (ttp) REVERT: A 1123 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7130 (ttp80) REVERT: A 1125 TYR cc_start: 0.6355 (p90) cc_final: 0.6059 (p90) REVERT: A 1134 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6267 (p90) REVERT: A 1191 ASN cc_start: 0.7482 (t0) cc_final: 0.6997 (p0) REVERT: B 96 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7744 (ttpt) REVERT: B 136 HIS cc_start: 0.7480 (m90) cc_final: 0.7127 (m-70) REVERT: B 150 SER cc_start: 0.7908 (t) cc_final: 0.7593 (m) REVERT: B 160 MET cc_start: 0.7414 (mmt) cc_final: 0.7059 (mmm) REVERT: B 184 LEU cc_start: 0.7468 (tp) cc_final: 0.7210 (tp) REVERT: B 205 MET cc_start: 0.7551 (mmm) cc_final: 0.7328 (mmt) REVERT: B 209 ASP cc_start: 0.7229 (t0) cc_final: 0.6880 (t0) REVERT: B 250 LYS cc_start: 0.7534 (mttt) cc_final: 0.7172 (mttp) REVERT: B 300 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 316 ASP cc_start: 0.8137 (t0) cc_final: 0.7814 (m-30) REVERT: B 320 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 322 SER cc_start: 0.8080 (t) cc_final: 0.7318 (p) REVERT: B 337 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 355 MET cc_start: 0.8071 (tmm) cc_final: 0.7616 (ttp) REVERT: B 383 MET cc_start: 0.7232 (tpp) cc_final: 0.6397 (mmm) REVERT: B 444 ASN cc_start: 0.7982 (t0) cc_final: 0.7713 (t0) REVERT: B 486 ILE cc_start: 0.8107 (mp) cc_final: 0.7861 (mm) REVERT: B 580 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6468 (tp30) REVERT: B 590 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6670 (mt-10) REVERT: B 591 LYS cc_start: 0.7316 (mtmt) cc_final: 0.7034 (mtpp) REVERT: B 621 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6229 (mt-10) REVERT: B 633 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7681 (mmtm) REVERT: B 640 ILE cc_start: 0.7341 (mt) cc_final: 0.7120 (tt) REVERT: B 810 MET cc_start: 0.4813 (ptp) cc_final: 0.4436 (ptt) REVERT: B 847 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6719 (mm-30) REVERT: B 849 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7069 (mt-10) REVERT: B 877 GLN cc_start: 0.7790 (tt0) cc_final: 0.7361 (tt0) REVERT: B 880 LYS cc_start: 0.7269 (ttpp) cc_final: 0.6940 (tttp) REVERT: B 881 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7040 (mt-10) REVERT: B 903 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7255 (ttm-80) REVERT: B 938 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7435 (mtp) REVERT: B 966 ASP cc_start: 0.7345 (t0) cc_final: 0.6692 (t0) REVERT: B 967 MET cc_start: 0.6444 (mmm) cc_final: 0.6225 (mmm) REVERT: B 972 PHE cc_start: 0.7261 (t80) cc_final: 0.6828 (t80) REVERT: B 990 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.6903 (mtt-85) REVERT: B 993 ASP cc_start: 0.7101 (t0) cc_final: 0.6858 (t0) REVERT: B 994 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7113 (mp0) REVERT: B 995 SER cc_start: 0.7637 (p) cc_final: 0.7310 (t) REVERT: B 999 PHE cc_start: 0.7364 (m-80) cc_final: 0.6754 (m-80) REVERT: B 1007 LYS cc_start: 0.7680 (tttt) cc_final: 0.6977 (tttp) REVERT: B 1033 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 1044 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6106 (mt-10) REVERT: B 1051 LYS cc_start: 0.8662 (mttm) cc_final: 0.8177 (mttm) REVERT: B 1054 ASN cc_start: 0.8440 (t0) cc_final: 0.8040 (t0) REVERT: B 1058 THR cc_start: 0.7601 (m) cc_final: 0.7181 (p) REVERT: B 1060 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7010 (mt-10) REVERT: B 1064 GLN cc_start: 0.7942 (mt0) cc_final: 0.7688 (mt0) REVERT: B 1072 ASP cc_start: 0.7295 (m-30) cc_final: 0.6731 (t0) REVERT: B 1123 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7446 (ttp80) REVERT: B 1134 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6020 (p90) REVERT: B 1191 ASN cc_start: 0.7525 (t0) cc_final: 0.7121 (p0) outliers start: 48 outliers final: 35 residues processed: 458 average time/residue: 0.3179 time to fit residues: 209.9052 Evaluate side-chains 465 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 426 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 502 HIS B1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16492 Z= 0.184 Angle : 0.499 10.842 22364 Z= 0.258 Chirality : 0.040 0.228 2688 Planarity : 0.004 0.048 2750 Dihedral : 3.787 39.707 2186 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.67 % Allowed : 16.99 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.19), residues: 2022 helix: 2.18 (0.13), residues: 1464 sheet: 1.28 (0.63), residues: 82 loop : -0.34 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 PHE 0.029 0.001 PHE B 769 TYR 0.019 0.001 TYR B 313 ARG 0.010 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 438 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7639 (t80) cc_final: 0.7262 (t80) REVERT: A 164 SER cc_start: 0.7933 (m) cc_final: 0.7697 (p) REVERT: A 250 LYS cc_start: 0.7566 (mttt) cc_final: 0.7326 (mttp) REVERT: A 289 PHE cc_start: 0.8138 (m-10) cc_final: 0.7822 (m-80) REVERT: A 316 ASP cc_start: 0.7987 (t0) cc_final: 0.7665 (m-30) REVERT: A 319 LEU cc_start: 0.8263 (mt) cc_final: 0.8016 (mp) REVERT: A 320 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 337 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 375 LYS cc_start: 0.8002 (mttt) cc_final: 0.7626 (ptmm) REVERT: A 383 MET cc_start: 0.7253 (tpp) cc_final: 0.6595 (mmm) REVERT: A 443 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 444 ASN cc_start: 0.8081 (t0) cc_final: 0.7725 (t0) REVERT: A 475 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7423 (mm-40) REVERT: A 479 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7280 (ttp80) REVERT: A 499 ARG cc_start: 0.6967 (ttm170) cc_final: 0.6699 (ttm170) REVERT: A 511 MET cc_start: 0.7087 (tmm) cc_final: 0.6811 (ttp) REVERT: A 580 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6629 (tp30) REVERT: A 591 LYS cc_start: 0.7329 (mtmt) cc_final: 0.7023 (mtpp) REVERT: A 628 VAL cc_start: 0.7681 (p) cc_final: 0.7109 (p) REVERT: A 633 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7532 (mtmm) REVERT: A 640 ILE cc_start: 0.7206 (mt) cc_final: 0.6992 (tt) REVERT: A 678 MET cc_start: 0.7113 (mmm) cc_final: 0.6487 (tmm) REVERT: A 740 PHE cc_start: 0.3979 (t80) cc_final: 0.3636 (t80) REVERT: A 810 MET cc_start: 0.4714 (ptp) cc_final: 0.4186 (ptp) REVERT: A 828 LYS cc_start: 0.7536 (mttt) cc_final: 0.7117 (mmmm) REVERT: A 847 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6510 (mm-30) REVERT: A 877 GLN cc_start: 0.7814 (tt0) cc_final: 0.7166 (tt0) REVERT: A 880 LYS cc_start: 0.7336 (tttm) cc_final: 0.7007 (tttp) REVERT: A 903 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7397 (ttm-80) REVERT: A 966 ASP cc_start: 0.7586 (t0) cc_final: 0.6958 (t0) REVERT: A 989 VAL cc_start: 0.7677 (p) cc_final: 0.7432 (m) REVERT: A 994 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 1003 SER cc_start: 0.7950 (t) cc_final: 0.7357 (m) REVERT: A 1007 LYS cc_start: 0.7660 (tttt) cc_final: 0.6943 (tttp) REVERT: A 1033 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6971 (mt-10) REVERT: A 1037 THR cc_start: 0.7930 (t) cc_final: 0.7716 (m) REVERT: A 1044 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5878 (mt-10) REVERT: A 1051 LYS cc_start: 0.8764 (mttm) cc_final: 0.8202 (mttm) REVERT: A 1054 ASN cc_start: 0.8270 (t0) cc_final: 0.7803 (t0) REVERT: A 1072 ASP cc_start: 0.7249 (m-30) cc_final: 0.6750 (t0) REVERT: A 1104 MET cc_start: 0.6356 (mtp) cc_final: 0.6105 (ttm) REVERT: A 1123 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7158 (ttp80) REVERT: A 1125 TYR cc_start: 0.6300 (p90) cc_final: 0.6010 (p90) REVERT: A 1134 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6259 (p90) REVERT: A 1169 ARG cc_start: 0.6310 (mtt180) cc_final: 0.5799 (mtt180) REVERT: A 1191 ASN cc_start: 0.7487 (t0) cc_final: 0.7002 (p0) REVERT: B 96 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7734 (ttpt) REVERT: B 136 HIS cc_start: 0.7492 (m90) cc_final: 0.7146 (m-70) REVERT: B 150 SER cc_start: 0.7914 (t) cc_final: 0.7566 (m) REVERT: B 160 MET cc_start: 0.7395 (mmt) cc_final: 0.7033 (mmm) REVERT: B 184 LEU cc_start: 0.7441 (tp) cc_final: 0.7184 (tp) REVERT: B 205 MET cc_start: 0.7540 (mmm) cc_final: 0.7312 (mmp) REVERT: B 209 ASP cc_start: 0.7223 (t0) cc_final: 0.6839 (t0) REVERT: B 250 LYS cc_start: 0.7528 (mttt) cc_final: 0.7167 (mttp) REVERT: B 296 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: B 300 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 316 ASP cc_start: 0.8149 (t0) cc_final: 0.7840 (m-30) REVERT: B 320 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 337 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 355 MET cc_start: 0.8100 (tmm) cc_final: 0.7636 (ttp) REVERT: B 383 MET cc_start: 0.7216 (tpp) cc_final: 0.6427 (mmm) REVERT: B 420 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7280 (mtt-85) REVERT: B 444 ASN cc_start: 0.7995 (t0) cc_final: 0.7707 (t0) REVERT: B 451 ILE cc_start: 0.7739 (mm) cc_final: 0.7236 (tp) REVERT: B 486 ILE cc_start: 0.8101 (mp) cc_final: 0.7856 (mm) REVERT: B 580 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6486 (tp30) REVERT: B 584 LEU cc_start: 0.7358 (mm) cc_final: 0.7136 (mm) REVERT: B 591 LYS cc_start: 0.7303 (mtmt) cc_final: 0.7025 (mtpp) REVERT: B 621 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6244 (mt-10) REVERT: B 632 LYS cc_start: 0.7584 (ttmt) cc_final: 0.6915 (ttmm) REVERT: B 633 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7652 (mmtm) REVERT: B 640 ILE cc_start: 0.7329 (mt) cc_final: 0.7121 (tt) REVERT: B 810 MET cc_start: 0.4810 (ptp) cc_final: 0.4427 (ptt) REVERT: B 847 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 849 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7103 (mt-10) REVERT: B 877 GLN cc_start: 0.7707 (tt0) cc_final: 0.7044 (tt0) REVERT: B 880 LYS cc_start: 0.7316 (ttpp) cc_final: 0.6983 (tttp) REVERT: B 903 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7238 (ttm-80) REVERT: B 966 ASP cc_start: 0.7341 (t0) cc_final: 0.6691 (t0) REVERT: B 967 MET cc_start: 0.6439 (mmm) cc_final: 0.6233 (mmm) REVERT: B 972 PHE cc_start: 0.7272 (t80) cc_final: 0.6813 (t80) REVERT: B 990 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.6902 (mtt-85) REVERT: B 993 ASP cc_start: 0.7104 (t0) cc_final: 0.6846 (t0) REVERT: B 994 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7138 (mp0) REVERT: B 995 SER cc_start: 0.7633 (p) cc_final: 0.7308 (t) REVERT: B 1007 LYS cc_start: 0.7699 (tttt) cc_final: 0.6989 (tttp) REVERT: B 1033 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7112 (mt-10) REVERT: B 1044 GLU cc_start: 0.6383 (mt-10) cc_final: 0.6103 (mt-10) REVERT: B 1051 LYS cc_start: 0.8677 (mttm) cc_final: 0.8188 (mttm) REVERT: B 1054 ASN cc_start: 0.8419 (t0) cc_final: 0.8041 (t0) REVERT: B 1058 THR cc_start: 0.7603 (m) cc_final: 0.7193 (p) REVERT: B 1060 GLU cc_start: 0.7957 (mm-30) cc_final: 0.6999 (mt-10) REVERT: B 1061 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7737 (p) REVERT: B 1064 GLN cc_start: 0.7942 (mt0) cc_final: 0.7646 (mt0) REVERT: B 1072 ASP cc_start: 0.7292 (m-30) cc_final: 0.6729 (t0) REVERT: B 1122 GLU cc_start: 0.7534 (tp30) cc_final: 0.7330 (tp30) REVERT: B 1123 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7437 (ttp80) REVERT: B 1134 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6018 (p90) REVERT: B 1191 ASN cc_start: 0.7513 (t0) cc_final: 0.7091 (p0) outliers start: 47 outliers final: 29 residues processed: 462 average time/residue: 0.3215 time to fit residues: 213.1195 Evaluate side-chains 470 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 437 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16492 Z= 0.204 Angle : 0.501 11.163 22364 Z= 0.259 Chirality : 0.040 0.227 2688 Planarity : 0.004 0.047 2750 Dihedral : 3.749 39.485 2186 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.44 % Allowed : 17.78 % Favored : 79.77 % 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: 2.40 (0.19), residues: 2022 helix: 2.20 (0.13), residues: 1464 sheet: 1.41 (0.63), residues: 82 loop : -0.28 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 PHE 0.030 0.001 PHE B 769 TYR 0.013 0.001 TYR B1009 ARG 0.011 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 439 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7629 (t80) cc_final: 0.7254 (t80) REVERT: A 164 SER cc_start: 0.7903 (m) cc_final: 0.7668 (p) REVERT: A 205 MET cc_start: 0.7527 (mmt) cc_final: 0.7132 (mmt) REVERT: A 209 ASP cc_start: 0.7255 (t0) cc_final: 0.7051 (t0) REVERT: A 250 LYS cc_start: 0.7579 (mttt) cc_final: 0.7331 (mttp) REVERT: A 289 PHE cc_start: 0.8149 (m-10) cc_final: 0.7826 (m-80) REVERT: A 300 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 316 ASP cc_start: 0.7992 (t0) cc_final: 0.7671 (m-30) REVERT: A 320 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 337 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 375 LYS cc_start: 0.7989 (mttt) cc_final: 0.7590 (ptmm) REVERT: A 383 MET cc_start: 0.7262 (tpp) cc_final: 0.6569 (mmm) REVERT: A 443 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 444 ASN cc_start: 0.8084 (t0) cc_final: 0.7721 (t0) REVERT: A 479 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7299 (ttp80) REVERT: A 499 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6705 (ttm170) REVERT: A 511 MET cc_start: 0.7080 (tmm) cc_final: 0.6809 (ttp) REVERT: A 580 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6627 (tp30) REVERT: A 590 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 591 LYS cc_start: 0.7313 (mtmt) cc_final: 0.7008 (mtpp) REVERT: A 633 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7538 (mtmm) REVERT: A 671 MET cc_start: 0.6537 (ppp) cc_final: 0.6258 (tmm) REVERT: A 678 MET cc_start: 0.7068 (mmm) cc_final: 0.6438 (tmm) REVERT: A 740 PHE cc_start: 0.3970 (t80) cc_final: 0.3611 (t80) REVERT: A 810 MET cc_start: 0.4704 (ptp) cc_final: 0.4164 (ptp) REVERT: A 828 LYS cc_start: 0.7538 (mttt) cc_final: 0.7120 (mmmm) REVERT: A 847 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6489 (mm-30) REVERT: A 877 GLN cc_start: 0.7799 (tt0) cc_final: 0.7164 (tt0) REVERT: A 880 LYS cc_start: 0.7371 (tttm) cc_final: 0.6941 (tttp) REVERT: A 903 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7448 (ttm-80) REVERT: A 966 ASP cc_start: 0.7607 (t0) cc_final: 0.7177 (t0) REVERT: A 989 VAL cc_start: 0.7677 (p) cc_final: 0.7436 (m) REVERT: A 994 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 1007 LYS cc_start: 0.7668 (tttt) cc_final: 0.7177 (tttm) REVERT: A 1033 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 1037 THR cc_start: 0.7912 (t) cc_final: 0.7704 (m) REVERT: A 1044 GLU cc_start: 0.6326 (mt-10) cc_final: 0.5849 (mt-10) REVERT: A 1051 LYS cc_start: 0.8736 (mttm) cc_final: 0.8195 (mttm) REVERT: A 1054 ASN cc_start: 0.8264 (t0) cc_final: 0.7820 (t0) REVERT: A 1060 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6853 (mt-10) REVERT: A 1072 ASP cc_start: 0.7262 (m-30) cc_final: 0.6974 (t0) REVERT: A 1104 MET cc_start: 0.6352 (mtp) cc_final: 0.6100 (ttm) REVERT: A 1123 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7187 (ttp80) REVERT: A 1125 TYR cc_start: 0.6247 (p90) cc_final: 0.5950 (p90) REVERT: A 1134 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6249 (p90) REVERT: A 1139 ASP cc_start: 0.7217 (m-30) cc_final: 0.6318 (m-30) REVERT: A 1169 ARG cc_start: 0.6304 (mtt180) cc_final: 0.5800 (mtt180) REVERT: A 1191 ASN cc_start: 0.7522 (t0) cc_final: 0.7047 (p0) REVERT: B 96 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7732 (ttpt) REVERT: B 136 HIS cc_start: 0.7476 (m90) cc_final: 0.7140 (m-70) REVERT: B 150 SER cc_start: 0.7918 (t) cc_final: 0.7570 (m) REVERT: B 160 MET cc_start: 0.7433 (mmt) cc_final: 0.7074 (mmm) REVERT: B 184 LEU cc_start: 0.7436 (tp) cc_final: 0.7186 (tp) REVERT: B 205 MET cc_start: 0.7497 (mmm) cc_final: 0.7276 (mmp) REVERT: B 209 ASP cc_start: 0.7223 (t0) cc_final: 0.6809 (t0) REVERT: B 250 LYS cc_start: 0.7523 (mttt) cc_final: 0.7206 (mttp) REVERT: B 296 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: B 300 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 316 ASP cc_start: 0.8167 (t0) cc_final: 0.7853 (m-30) REVERT: B 320 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 337 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 355 MET cc_start: 0.8107 (tmm) cc_final: 0.7636 (ttp) REVERT: B 383 MET cc_start: 0.7243 (tpp) cc_final: 0.6425 (mmm) REVERT: B 444 ASN cc_start: 0.8027 (t0) cc_final: 0.7735 (t0) REVERT: B 486 ILE cc_start: 0.8034 (mp) cc_final: 0.7800 (mm) REVERT: B 516 ARG cc_start: 0.8072 (ptm160) cc_final: 0.7856 (ptm160) REVERT: B 580 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6493 (tp30) REVERT: B 584 LEU cc_start: 0.7367 (mm) cc_final: 0.7112 (mm) REVERT: B 590 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6802 (mt-10) REVERT: B 591 LYS cc_start: 0.7295 (mtmt) cc_final: 0.7031 (mtpp) REVERT: B 609 ARG cc_start: 0.7270 (mtp180) cc_final: 0.6980 (mtp180) REVERT: B 621 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6268 (mt-10) REVERT: B 632 LYS cc_start: 0.7515 (ttmt) cc_final: 0.7210 (ttmm) REVERT: B 633 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7669 (mmtm) REVERT: B 810 MET cc_start: 0.4803 (ptp) cc_final: 0.4411 (ptt) REVERT: B 847 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6666 (mm-30) REVERT: B 877 GLN cc_start: 0.7723 (tt0) cc_final: 0.7311 (tt0) REVERT: B 880 LYS cc_start: 0.7314 (ttpp) cc_final: 0.6977 (tttp) REVERT: B 881 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 903 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7261 (ttm-80) REVERT: B 966 ASP cc_start: 0.7338 (t0) cc_final: 0.6731 (t0) REVERT: B 967 MET cc_start: 0.6461 (mmm) cc_final: 0.6252 (mmm) REVERT: B 972 PHE cc_start: 0.7294 (t80) cc_final: 0.6839 (t80) REVERT: B 990 ARG cc_start: 0.7527 (mtt-85) cc_final: 0.6905 (mtt-85) REVERT: B 993 ASP cc_start: 0.7123 (t0) cc_final: 0.6855 (t0) REVERT: B 995 SER cc_start: 0.7645 (p) cc_final: 0.7327 (t) REVERT: B 999 PHE cc_start: 0.7351 (m-80) cc_final: 0.6781 (m-80) REVERT: B 1007 LYS cc_start: 0.7684 (tttt) cc_final: 0.6984 (tttp) REVERT: B 1033 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 1044 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6106 (mt-10) REVERT: B 1051 LYS cc_start: 0.8685 (mttm) cc_final: 0.8196 (mttm) REVERT: B 1054 ASN cc_start: 0.8408 (t0) cc_final: 0.8057 (t0) REVERT: B 1058 THR cc_start: 0.7608 (m) cc_final: 0.7183 (p) REVERT: B 1060 GLU cc_start: 0.7968 (mm-30) cc_final: 0.6993 (mt-10) REVERT: B 1061 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 1072 ASP cc_start: 0.7294 (m-30) cc_final: 0.6720 (t0) REVERT: B 1122 GLU cc_start: 0.7544 (tp30) cc_final: 0.7324 (tp30) REVERT: B 1123 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7448 (ttp80) REVERT: B 1134 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6009 (p90) REVERT: B 1191 ASN cc_start: 0.7531 (t0) cc_final: 0.7106 (p0) outliers start: 43 outliers final: 33 residues processed: 459 average time/residue: 0.3182 time to fit residues: 210.1956 Evaluate side-chains 471 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 434 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 502 HIS B 691 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16492 Z= 0.259 Angle : 0.532 11.769 22364 Z= 0.274 Chirality : 0.042 0.195 2688 Planarity : 0.004 0.046 2750 Dihedral : 3.786 39.724 2186 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.44 % Allowed : 18.30 % Favored : 79.26 % 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: 2.28 (0.19), residues: 2022 helix: 2.10 (0.13), residues: 1468 sheet: 1.46 (0.64), residues: 82 loop : -0.33 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 962 HIS 0.007 0.001 HIS B1120 PHE 0.031 0.001 PHE B 769 TYR 0.021 0.001 TYR B 313 ARG 0.011 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 433 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7678 (t80) cc_final: 0.7295 (t80) REVERT: A 164 SER cc_start: 0.7935 (m) cc_final: 0.7693 (p) REVERT: A 205 MET cc_start: 0.7584 (mmt) cc_final: 0.7190 (mmt) REVERT: A 209 ASP cc_start: 0.7322 (t0) cc_final: 0.7118 (t0) REVERT: A 250 LYS cc_start: 0.7584 (mttt) cc_final: 0.7337 (mttp) REVERT: A 289 PHE cc_start: 0.8176 (m-10) cc_final: 0.7853 (m-80) REVERT: A 300 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 316 ASP cc_start: 0.7983 (t0) cc_final: 0.7656 (m-30) REVERT: A 320 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 337 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 339 THR cc_start: 0.8200 (m) cc_final: 0.7965 (p) REVERT: A 375 LYS cc_start: 0.7995 (mttt) cc_final: 0.7595 (ptmm) REVERT: A 383 MET cc_start: 0.7244 (tpp) cc_final: 0.6595 (mmm) REVERT: A 443 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 444 ASN cc_start: 0.8070 (t0) cc_final: 0.7700 (t0) REVERT: A 475 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7546 (mm-40) REVERT: A 479 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7292 (ttp80) REVERT: A 499 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6731 (ttm170) REVERT: A 511 MET cc_start: 0.7124 (tmm) cc_final: 0.6867 (ttp) REVERT: A 580 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6638 (tp30) REVERT: A 587 LEU cc_start: 0.7075 (mm) cc_final: 0.6862 (mp) REVERT: A 591 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7010 (mtpp) REVERT: A 626 ILE cc_start: 0.7594 (mt) cc_final: 0.7342 (tt) REVERT: A 633 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7515 (mtmm) REVERT: A 671 MET cc_start: 0.6558 (ppp) cc_final: 0.6233 (tmm) REVERT: A 678 MET cc_start: 0.7000 (mmm) cc_final: 0.6723 (tmm) REVERT: A 740 PHE cc_start: 0.4007 (t80) cc_final: 0.3626 (t80) REVERT: A 810 MET cc_start: 0.4744 (ptp) cc_final: 0.4191 (ptp) REVERT: A 828 LYS cc_start: 0.7566 (mttt) cc_final: 0.7033 (mmmm) REVERT: A 847 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6413 (mm-30) REVERT: A 877 GLN cc_start: 0.7803 (tt0) cc_final: 0.7145 (tt0) REVERT: A 880 LYS cc_start: 0.7336 (tttm) cc_final: 0.6918 (tttp) REVERT: A 903 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7461 (ttm-80) REVERT: A 966 ASP cc_start: 0.7633 (t0) cc_final: 0.7054 (t0) REVERT: A 972 PHE cc_start: 0.6916 (t80) cc_final: 0.6631 (t80) REVERT: A 989 VAL cc_start: 0.7735 (p) cc_final: 0.7479 (m) REVERT: A 994 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 1007 LYS cc_start: 0.7656 (tttt) cc_final: 0.6981 (tttp) REVERT: A 1033 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 1037 THR cc_start: 0.7911 (t) cc_final: 0.7689 (m) REVERT: A 1044 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5879 (mt-10) REVERT: A 1051 LYS cc_start: 0.8736 (mttm) cc_final: 0.8207 (mttm) REVERT: A 1054 ASN cc_start: 0.8264 (t0) cc_final: 0.7826 (t0) REVERT: A 1060 GLU cc_start: 0.7942 (mm-30) cc_final: 0.6884 (mt-10) REVERT: A 1072 ASP cc_start: 0.7264 (m-30) cc_final: 0.6738 (t0) REVERT: A 1104 MET cc_start: 0.6412 (mtp) cc_final: 0.6195 (ttp) REVERT: A 1123 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7173 (ttp80) REVERT: A 1125 TYR cc_start: 0.6227 (p90) cc_final: 0.5977 (p90) REVERT: A 1134 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6270 (p90) REVERT: A 1169 ARG cc_start: 0.6319 (mtt180) cc_final: 0.5814 (mtt180) REVERT: B 96 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7746 (ttpt) REVERT: B 136 HIS cc_start: 0.7483 (m90) cc_final: 0.7131 (m-70) REVERT: B 150 SER cc_start: 0.7921 (t) cc_final: 0.7570 (m) REVERT: B 160 MET cc_start: 0.7449 (mmt) cc_final: 0.7195 (mmm) REVERT: B 184 LEU cc_start: 0.7460 (tp) cc_final: 0.7208 (tp) REVERT: B 205 MET cc_start: 0.7522 (mmm) cc_final: 0.7307 (mmt) REVERT: B 209 ASP cc_start: 0.7250 (t0) cc_final: 0.6797 (t0) REVERT: B 250 LYS cc_start: 0.7520 (mttt) cc_final: 0.7167 (mttp) REVERT: B 296 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: B 300 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 316 ASP cc_start: 0.8165 (t0) cc_final: 0.7841 (m-30) REVERT: B 320 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 337 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 355 MET cc_start: 0.8089 (tmm) cc_final: 0.7615 (ttp) REVERT: B 383 MET cc_start: 0.7245 (tpp) cc_final: 0.6394 (mmm) REVERT: B 444 ASN cc_start: 0.8028 (t0) cc_final: 0.7691 (t0) REVERT: B 486 ILE cc_start: 0.8045 (mp) cc_final: 0.7814 (mm) REVERT: B 580 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6506 (tp30) REVERT: B 591 LYS cc_start: 0.7312 (mtmt) cc_final: 0.7036 (mtpp) REVERT: B 609 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6973 (mtp180) REVERT: B 621 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6341 (mt-10) REVERT: B 632 LYS cc_start: 0.7595 (ttmt) cc_final: 0.6950 (ttmm) REVERT: B 633 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7671 (mmtm) REVERT: B 678 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6210 (mmm) REVERT: B 810 MET cc_start: 0.4824 (ptp) cc_final: 0.4434 (ptt) REVERT: B 847 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6709 (mm-30) REVERT: B 877 GLN cc_start: 0.7727 (tt0) cc_final: 0.7067 (tt0) REVERT: B 880 LYS cc_start: 0.7319 (ttpp) cc_final: 0.6980 (tttp) REVERT: B 903 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7269 (ttm-80) REVERT: B 926 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5909 (pt0) REVERT: B 938 MET cc_start: 0.7805 (mtp) cc_final: 0.7418 (mtp) REVERT: B 966 ASP cc_start: 0.7336 (t0) cc_final: 0.6716 (t0) REVERT: B 967 MET cc_start: 0.6477 (mmm) cc_final: 0.6261 (mmm) REVERT: B 972 PHE cc_start: 0.7285 (t80) cc_final: 0.6827 (t80) REVERT: B 993 ASP cc_start: 0.7136 (t0) cc_final: 0.6866 (t0) REVERT: B 995 SER cc_start: 0.7683 (p) cc_final: 0.7390 (t) REVERT: B 999 PHE cc_start: 0.7343 (m-80) cc_final: 0.6835 (m-80) REVERT: B 1007 LYS cc_start: 0.7660 (tttt) cc_final: 0.6967 (tttp) REVERT: B 1033 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 1044 GLU cc_start: 0.6382 (mt-10) cc_final: 0.6038 (mt-10) REVERT: B 1051 LYS cc_start: 0.8683 (mttm) cc_final: 0.8183 (mttm) REVERT: B 1054 ASN cc_start: 0.8400 (t0) cc_final: 0.8060 (t0) REVERT: B 1058 THR cc_start: 0.7609 (m) cc_final: 0.7172 (p) REVERT: B 1060 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7021 (mt-10) REVERT: B 1061 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7662 (p) REVERT: B 1072 ASP cc_start: 0.7305 (m-30) cc_final: 0.6732 (t0) REVERT: B 1122 GLU cc_start: 0.7571 (tp30) cc_final: 0.7323 (tp30) REVERT: B 1123 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7499 (ttp80) REVERT: B 1134 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6004 (p90) REVERT: B 1191 ASN cc_start: 0.7549 (t0) cc_final: 0.7110 (p0) outliers start: 43 outliers final: 34 residues processed: 456 average time/residue: 0.3308 time to fit residues: 217.0989 Evaluate side-chains 467 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 427 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.0870 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16492 Z= 0.196 Angle : 0.516 12.197 22364 Z= 0.264 Chirality : 0.041 0.211 2688 Planarity : 0.004 0.047 2750 Dihedral : 3.762 39.556 2186 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 18.41 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 2022 helix: 2.16 (0.13), residues: 1468 sheet: 1.46 (0.64), residues: 82 loop : -0.27 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.005 0.001 HIS B1120 PHE 0.031 0.001 PHE B 769 TYR 0.014 0.001 TYR B1009 ARG 0.010 0.000 ARG A 887 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 438 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7639 (t80) cc_final: 0.7228 (t80) REVERT: A 164 SER cc_start: 0.7906 (m) cc_final: 0.7672 (p) REVERT: A 205 MET cc_start: 0.7572 (mmt) cc_final: 0.7217 (mmt) REVERT: A 209 ASP cc_start: 0.7323 (t0) cc_final: 0.7071 (t0) REVERT: A 250 LYS cc_start: 0.7576 (mttt) cc_final: 0.7329 (mttp) REVERT: A 289 PHE cc_start: 0.8160 (m-10) cc_final: 0.7842 (m-80) REVERT: A 316 ASP cc_start: 0.8024 (t0) cc_final: 0.7711 (m-30) REVERT: A 320 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 337 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 339 THR cc_start: 0.8245 (m) cc_final: 0.8003 (p) REVERT: A 351 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7818 (ttm-80) REVERT: A 375 LYS cc_start: 0.7988 (mttt) cc_final: 0.7601 (ptmm) REVERT: A 383 MET cc_start: 0.7246 (tpp) cc_final: 0.6617 (mmm) REVERT: A 443 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 444 ASN cc_start: 0.8069 (t0) cc_final: 0.7719 (t0) REVERT: A 499 ARG cc_start: 0.6971 (ttm170) cc_final: 0.6732 (ttm170) REVERT: A 511 MET cc_start: 0.7122 (tmm) cc_final: 0.6797 (ttp) REVERT: A 580 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6644 (tp30) REVERT: A 587 LEU cc_start: 0.7054 (mm) cc_final: 0.6844 (mp) REVERT: A 591 LYS cc_start: 0.7352 (mtmt) cc_final: 0.7055 (mtpp) REVERT: A 626 ILE cc_start: 0.7597 (mt) cc_final: 0.7324 (tt) REVERT: A 633 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7520 (mtmm) REVERT: A 671 MET cc_start: 0.6561 (ppp) cc_final: 0.6243 (tmm) REVERT: A 678 MET cc_start: 0.6959 (mmm) cc_final: 0.6691 (tmm) REVERT: A 740 PHE cc_start: 0.3969 (t80) cc_final: 0.3605 (t80) REVERT: A 810 MET cc_start: 0.4731 (ptp) cc_final: 0.4173 (ptp) REVERT: A 828 LYS cc_start: 0.7542 (mttt) cc_final: 0.7081 (mmmm) REVERT: A 847 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6422 (mm-30) REVERT: A 877 GLN cc_start: 0.7785 (tt0) cc_final: 0.7150 (tt0) REVERT: A 880 LYS cc_start: 0.7371 (tttm) cc_final: 0.6935 (tttp) REVERT: A 903 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7434 (ttm-80) REVERT: A 938 MET cc_start: 0.7753 (mtp) cc_final: 0.7333 (mtp) REVERT: A 966 ASP cc_start: 0.7561 (t0) cc_final: 0.7011 (t0) REVERT: A 972 PHE cc_start: 0.6918 (t80) cc_final: 0.6557 (t80) REVERT: A 994 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 1007 LYS cc_start: 0.7651 (tttt) cc_final: 0.6955 (tttp) REVERT: A 1033 GLU cc_start: 0.7729 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 1037 THR cc_start: 0.7900 (t) cc_final: 0.7669 (m) REVERT: A 1044 GLU cc_start: 0.6335 (mt-10) cc_final: 0.5865 (mt-10) REVERT: A 1051 LYS cc_start: 0.8753 (mttm) cc_final: 0.8224 (mttm) REVERT: A 1054 ASN cc_start: 0.8267 (t0) cc_final: 0.7819 (t0) REVERT: A 1060 GLU cc_start: 0.7912 (mm-30) cc_final: 0.6834 (mt-10) REVERT: A 1072 ASP cc_start: 0.7141 (m-30) cc_final: 0.6624 (t0) REVERT: A 1104 MET cc_start: 0.6369 (mtp) cc_final: 0.6101 (ttm) REVERT: A 1123 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7093 (ttp80) REVERT: A 1125 TYR cc_start: 0.6192 (p90) cc_final: 0.5949 (p90) REVERT: A 1134 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.6278 (p90) REVERT: A 1169 ARG cc_start: 0.6327 (mtt180) cc_final: 0.5830 (mtt180) REVERT: A 1191 ASN cc_start: 0.7545 (t0) cc_final: 0.7101 (p0) REVERT: B 96 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7721 (ttpt) REVERT: B 136 HIS cc_start: 0.7486 (m90) cc_final: 0.7134 (m-70) REVERT: B 150 SER cc_start: 0.7935 (t) cc_final: 0.7568 (m) REVERT: B 160 MET cc_start: 0.7438 (mmt) cc_final: 0.7184 (mmm) REVERT: B 184 LEU cc_start: 0.7430 (tp) cc_final: 0.7184 (tp) REVERT: B 205 MET cc_start: 0.7529 (mmm) cc_final: 0.7308 (mmp) REVERT: B 209 ASP cc_start: 0.7260 (t0) cc_final: 0.6771 (t0) REVERT: B 250 LYS cc_start: 0.7529 (mttt) cc_final: 0.7173 (mttp) REVERT: B 296 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: B 300 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7414 (mt-10) REVERT: B 316 ASP cc_start: 0.8149 (t0) cc_final: 0.7824 (m-30) REVERT: B 320 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 337 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 355 MET cc_start: 0.8084 (tmm) cc_final: 0.7583 (ttp) REVERT: B 383 MET cc_start: 0.7233 (tpp) cc_final: 0.6625 (mmm) REVERT: B 444 ASN cc_start: 0.7984 (t0) cc_final: 0.7759 (t0) REVERT: B 486 ILE cc_start: 0.8037 (mp) cc_final: 0.7812 (mm) REVERT: B 580 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6454 (tp30) REVERT: B 591 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7033 (mtpp) REVERT: B 609 ARG cc_start: 0.7307 (mtp180) cc_final: 0.7008 (mtp180) REVERT: B 621 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 626 ILE cc_start: 0.8082 (mt) cc_final: 0.7880 (tt) REVERT: B 632 LYS cc_start: 0.7523 (ttmt) cc_final: 0.6874 (ttmm) REVERT: B 633 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7671 (mmtm) REVERT: B 678 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6193 (mmm) REVERT: B 810 MET cc_start: 0.4803 (ptp) cc_final: 0.4403 (ptt) REVERT: B 847 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 877 GLN cc_start: 0.7710 (tt0) cc_final: 0.7076 (tt0) REVERT: B 880 LYS cc_start: 0.7315 (ttpp) cc_final: 0.6975 (tttp) REVERT: B 903 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7249 (ttm-80) REVERT: B 966 ASP cc_start: 0.7329 (t0) cc_final: 0.6733 (t0) REVERT: B 967 MET cc_start: 0.6463 (mmm) cc_final: 0.6261 (mmm) REVERT: B 972 PHE cc_start: 0.7271 (t80) cc_final: 0.6769 (t80) REVERT: B 993 ASP cc_start: 0.7134 (t0) cc_final: 0.6861 (t0) REVERT: B 995 SER cc_start: 0.7705 (p) cc_final: 0.7391 (t) REVERT: B 999 PHE cc_start: 0.7333 (m-80) cc_final: 0.6819 (m-80) REVERT: B 1007 LYS cc_start: 0.7683 (tttt) cc_final: 0.6970 (tttp) REVERT: B 1033 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 1044 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6113 (mt-10) REVERT: B 1051 LYS cc_start: 0.8695 (mttm) cc_final: 0.8226 (mttm) REVERT: B 1054 ASN cc_start: 0.8373 (t0) cc_final: 0.8042 (t0) REVERT: B 1058 THR cc_start: 0.7612 (m) cc_final: 0.7195 (p) REVERT: B 1060 GLU cc_start: 0.7976 (mm-30) cc_final: 0.6956 (mt-10) REVERT: B 1061 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 1072 ASP cc_start: 0.7298 (m-30) cc_final: 0.6755 (t0) REVERT: B 1123 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7476 (ttp80) REVERT: B 1134 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.5996 (p90) REVERT: B 1191 ASN cc_start: 0.7535 (t0) cc_final: 0.7102 (p0) outliers start: 42 outliers final: 34 residues processed: 458 average time/residue: 0.3296 time to fit residues: 213.7578 Evaluate side-chains 472 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 433 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 981 HIS A1064 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130771 restraints weight = 21951.919| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.67 r_work: 0.3456 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16492 Z= 0.166 Angle : 0.504 12.249 22364 Z= 0.257 Chirality : 0.040 0.296 2688 Planarity : 0.004 0.047 2750 Dihedral : 3.654 39.096 2186 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.93 % Allowed : 18.75 % Favored : 79.32 % 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: 2.52 (0.19), residues: 2022 helix: 2.26 (0.13), residues: 1466 sheet: 1.57 (0.64), residues: 82 loop : -0.19 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 278 HIS 0.003 0.001 HIS B 676 PHE 0.031 0.001 PHE B 769 TYR 0.014 0.001 TYR B1009 ARG 0.010 0.000 ARG A 887 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4540.06 seconds wall clock time: 82 minutes 36.74 seconds (4956.74 seconds total)