Starting phenix.real_space_refine on Sun Apr 7 18:07:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxc_17264/04_2024/8oxc_17264_updated.pdb" } resolution = 2.58 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= 1.000 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7199 2.51 5 N 1832 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1116": "OD1" <-> "OD2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 248": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11143 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, 'PIE': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 6.07, per 1000 atoms: 0.54 Number of scatterers: 11143 At special positions: 0 Unit cell: (85.404, 89.933, 178.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2055 8.00 N 1832 7.00 C 7199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.05 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.9 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 8 sheets defined 44.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.812A pdb=" N GLN A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 116 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 141 through 174 removed outlier: 3.763A pdb=" N LEU A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.639A pdb=" N LEU A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 154 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 155 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 162 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 164 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 170 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.908A pdb=" N GLN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.503A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 332 through 365 removed outlier: 3.635A pdb=" N THR A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 395 removed outlier: 4.117A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.610A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 533 Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 628 removed outlier: 4.063A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 758 through 770 removed outlier: 3.587A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 770 " --> pdb=" O HIS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 840 through 858 Processing helix chain 'A' and resid 870 through 884 removed outlier: 3.521A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.843A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.664A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 971 removed outlier: 3.994A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 5.190A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1016 through 1023 Processing helix chain 'A' and resid 1030 through 1056 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.519A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1113 removed outlier: 3.720A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 3.528A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix removed outlier: 3.515A pdb=" N ALA A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1181 Processing helix chain 'B' and resid 50 through 73 removed outlier: 4.053A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 150 No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 323 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.877A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.835A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 277 through 281 removed outlier: 4.197A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 906 through 909 removed outlier: 6.432A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.807A pdb=" N CYS A 469 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 658 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER A 580 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 569 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 5.839A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.166A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1167 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: 3.37 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1783 1.31 - 1.44: 3165 1.44 - 1.56: 6351 1.56 - 1.69: 7 1.69 - 1.81: 83 Bond restraints: 11389 Sorted by residual: bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.590 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CA ASP A 260 " pdb=" CB ASP A 260 " ideal model delta sigma weight residual 1.531 1.577 -0.046 3.12e-02 1.03e+03 2.21e+00 bond pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.410 1.438 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.89e+00 ... (remaining 11384 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 183 105.80 - 112.86: 6078 112.86 - 119.92: 3797 119.92 - 126.97: 5238 126.97 - 134.03: 131 Bond angle restraints: 15427 Sorted by residual: angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.34 5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" C ASN A 472 " pdb=" CA ASN A 472 " pdb=" CB ASN A 472 " ideal model delta sigma weight residual 110.42 116.17 -5.75 1.99e+00 2.53e-01 8.34e+00 angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 105.66 7.29 3.00e+00 1.11e-01 5.91e+00 angle pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 113.24 106.06 7.18 3.00e+00 1.11e-01 5.74e+00 angle pdb=" N ASN A 472 " pdb=" CA ASN A 472 " pdb=" C ASN A 472 " ideal model delta sigma weight residual 110.80 106.22 4.58 2.13e+00 2.20e-01 4.63e+00 ... (remaining 15422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 6374 23.57 - 47.15: 385 47.15 - 70.72: 45 70.72 - 94.30: 18 94.30 - 117.87: 6 Dihedral angle restraints: 6828 sinusoidal: 2836 harmonic: 3992 Sorted by residual: dihedral pdb=" CA THR A 398 " pdb=" C THR A 398 " pdb=" N MET A 399 " pdb=" CA MET A 399 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 170.84 117.87 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -68.44 116.06 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 6825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1413 0.049 - 0.098: 258 0.098 - 0.146: 57 0.146 - 0.195: 3 0.195 - 0.244: 1 Chirality restraints: 1732 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB THR A1152 " pdb=" CA THR A1152 " pdb=" OG1 THR A1152 " pdb=" CG2 THR A1152 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 5.77e-01 ... (remaining 1729 not shown) Planarity restraints: 1941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO A 793 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 170 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 109 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.032 5.00e-02 4.00e+02 ... (remaining 1938 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 8497 3.11 - 3.70: 17472 3.70 - 4.30: 26877 4.30 - 4.90: 43746 Nonbonded interactions: 96692 Sorted by model distance: nonbonded pdb=" O3 NAG C 2 " pdb=" O2 BMA C 3 " model vdw 1.911 2.440 nonbonded pdb=" O GLN A 65 " pdb=" OH TYR A 92 " model vdw 1.945 2.440 nonbonded pdb=" O THR A 978 " pdb=" OH TYR A1069 " model vdw 1.974 2.440 nonbonded pdb=" OG1 THR A 576 " pdb=" O TYR A 588 " model vdw 2.017 2.440 nonbonded pdb=" OD1 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 2.019 3.040 ... (remaining 96687 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=0.00 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 15.210 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11389 Z= 0.191 Angle : 0.539 7.293 15427 Z= 0.276 Chirality : 0.040 0.244 1732 Planarity : 0.004 0.063 1938 Dihedral : 15.405 117.869 4247 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.08 % Allowed : 0.00 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1349 helix: 0.03 (0.21), residues: 592 sheet: -0.17 (0.38), residues: 190 loop : -0.86 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 359 PHE 0.021 0.001 PHE A 113 TYR 0.025 0.001 TYR A 588 ARG 0.004 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8334 (mttt) cc_final: 0.7938 (mttt) REVERT: A 195 GLN cc_start: 0.7846 (mt0) cc_final: 0.7436 (mt0) REVERT: A 1055 TYR cc_start: 0.6542 (m-80) cc_final: 0.5657 (m-80) REVERT: A 1091 ASP cc_start: 0.7607 (m-30) cc_final: 0.7257 (m-30) REVERT: B 186 PHE cc_start: 0.7305 (m-80) cc_final: 0.7060 (m-80) REVERT: B 244 ASP cc_start: 0.7393 (t70) cc_final: 0.6580 (t70) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 1.1838 time to fit residues: 221.3063 Evaluate side-chains 125 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 447 GLN A 872 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11389 Z= 0.250 Angle : 0.602 9.227 15427 Z= 0.307 Chirality : 0.045 0.288 1732 Planarity : 0.005 0.056 1938 Dihedral : 10.327 109.169 1629 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.01 % Allowed : 9.52 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1349 helix: 0.38 (0.21), residues: 596 sheet: 0.02 (0.39), residues: 188 loop : -0.84 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 669 HIS 0.003 0.001 HIS A 359 PHE 0.020 0.002 PHE A 666 TYR 0.019 0.002 TYR A 658 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8245 (mttt) cc_final: 0.7828 (mttt) REVERT: A 195 GLN cc_start: 0.7788 (mt0) cc_final: 0.7406 (mt0) REVERT: A 1055 TYR cc_start: 0.6440 (m-10) cc_final: 0.5763 (m-10) REVERT: A 1091 ASP cc_start: 0.7604 (m-30) cc_final: 0.7202 (m-30) REVERT: A 1168 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6601 (pp-130) REVERT: B 59 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7499 (tp) REVERT: B 244 ASP cc_start: 0.7410 (t70) cc_final: 0.6595 (t70) outliers start: 24 outliers final: 13 residues processed: 157 average time/residue: 1.1318 time to fit residues: 194.1886 Evaluate side-chains 134 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 447 GLN A 796 ASN A 852 ASN A 917 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11389 Z= 0.188 Angle : 0.541 9.487 15427 Z= 0.275 Chirality : 0.042 0.284 1732 Planarity : 0.004 0.053 1938 Dihedral : 9.315 106.067 1629 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.76 % Allowed : 11.36 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1349 helix: 0.64 (0.21), residues: 597 sheet: 0.05 (0.39), residues: 185 loop : -0.78 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 510 PHE 0.021 0.001 PHE A 666 TYR 0.013 0.001 TYR A 658 ARG 0.008 0.000 ARG A1141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8255 (mttt) cc_final: 0.7836 (mttt) REVERT: A 195 GLN cc_start: 0.7785 (mt0) cc_final: 0.7395 (mt0) REVERT: A 1055 TYR cc_start: 0.6461 (m-10) cc_final: 0.5908 (m-10) REVERT: A 1168 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6639 (pp-130) outliers start: 33 outliers final: 16 residues processed: 152 average time/residue: 1.1463 time to fit residues: 191.0901 Evaluate side-chains 143 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11389 Z= 0.197 Angle : 0.539 9.584 15427 Z= 0.273 Chirality : 0.042 0.271 1732 Planarity : 0.004 0.051 1938 Dihedral : 8.763 104.492 1629 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.43 % Allowed : 12.11 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1349 helix: 0.75 (0.21), residues: 597 sheet: 0.32 (0.40), residues: 171 loop : -0.85 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 PHE 0.019 0.001 PHE A 666 TYR 0.014 0.001 TYR A 658 ARG 0.007 0.000 ARG A1141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8244 (mttt) cc_final: 0.7836 (mttt) REVERT: A 195 GLN cc_start: 0.7775 (mt0) cc_final: 0.7390 (mt0) REVERT: A 337 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6620 (mmm) REVERT: A 365 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6247 (mt0) REVERT: A 399 MET cc_start: 0.7509 (mmm) cc_final: 0.7179 (mmm) REVERT: A 1055 TYR cc_start: 0.6404 (m-10) cc_final: 0.5787 (m-10) REVERT: A 1091 ASP cc_start: 0.7619 (m-30) cc_final: 0.7241 (m-30) REVERT: A 1142 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: A 1168 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6674 (pp-130) outliers start: 41 outliers final: 19 residues processed: 157 average time/residue: 1.0741 time to fit residues: 184.8983 Evaluate side-chains 144 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 104 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11389 Z= 0.179 Angle : 0.523 9.562 15427 Z= 0.266 Chirality : 0.042 0.269 1732 Planarity : 0.004 0.050 1938 Dihedral : 8.502 106.328 1629 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.51 % Allowed : 13.20 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1349 helix: 0.83 (0.22), residues: 597 sheet: 0.48 (0.39), residues: 185 loop : -0.89 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.002 0.000 HIS A 417 PHE 0.019 0.001 PHE A 666 TYR 0.014 0.001 TYR A 658 ARG 0.006 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8225 (mttt) cc_final: 0.7825 (mttt) REVERT: A 195 GLN cc_start: 0.7755 (mt0) cc_final: 0.7374 (mt0) REVERT: A 330 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7415 (mtp180) REVERT: A 337 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6638 (mmm) REVERT: A 365 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6191 (mt0) REVERT: A 808 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: A 1055 TYR cc_start: 0.6390 (m-10) cc_final: 0.5670 (m-10) REVERT: A 1091 ASP cc_start: 0.7614 (m-30) cc_final: 0.7285 (m-30) REVERT: A 1168 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6683 (pp-130) outliers start: 42 outliers final: 22 residues processed: 150 average time/residue: 1.1065 time to fit residues: 182.5788 Evaluate side-chains 152 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11389 Z= 0.303 Angle : 0.585 9.581 15427 Z= 0.298 Chirality : 0.044 0.265 1732 Planarity : 0.004 0.052 1938 Dihedral : 8.283 107.540 1629 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.17 % Allowed : 14.62 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1349 helix: 0.56 (0.21), residues: 598 sheet: 0.40 (0.38), residues: 188 loop : -1.00 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 669 HIS 0.003 0.001 HIS A 417 PHE 0.019 0.002 PHE A 961 TYR 0.018 0.002 TYR A1055 ARG 0.006 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8261 (mttt) cc_final: 0.7854 (mttt) REVERT: A 195 GLN cc_start: 0.7808 (mt0) cc_final: 0.7418 (mt0) REVERT: A 337 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6715 (mmm) REVERT: A 365 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: A 808 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: A 1055 TYR cc_start: 0.6124 (m-10) cc_final: 0.5268 (m-10) REVERT: A 1091 ASP cc_start: 0.7642 (m-30) cc_final: 0.7270 (m-30) REVERT: A 1168 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6703 (pp-130) outliers start: 38 outliers final: 20 residues processed: 159 average time/residue: 1.0682 time to fit residues: 186.5695 Evaluate side-chains 145 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0980 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11389 Z= 0.162 Angle : 0.525 9.635 15427 Z= 0.267 Chirality : 0.042 0.408 1732 Planarity : 0.004 0.052 1938 Dihedral : 7.851 103.184 1629 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1349 helix: 0.83 (0.22), residues: 597 sheet: 0.46 (0.38), residues: 192 loop : -0.91 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.002 0.000 HIS A 449 PHE 0.017 0.001 PHE A 666 TYR 0.016 0.001 TYR A 658 ARG 0.006 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8196 (mttt) cc_final: 0.7796 (mttt) REVERT: A 195 GLN cc_start: 0.7793 (mt0) cc_final: 0.7414 (mt0) REVERT: A 330 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7418 (mtp180) REVERT: A 337 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6598 (mmm) REVERT: A 365 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6055 (mt0) REVERT: A 1055 TYR cc_start: 0.6115 (m-10) cc_final: 0.5258 (m-10) REVERT: A 1168 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6679 (pp-130) REVERT: B 307 ARG cc_start: 0.7265 (mtp85) cc_final: 0.6998 (mtt-85) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 1.0905 time to fit residues: 179.3593 Evaluate side-chains 145 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.003 0.058 11389 Z= 0.199 Angle : 0.544 9.516 15427 Z= 0.275 Chirality : 0.042 0.288 1732 Planarity : 0.004 0.051 1938 Dihedral : 7.664 107.443 1629 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.51 % Allowed : 16.37 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1349 helix: 0.76 (0.22), residues: 604 sheet: 0.49 (0.38), residues: 186 loop : -0.90 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.002 0.000 HIS A 417 PHE 0.014 0.001 PHE A 666 TYR 0.016 0.001 TYR A 658 ARG 0.004 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8221 (mttt) cc_final: 0.7819 (mttt) REVERT: A 195 GLN cc_start: 0.7814 (mt0) cc_final: 0.7439 (mt0) REVERT: A 330 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7522 (mtm180) REVERT: A 337 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6638 (mmm) REVERT: A 365 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6001 (mt0) REVERT: A 808 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: A 1055 TYR cc_start: 0.6124 (m-10) cc_final: 0.5290 (m-10) REVERT: A 1168 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6684 (pp-130) REVERT: B 263 THR cc_start: 0.8507 (p) cc_final: 0.8276 (p) REVERT: B 277 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 1.0903 time to fit residues: 179.5974 Evaluate side-chains 143 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 79 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 11389 Z= 0.157 Angle : 0.519 9.804 15427 Z= 0.263 Chirality : 0.041 0.269 1732 Planarity : 0.004 0.050 1938 Dihedral : 7.288 103.357 1629 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.59 % Allowed : 16.62 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1349 helix: 0.84 (0.22), residues: 607 sheet: 0.50 (0.37), residues: 192 loop : -0.84 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.002 0.000 HIS A1039 PHE 0.012 0.001 PHE A 666 TYR 0.016 0.001 TYR A 658 ARG 0.004 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8201 (mttt) cc_final: 0.7800 (mttt) REVERT: A 195 GLN cc_start: 0.7800 (mt0) cc_final: 0.7542 (mt0) REVERT: A 330 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7441 (mtp180) REVERT: A 337 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6591 (mmm) REVERT: A 365 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.5860 (mt0) REVERT: A 808 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: A 1010 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7824 (mtpt) REVERT: A 1055 TYR cc_start: 0.6092 (m-10) cc_final: 0.5329 (m-10) REVERT: A 1168 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6653 (pp-130) REVERT: A 1180 LYS cc_start: 0.7367 (tptt) cc_final: 0.6714 (ttmt) REVERT: B 59 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7324 (tp) outliers start: 31 outliers final: 18 residues processed: 162 average time/residue: 1.1535 time to fit residues: 204.9592 Evaluate side-chains 154 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 123 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11389 Z= 0.285 Angle : 0.997 59.183 15427 Z= 0.520 Chirality : 0.045 0.356 1732 Planarity : 0.005 0.092 1938 Dihedral : 7.348 103.598 1629 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.26 % Allowed : 17.54 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1349 helix: 0.84 (0.22), residues: 607 sheet: 0.52 (0.37), residues: 192 loop : -0.83 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.002 0.000 HIS A 449 PHE 0.012 0.001 PHE A 666 TYR 0.016 0.001 TYR A 658 ARG 0.012 0.000 ARG A1141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8211 (mttt) cc_final: 0.7810 (mttt) REVERT: A 195 GLN cc_start: 0.7806 (mt0) cc_final: 0.7547 (mt0) REVERT: A 330 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7519 (mtm180) REVERT: A 337 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6607 (mmm) REVERT: A 365 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.5870 (mt0) REVERT: A 808 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 1010 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7820 (mtpt) REVERT: A 1055 TYR cc_start: 0.6107 (m-10) cc_final: 0.5342 (m-10) REVERT: A 1168 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6666 (pp-130) REVERT: A 1180 LYS cc_start: 0.7373 (tptt) cc_final: 0.6758 (ttmt) REVERT: B 59 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7342 (tp) REVERT: B 139 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7048 (t70) outliers start: 27 outliers final: 15 residues processed: 150 average time/residue: 1.1210 time to fit residues: 183.8051 Evaluate side-chains 152 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.182031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127301 restraints weight = 11694.671| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.27 r_work: 0.3602 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11389 Z= 0.282 Angle : 0.996 58.972 15427 Z= 0.520 Chirality : 0.045 0.356 1732 Planarity : 0.005 0.091 1938 Dihedral : 7.348 103.598 1629 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 17.88 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1349 helix: 0.84 (0.22), residues: 607 sheet: 0.52 (0.37), residues: 192 loop : -0.83 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.002 0.000 HIS A 449 PHE 0.012 0.001 PHE A 666 TYR 0.016 0.001 TYR A 658 ARG 0.011 0.000 ARG A1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.00 seconds wall clock time: 79 minutes 13.45 seconds (4753.45 seconds total)