Starting phenix.real_space_refine on Thu Mar 14 18:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsu_30167/03_2024/7bsu_30167_trim_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 Be 1 3.05 5 C 6076 2.51 5 N 1503 2.21 5 O 1695 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A ASP 752": "OD1" <-> "OD2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9325 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6591 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 791} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'AH2': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.39, per 1000 atoms: 0.58 Number of scatterers: 9325 At special positions: 0 Unit cell: (114.54, 83.83, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 1695 8.00 N 1503 7.00 C 6076 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 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 Links applied NAG-ASN " NAG C 404 " - " ASN C 294 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 6 sheets defined 31.5% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.987A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.583A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.508A pdb=" N LEU A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 4.241A pdb=" N THR A 100 " --> pdb=" O PHE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.842A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.543A pdb=" N ILE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.563A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.312A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.546A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 712 through 715 No H-bonds generated for 'chain 'A' and resid 712 through 715' Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.542A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 804 removed outlier: 3.511A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.523A pdb=" N LYS A 856 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 857 " --> pdb=" O HIS A 854 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 889 removed outlier: 3.549A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 878 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 905 through 913 removed outlier: 3.716A pdb=" N THR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 926 No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 953 through 974 removed outlier: 3.571A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1008 Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1030 through 1040 removed outlier: 3.528A pdb=" N VAL A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 3.797A pdb=" N SER A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1067 No H-bonds generated for 'chain 'A' and resid 1064 through 1067' Processing helix chain 'A' and resid 1070 through 1073 No H-bonds generated for 'chain 'A' and resid 1070 through 1073' Processing helix chain 'A' and resid 1080 through 1087 removed outlier: 3.743A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.705A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.735A pdb=" N THR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 324 through 345 removed outlier: 3.592A pdb=" N ILE C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 125 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.963A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 847 through 849 removed outlier: 3.938A pdb=" N TYR A 847 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 813 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 815 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 785 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.203A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 104 through 110 removed outlier: 3.517A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 513 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: 2.57 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2858 1.34 - 1.46: 2021 1.46 - 1.58: 4602 1.58 - 1.70: 3 1.70 - 1.82: 71 Bond restraints: 9555 Sorted by residual: bond pdb=" F3 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.529 1.763 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.535 1.766 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.542 1.767 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CG BFD A 409 " pdb=" OD1 BFD A 409 " ideal model delta sigma weight residual 1.269 1.447 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C17 P5S A1101 " pdb=" O19 P5S A1101 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 9550 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.13: 262 107.13 - 113.90: 5418 113.90 - 120.67: 3887 120.67 - 127.43: 3292 127.43 - 134.20: 98 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N ILE A 385 " pdb=" CA ILE A 385 " pdb=" C ILE A 385 " ideal model delta sigma weight residual 113.71 107.71 6.00 9.50e-01 1.11e+00 3.99e+01 angle pdb=" N ILE A 293 " pdb=" CA ILE A 293 " pdb=" C ILE A 293 " ideal model delta sigma weight residual 113.42 108.88 4.54 1.17e+00 7.31e-01 1.51e+01 angle pdb=" OG P5S A1101 " pdb=" P12 P5S A1101 " pdb=" O16 P5S A1101 " ideal model delta sigma weight residual 98.42 110.01 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 P5S A1101 " pdb=" P12 P5S A1101 " pdb=" O15 P5S A1101 " ideal model delta sigma weight residual 120.39 109.61 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C THR A 408 " pdb=" N BFD A 409 " pdb=" CA BFD A 409 " ideal model delta sigma weight residual 121.70 127.50 -5.80 1.80e+00 3.09e-01 1.04e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 5232 25.13 - 50.25: 383 50.25 - 75.38: 79 75.38 - 100.50: 19 100.50 - 125.63: 13 Dihedral angle restraints: 5726 sinusoidal: 2384 harmonic: 3342 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual -86.00 -49.28 -36.72 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CA THR C 263 " pdb=" C THR C 263 " pdb=" N ALA C 264 " pdb=" CA ALA C 264 " ideal model delta harmonic sigma weight residual 180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C22 P5S A1101 " pdb=" C23 P5S A1101 " pdb=" C24 P5S A1101 " pdb=" C25 P5S A1101 " ideal model delta sinusoidal sigma weight residual -179.61 -53.98 -125.63 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 5723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1282 0.060 - 0.120: 171 0.120 - 0.180: 5 0.180 - 0.240: 2 0.240 - 0.299: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2 P5S A1101 " pdb=" C1 P5S A1101 " pdb=" C3 P5S A1101 " pdb=" O37 P5S A1101 " both_signs ideal model delta sigma weight residual False 2.32 2.54 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA BFD A 409 " pdb=" N BFD A 409 " pdb=" C BFD A 409 " pdb=" CB BFD A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1458 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.349 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " 0.188 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" C7 NAG C 405 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.181 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG C 401 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.144 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 29 2.28 - 2.94: 4681 2.94 - 3.59: 12190 3.59 - 4.25: 22823 4.25 - 4.90: 38618 Nonbonded interactions: 78341 Sorted by model distance: nonbonded pdb=" F2 BFD A 409 " pdb=" ND2 ASN A 819 " model vdw 1.626 2.470 nonbonded pdb=" O4 NAG C 401 " pdb=" O5 NAG C 402 " model vdw 1.876 2.440 nonbonded pdb=" F1 BFD A 409 " pdb="MG MG A1100 " model vdw 1.976 2.120 nonbonded pdb=" O LEU A 162 " pdb=" OG1 THR A 193 " model vdw 2.003 2.440 nonbonded pdb=" OG SER A 282 " pdb=" OE2 GLU A 398 " model vdw 2.008 2.440 ... (remaining 78336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.030 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.006 0.234 9555 Z= 0.370 Angle : 0.603 11.586 12957 Z= 0.325 Chirality : 0.041 0.299 1461 Planarity : 0.010 0.297 1609 Dihedral : 19.316 125.631 3561 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 7.59 % Allowed : 20.79 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -6.52 (0.16), residues: 1125 helix: -5.01 (0.09), residues: 482 sheet: -3.22 (0.37), residues: 149 loop : -3.81 (0.21), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.008 0.001 PHE A 72 TYR 0.011 0.001 TYR C 134 ARG 0.001 0.000 ARG A 843 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 130 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8365 (tttm) cc_final: 0.8111 (ttmt) REVERT: A 126 TYR cc_start: 0.8551 (m-80) cc_final: 0.8272 (m-80) REVERT: A 206 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7367 (mmt90) REVERT: A 213 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8592 (mm110) REVERT: A 224 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6065 (ttm-80) REVERT: A 266 MET cc_start: 0.7087 (mmp) cc_final: 0.6711 (ttt) REVERT: A 382 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8019 (t70) REVERT: C 200 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8248 (tttt) REVERT: C 279 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (mttt) outliers start: 77 outliers final: 64 residues processed: 197 average time/residue: 0.2346 time to fit residues: 62.3094 Evaluate side-chains 188 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 122 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 38 GLN A 43 ASN A 59 ASN A 63 GLN A 114 HIS A 275 GLN A 386 ASN A 397 ASN A 653 GLN A 694 ASN A 744 HIS A 745 GLN A 761 ASN A 794 GLN A 828 HIS A 862 HIS A 864 HIS A 872 HIS A 875 GLN A 928 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 152 ASN C 216 ASN ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9555 Z= 0.282 Angle : 0.658 8.581 12957 Z= 0.332 Chirality : 0.046 0.259 1461 Planarity : 0.005 0.052 1609 Dihedral : 14.862 118.683 1495 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 7.00 % Allowed : 20.00 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -5.07 (0.20), residues: 1125 helix: -3.98 (0.14), residues: 475 sheet: -2.38 (0.39), residues: 156 loop : -2.90 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 PHE 0.014 0.002 PHE A 995 TYR 0.014 0.002 TYR C 121 ARG 0.003 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 123 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7733 (m-80) cc_final: 0.7293 (m-80) REVERT: A 126 TYR cc_start: 0.8413 (m-80) cc_final: 0.8058 (m-80) REVERT: A 135 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7521 (ttp80) REVERT: A 142 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6928 (mtpp) REVERT: A 224 ARG cc_start: 0.6716 (ttm170) cc_final: 0.6034 (ttm-80) REVERT: A 266 MET cc_start: 0.7055 (mmp) cc_final: 0.6670 (ttt) REVERT: A 382 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8096 (t70) REVERT: A 777 GLN cc_start: 0.8246 (mt0) cc_final: 0.7883 (mt0) REVERT: A 926 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8748 (pp) REVERT: C 59 LEU cc_start: 0.8188 (tt) cc_final: 0.7530 (mt) REVERT: C 200 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8248 (tttm) REVERT: C 228 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7986 (mmtp) outliers start: 71 outliers final: 50 residues processed: 186 average time/residue: 0.2278 time to fit residues: 58.2611 Evaluate side-chains 170 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 117 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 0.0020 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 114 HIS A 745 GLN A 761 ASN A1051 GLN ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9555 Z= 0.152 Angle : 0.555 8.568 12957 Z= 0.279 Chirality : 0.042 0.267 1461 Planarity : 0.004 0.049 1609 Dihedral : 11.958 104.499 1438 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.40 % Allowed : 20.89 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.81 (0.22), residues: 1125 helix: -2.74 (0.19), residues: 470 sheet: -1.81 (0.41), residues: 162 loop : -2.41 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.007 0.001 HIS A 929 PHE 0.012 0.001 PHE A 995 TYR 0.018 0.001 TYR A 722 ARG 0.003 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 136 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7553 (m-80) cc_final: 0.7008 (m-80) REVERT: A 126 TYR cc_start: 0.8308 (m-80) cc_final: 0.7930 (m-80) REVERT: A 135 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7583 (tmm-80) REVERT: A 206 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7650 (mmt90) REVERT: A 224 ARG cc_start: 0.6657 (ttm170) cc_final: 0.6019 (ttm-80) REVERT: A 266 MET cc_start: 0.7026 (mmp) cc_final: 0.6669 (ttt) REVERT: A 926 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8612 (pp) REVERT: A 1050 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: C 59 LEU cc_start: 0.8095 (tt) cc_final: 0.7572 (mt) REVERT: C 200 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8205 (tttm) REVERT: C 228 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7979 (mmtp) outliers start: 65 outliers final: 46 residues processed: 185 average time/residue: 0.2233 time to fit residues: 56.6597 Evaluate side-chains 167 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 119 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 0.0070 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 106 GLN A 114 HIS ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN A 745 GLN A 761 ASN A1051 GLN A1089 ASN ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9555 Z= 0.257 Angle : 0.589 7.884 12957 Z= 0.297 Chirality : 0.045 0.308 1461 Planarity : 0.004 0.051 1609 Dihedral : 10.927 88.602 1417 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.80 % Allowed : 20.69 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.22 (0.23), residues: 1125 helix: -2.19 (0.21), residues: 477 sheet: -1.35 (0.43), residues: 156 loop : -2.22 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.013 0.001 PHE A1055 TYR 0.014 0.001 TYR A 311 ARG 0.003 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 121 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7616 (m-80) cc_final: 0.7040 (m-80) REVERT: A 58 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7808 (ttmm) REVERT: A 126 TYR cc_start: 0.8313 (m-80) cc_final: 0.7902 (m-80) REVERT: A 135 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7549 (tmm-80) REVERT: A 142 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6790 (mtpp) REVERT: A 206 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7481 (mmt90) REVERT: A 224 ARG cc_start: 0.6688 (ttm170) cc_final: 0.6058 (ttm-80) REVERT: A 266 MET cc_start: 0.7090 (mmp) cc_final: 0.6790 (ttt) REVERT: A 281 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7984 (ptm-80) REVERT: A 359 MET cc_start: 0.9092 (ttp) cc_final: 0.8873 (ttm) REVERT: A 926 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 1050 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: A 1089 ASN cc_start: 0.6820 (m-40) cc_final: 0.6617 (m110) REVERT: C 59 LEU cc_start: 0.8039 (tt) cc_final: 0.7526 (mt) REVERT: C 200 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8235 (tttm) REVERT: C 228 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7981 (mmtp) outliers start: 69 outliers final: 53 residues processed: 175 average time/residue: 0.2389 time to fit residues: 57.0103 Evaluate side-chains 173 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A 761 ASN A1051 GLN C 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9555 Z= 0.242 Angle : 0.571 7.804 12957 Z= 0.287 Chirality : 0.045 0.325 1461 Planarity : 0.004 0.046 1609 Dihedral : 10.420 86.990 1417 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 7.09 % Allowed : 20.89 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.84 (0.24), residues: 1125 helix: -1.80 (0.22), residues: 479 sheet: -1.16 (0.44), residues: 149 loop : -2.09 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.013 0.001 PHE A1055 TYR 0.012 0.001 TYR A 311 ARG 0.003 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 118 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7526 (m-80) cc_final: 0.6927 (m-80) REVERT: A 58 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7801 (ttmm) REVERT: A 126 TYR cc_start: 0.8327 (m-80) cc_final: 0.7942 (m-80) REVERT: A 135 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7556 (tmm-80) REVERT: A 142 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6803 (mtpp) REVERT: A 224 ARG cc_start: 0.6616 (ttm170) cc_final: 0.6005 (ttm-80) REVERT: A 266 MET cc_start: 0.7094 (mmp) cc_final: 0.6747 (ttt) REVERT: A 281 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8165 (ptm-80) REVERT: A 926 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 1050 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: A 1089 ASN cc_start: 0.6771 (m-40) cc_final: 0.6531 (m110) REVERT: C 59 LEU cc_start: 0.8012 (tt) cc_final: 0.7506 (mt) REVERT: C 200 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8229 (tttm) REVERT: C 228 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7968 (mmtp) outliers start: 72 outliers final: 57 residues processed: 176 average time/residue: 0.2326 time to fit residues: 55.7065 Evaluate side-chains 175 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 114 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A 761 ASN A1051 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9555 Z= 0.296 Angle : 0.592 7.527 12957 Z= 0.297 Chirality : 0.046 0.307 1461 Planarity : 0.004 0.048 1609 Dihedral : 10.155 86.759 1414 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 7.68 % Allowed : 20.89 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.70 (0.24), residues: 1125 helix: -1.64 (0.22), residues: 480 sheet: -1.11 (0.44), residues: 149 loop : -2.05 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.013 0.001 PHE A1055 TYR 0.014 0.001 TYR A 311 ARG 0.002 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 116 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7613 (m-80) cc_final: 0.6905 (m-80) REVERT: A 126 TYR cc_start: 0.8278 (m-80) cc_final: 0.7945 (m-80) REVERT: A 135 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7542 (tmm-80) REVERT: A 142 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6915 (mtpp) REVERT: A 206 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7526 (mmt90) REVERT: A 224 ARG cc_start: 0.6566 (ttm170) cc_final: 0.5954 (ttm-80) REVERT: A 266 MET cc_start: 0.7109 (mmp) cc_final: 0.6721 (ttt) REVERT: A 281 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8022 (ptm-80) REVERT: A 926 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 1089 ASN cc_start: 0.6749 (m-40) cc_final: 0.6478 (m110) REVERT: C 59 LEU cc_start: 0.8049 (tt) cc_final: 0.7543 (mt) REVERT: C 200 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8249 (tttm) REVERT: C 228 LYS cc_start: 0.8257 (mmmm) cc_final: 0.8013 (mmtp) outliers start: 78 outliers final: 63 residues processed: 178 average time/residue: 0.1982 time to fit residues: 48.8035 Evaluate side-chains 178 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 112 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A1051 GLN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9555 Z= 0.167 Angle : 0.529 7.258 12957 Z= 0.267 Chirality : 0.042 0.262 1461 Planarity : 0.004 0.046 1609 Dihedral : 9.366 84.265 1408 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.90 % Allowed : 21.97 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.32 (0.24), residues: 1125 helix: -1.25 (0.23), residues: 475 sheet: -0.90 (0.44), residues: 155 loop : -1.93 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.013 0.001 PHE A1055 TYR 0.013 0.001 TYR A 324 ARG 0.001 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 119 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7468 (m-80) cc_final: 0.6888 (m-80) REVERT: A 58 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7818 (mtpp) REVERT: A 126 TYR cc_start: 0.8203 (m-80) cc_final: 0.7835 (m-80) REVERT: A 206 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7661 (mmt90) REVERT: A 224 ARG cc_start: 0.6411 (ttm170) cc_final: 0.5863 (ttm-80) REVERT: A 266 MET cc_start: 0.7027 (mmp) cc_final: 0.6661 (ttt) REVERT: A 281 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8212 (ptm-80) REVERT: A 926 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 979 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7429 (mm110) REVERT: A 1050 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: A 1089 ASN cc_start: 0.6667 (m-40) cc_final: 0.6446 (m110) REVERT: C 59 LEU cc_start: 0.8001 (tt) cc_final: 0.7488 (mt) REVERT: C 79 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: C 200 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8220 (tttm) outliers start: 70 outliers final: 53 residues processed: 175 average time/residue: 0.2297 time to fit residues: 55.0724 Evaluate side-chains 172 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 114 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A1051 GLN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9555 Z= 0.151 Angle : 0.511 8.498 12957 Z= 0.259 Chirality : 0.042 0.261 1461 Planarity : 0.004 0.049 1609 Dihedral : 8.869 79.635 1404 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.11 % Allowed : 22.56 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.98 (0.25), residues: 1125 helix: -0.88 (0.24), residues: 476 sheet: -0.88 (0.43), residues: 163 loop : -1.82 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.013 0.001 PHE A1055 TYR 0.013 0.001 TYR A 324 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 116 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7367 (m-80) cc_final: 0.6872 (m-80) REVERT: A 58 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7793 (mtpp) REVERT: A 126 TYR cc_start: 0.8217 (m-80) cc_final: 0.7738 (m-80) REVERT: A 185 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7964 (mptt) REVERT: A 206 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7666 (mmt90) REVERT: A 224 ARG cc_start: 0.6249 (ttm170) cc_final: 0.5735 (ttm-80) REVERT: A 266 MET cc_start: 0.6993 (mmp) cc_final: 0.6654 (ttt) REVERT: A 281 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8204 (ptm-80) REVERT: A 926 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8580 (pp) REVERT: A 979 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7342 (mm110) REVERT: A 1050 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: C 59 LEU cc_start: 0.8032 (tt) cc_final: 0.7514 (mt) REVERT: C 200 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8202 (tttm) outliers start: 62 outliers final: 50 residues processed: 167 average time/residue: 0.2368 time to fit residues: 53.7261 Evaluate side-chains 168 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A1051 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9555 Z= 0.157 Angle : 0.511 6.893 12957 Z= 0.259 Chirality : 0.042 0.250 1461 Planarity : 0.003 0.046 1609 Dihedral : 8.582 74.512 1402 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.91 % Allowed : 22.46 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.73 (0.25), residues: 1125 helix: -0.66 (0.24), residues: 475 sheet: -0.73 (0.44), residues: 161 loop : -1.71 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.011 0.001 PHE A 995 TYR 0.013 0.001 TYR A 324 ARG 0.001 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 117 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7292 (m-80) cc_final: 0.6775 (m-80) REVERT: A 58 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7804 (mtpp) REVERT: A 126 TYR cc_start: 0.8231 (m-80) cc_final: 0.7856 (m-80) REVERT: A 142 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6768 (mtpp) REVERT: A 185 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7992 (mptt) REVERT: A 206 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7683 (mmt90) REVERT: A 266 MET cc_start: 0.6980 (mmp) cc_final: 0.6565 (ttt) REVERT: A 281 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8211 (ptm-80) REVERT: A 297 PHE cc_start: 0.8070 (m-80) cc_final: 0.7829 (m-80) REVERT: A 926 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 979 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7317 (mm110) REVERT: A 1050 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: C 59 LEU cc_start: 0.8032 (tt) cc_final: 0.7491 (mt) REVERT: C 200 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8196 (tttm) outliers start: 60 outliers final: 49 residues processed: 166 average time/residue: 0.2446 time to fit residues: 54.5928 Evaluate side-chains 165 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 111 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A1051 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9555 Z= 0.244 Angle : 0.554 8.195 12957 Z= 0.279 Chirality : 0.044 0.263 1461 Planarity : 0.004 0.049 1609 Dihedral : 8.728 73.163 1402 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.62 % Allowed : 22.86 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.78 (0.25), residues: 1125 helix: -0.78 (0.23), residues: 479 sheet: -0.65 (0.47), residues: 147 loop : -1.66 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 PHE 0.012 0.001 PHE A1055 TYR 0.013 0.001 TYR A 311 ARG 0.002 0.000 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 111 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7490 (m-80) cc_final: 0.6934 (m-80) REVERT: A 142 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6679 (mtpp) REVERT: A 206 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7702 (mmt90) REVERT: A 266 MET cc_start: 0.7033 (mmp) cc_final: 0.6684 (ttt) REVERT: A 281 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8145 (ptm-80) REVERT: A 926 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8683 (pp) REVERT: A 979 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7586 (mm110) REVERT: A 1050 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: C 59 LEU cc_start: 0.8036 (tt) cc_final: 0.7502 (mt) REVERT: C 200 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8234 (tttm) outliers start: 57 outliers final: 50 residues processed: 158 average time/residue: 0.2240 time to fit residues: 48.7783 Evaluate side-chains 164 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 109 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A1051 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100072 restraints weight = 10529.090| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.68 r_work: 0.2793 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9555 Z= 0.173 Angle : 0.516 6.544 12957 Z= 0.262 Chirality : 0.042 0.252 1461 Planarity : 0.004 0.045 1609 Dihedral : 8.353 70.181 1402 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.81 % Allowed : 22.96 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.55 (0.25), residues: 1125 helix: -0.55 (0.24), residues: 474 sheet: -0.63 (0.47), residues: 148 loop : -1.54 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.011 0.001 PHE A 995 TYR 0.012 0.001 TYR A 324 ARG 0.002 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.91 seconds wall clock time: 42 minutes 17.47 seconds (2537.47 seconds total)