Starting phenix.real_space_refine on Thu Feb 15 10:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whw_32513/02_2024/7whw_32513_updated.pdb" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7706 2.51 5 N 1987 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 909": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11978 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8973 Classifications: {'peptide': 1126} Link IDs: {'PTRANS': 35, 'TRANS': 1090} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.09, per 1000 atoms: 0.59 Number of scatterers: 11978 At special positions: 0 Unit cell: (136.96, 109.14, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 3 15.00 Mg 1 11.99 O 2224 8.00 N 1987 7.00 C 7706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2782 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 35.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.869A pdb=" N HIS A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.938A pdb=" N PHE A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 242 through 274 Proline residue: A 246 - end of helix removed outlier: 5.026A pdb=" N VAL A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 252 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 257 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 259 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG A 264 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 267 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 270 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 271 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 272 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 544 through 575 removed outlier: 4.836A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.702A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 633 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 709 through 719 removed outlier: 3.631A pdb=" N GLU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.548A pdb=" N GLU A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 811 removed outlier: 3.569A pdb=" N ALA A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.969A pdb=" N LEU A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 934 removed outlier: 5.439A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 940 removed outlier: 4.563A pdb=" N ARG A 940 " --> pdb=" O LEU A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 937 through 940' Processing helix chain 'A' and resid 943 through 949 removed outlier: 3.527A pdb=" N VAL A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'A' and resid 1035 through 1045 removed outlier: 3.532A pdb=" N LYS A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1074 through 1080 Processing helix chain 'A' and resid 1087 through 1095 removed outlier: 3.674A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1120 Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1137 through 1140 No H-bonds generated for 'chain 'A' and resid 1137 through 1140' Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.841A pdb=" N ALA A1170 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1174 " --> pdb=" O ARG A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1199 Proline residue: A1189 - end of helix removed outlier: 3.514A pdb=" N ASN A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1239 Processing helix chain 'A' and resid 1248 through 1251 No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1253 through 1260 removed outlier: 3.577A pdb=" N VAL A1258 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1292 Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1308 through 1330 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 4.016A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1376 through 1385 removed outlier: 3.736A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1403 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1407 through 1416 Processing helix chain 'B' and resid 72 through 97 removed outlier: 3.535A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.561A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 373 through 397 removed outlier: 4.365A pdb=" N TRP B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.562A pdb=" N GLY A 520 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 430 through 433 Processing sheet with id= C, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.417A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 498 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 487 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 496 " --> pdb=" O TRP A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 682 through 684 Processing sheet with id= E, first strand: chain 'A' and resid 780 through 783 removed outlier: 3.504A pdb=" N ASP A 793 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 825 through 827 Processing sheet with id= G, first strand: chain 'A' and resid 848 through 851 removed outlier: 5.865A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1145 through 1147 removed outlier: 6.234A pdb=" N TYR A1161 " --> pdb=" O GLY A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.032A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 141 through 145 337 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2962 1.33 - 1.45: 2814 1.45 - 1.58: 6390 1.58 - 1.70: 6 1.70 - 1.82: 86 Bond restraints: 12258 Sorted by residual: bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.605 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.603 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C4 ACP A1601 " pdb=" C5 ACP A1601 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3G ACP A1601 " pdb=" PG ACP A1601 " ideal model delta sigma weight residual 1.532 1.608 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 ACP A1601 " pdb=" C6 ACP A1601 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 12253 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.63: 185 104.63 - 112.54: 6027 112.54 - 120.45: 5797 120.45 - 128.36: 4516 128.36 - 136.27: 109 Bond angle restraints: 16634 Sorted by residual: angle pdb=" N ILE A1086 " pdb=" CA ILE A1086 " pdb=" C ILE A1086 " ideal model delta sigma weight residual 113.53 107.28 6.25 9.80e-01 1.04e+00 4.07e+01 angle pdb=" CA ARG A1333 " pdb=" CB ARG A1333 " pdb=" CG ARG A1333 " ideal model delta sigma weight residual 114.10 124.64 -10.54 2.00e+00 2.50e-01 2.78e+01 angle pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta sigma weight residual 122.21 114.02 8.19 1.62e+00 3.81e-01 2.56e+01 angle pdb=" N LEU A1101 " pdb=" CA LEU A1101 " pdb=" C LEU A1101 " ideal model delta sigma weight residual 112.13 119.02 -6.89 1.37e+00 5.33e-01 2.53e+01 angle pdb=" C ASN B 240 " pdb=" CA ASN B 240 " pdb=" CB ASN B 240 " ideal model delta sigma weight residual 110.90 103.68 7.22 1.58e+00 4.01e-01 2.09e+01 ... (remaining 16629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 7121 28.61 - 57.21: 174 57.21 - 85.82: 14 85.82 - 114.43: 5 114.43 - 143.03: 1 Dihedral angle restraints: 7315 sinusoidal: 2977 harmonic: 4338 Sorted by residual: dihedral pdb=" CA TYR A1219 " pdb=" C TYR A1219 " pdb=" N THR A1220 " pdb=" CA THR A1220 " ideal model delta harmonic sigma weight residual 180.00 134.93 45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA VAL A1100 " pdb=" C VAL A1100 " pdb=" N LEU A1101 " pdb=" CA LEU A1101 " ideal model delta harmonic sigma weight residual -180.00 -141.67 -38.33 0 5.00e+00 4.00e-02 5.88e+01 dihedral pdb=" CA LEU A1101 " pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -143.79 -36.21 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 7312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1393 0.070 - 0.139: 389 0.139 - 0.209: 50 0.209 - 0.278: 17 0.278 - 0.348: 3 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG A1333 " pdb=" N ARG A1333 " pdb=" C ARG A1333 " pdb=" CB ARG A1333 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ASN A 675 " pdb=" N ASN A 675 " pdb=" C ASN A 675 " pdb=" CB ASN A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1849 not shown) Planarity restraints: 2107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.031 2.00e-02 2.50e+03 6.09e-02 3.70e+01 pdb=" C PHE B 398 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.028 2.00e-02 2.50e+03 5.36e-02 2.87e+01 pdb=" C VAL A1408 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.034 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.029 2.00e-02 2.50e+03 3.24e-02 2.62e+01 pdb=" CG TRP B 142 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.001 2.00e-02 2.50e+03 ... (remaining 2104 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 226 2.67 - 3.22: 11225 3.22 - 3.78: 19799 3.78 - 4.34: 26849 4.34 - 4.90: 42897 Nonbonded interactions: 100996 Sorted by model distance: nonbonded pdb=" O3G ACP A1601 " pdb="MG MG A1602 " model vdw 2.107 2.170 nonbonded pdb=" O THR A 669 " pdb=" OG1 THR A 673 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.220 2.440 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.251 2.440 nonbonded pdb=" OG SER A1106 " pdb=" OE1 GLN A1109 " model vdw 2.273 2.440 ... (remaining 100991 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: 1.310 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: 7.050 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 36.910 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.009 0.098 12258 Z= 0.610 Angle : 1.166 14.996 16634 Z= 0.622 Chirality : 0.067 0.348 1852 Planarity : 0.007 0.061 2106 Dihedral : 12.722 143.034 4527 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -5.16 (0.16), residues: 1480 helix: -4.19 (0.10), residues: 558 sheet: -2.77 (0.35), residues: 165 loop : -2.93 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP B 142 HIS 0.013 0.002 HIS B 186 PHE 0.051 0.004 PHE B 243 TYR 0.053 0.004 TYR A1217 ARG 0.021 0.001 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.6781 (t) cc_final: 0.6492 (p) REVERT: A 265 ARG cc_start: 0.6690 (tpt-90) cc_final: 0.6443 (tpt-90) REVERT: A 485 MET cc_start: -0.0067 (ppp) cc_final: -0.0306 (ttp) REVERT: A 532 MET cc_start: 0.1316 (mtt) cc_final: 0.0144 (tpp) REVERT: A 561 PHE cc_start: 0.7455 (m-80) cc_final: 0.6765 (t80) REVERT: A 562 ILE cc_start: 0.8525 (mm) cc_final: 0.8299 (mt) REVERT: A 903 TYR cc_start: 0.6586 (m-10) cc_final: 0.6327 (m-10) REVERT: A 906 GLU cc_start: 0.6525 (pt0) cc_final: 0.6232 (pt0) REVERT: A 1006 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (pp) REVERT: A 1044 TYR cc_start: 0.7883 (m-80) cc_final: 0.7667 (m-80) REVERT: A 1068 TYR cc_start: 0.8119 (m-80) cc_final: 0.7806 (m-10) REVERT: A 1088 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7665 (mtp180) REVERT: A 1196 MET cc_start: 0.8197 (tpp) cc_final: 0.7988 (mmm) REVERT: B 188 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6852 (ttp-170) REVERT: B 315 MET cc_start: 0.8751 (mmm) cc_final: 0.8490 (mmm) outliers start: 7 outliers final: 3 residues processed: 233 average time/residue: 0.2758 time to fit residues: 89.4064 Evaluate side-chains 142 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 738 GLN A1004 ASN A1139 GLN A1176 HIS A1307 HIS A1419 HIS B 67 ASN B 155 GLN B 256 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12258 Z= 0.278 Angle : 0.720 12.579 16634 Z= 0.369 Chirality : 0.047 0.171 1852 Planarity : 0.005 0.056 2106 Dihedral : 10.321 143.322 1724 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 2.09 % Allowed : 8.36 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.74 (0.19), residues: 1480 helix: -2.40 (0.18), residues: 545 sheet: -2.82 (0.35), residues: 163 loop : -2.45 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 142 HIS 0.004 0.001 HIS B 347 PHE 0.018 0.002 PHE A 679 TYR 0.029 0.002 TYR A1219 ARG 0.007 0.001 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 519 MET cc_start: 0.3403 (mtt) cc_final: 0.2366 (mmt) REVERT: A 532 MET cc_start: 0.1649 (mtt) cc_final: 0.0403 (mmp) REVERT: A 561 PHE cc_start: 0.7651 (m-80) cc_final: 0.6922 (t80) REVERT: A 691 ARG cc_start: 0.6849 (ttp-170) cc_final: 0.6483 (tpp-160) REVERT: A 740 TYR cc_start: 0.5773 (p90) cc_final: 0.4344 (p90) REVERT: A 847 LYS cc_start: 0.6747 (mttt) cc_final: 0.6458 (mttt) REVERT: A 1004 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7095 (t0) REVERT: A 1006 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7790 (pp) REVERT: A 1059 LYS cc_start: 0.7435 (ptpp) cc_final: 0.7139 (ptmt) REVERT: A 1088 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.6893 (mtp180) REVERT: A 1196 MET cc_start: 0.8243 (tpp) cc_final: 0.7977 (mmm) REVERT: B 323 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8139 (mt) outliers start: 27 outliers final: 13 residues processed: 163 average time/residue: 0.2624 time to fit residues: 61.5288 Evaluate side-chains 131 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12258 Z= 0.298 Angle : 0.675 9.653 16634 Z= 0.345 Chirality : 0.046 0.167 1852 Planarity : 0.004 0.044 2106 Dihedral : 9.621 143.354 1724 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.70 % Rotamer: Outliers : 3.02 % Allowed : 10.14 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.07 (0.20), residues: 1480 helix: -1.58 (0.20), residues: 555 sheet: -2.65 (0.36), residues: 164 loop : -2.23 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 142 HIS 0.004 0.001 HIS B 347 PHE 0.015 0.002 PHE A1341 TYR 0.027 0.002 TYR A1219 ARG 0.005 0.001 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 519 MET cc_start: 0.3155 (mtt) cc_final: 0.2264 (mmt) REVERT: A 532 MET cc_start: 0.1690 (mtt) cc_final: 0.0142 (mmm) REVERT: A 561 PHE cc_start: 0.7778 (m-80) cc_final: 0.6907 (t80) REVERT: A 691 ARG cc_start: 0.6795 (ttp-170) cc_final: 0.6508 (tpp-160) REVERT: A 730 LEU cc_start: 0.1999 (OUTLIER) cc_final: 0.1242 (mt) REVERT: A 1006 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7739 (pp) REVERT: A 1059 LYS cc_start: 0.7495 (ptpp) cc_final: 0.7264 (ptmt) REVERT: A 1088 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6878 (mtp180) REVERT: A 1089 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: A 1196 MET cc_start: 0.8274 (tpp) cc_final: 0.7959 (mmm) REVERT: B 359 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8576 (pt) outliers start: 39 outliers final: 23 residues processed: 152 average time/residue: 0.2865 time to fit residues: 64.2162 Evaluate side-chains 136 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12258 Z= 0.224 Angle : 0.613 8.544 16634 Z= 0.314 Chirality : 0.044 0.161 1852 Planarity : 0.004 0.043 2106 Dihedral : 8.944 139.737 1724 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.33 % Allowed : 11.15 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.59 (0.21), residues: 1480 helix: -1.03 (0.21), residues: 560 sheet: -2.38 (0.37), residues: 174 loop : -2.08 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 142 HIS 0.004 0.001 HIS B 347 PHE 0.012 0.002 PHE A1191 TYR 0.028 0.002 TYR A1219 ARG 0.004 0.000 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8099 (t80) REVERT: A 224 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8394 (tm) REVERT: A 519 MET cc_start: 0.3160 (mtt) cc_final: 0.2025 (mmt) REVERT: A 532 MET cc_start: 0.1737 (mtt) cc_final: 0.0143 (mmm) REVERT: A 561 PHE cc_start: 0.7661 (m-80) cc_final: 0.6892 (t80) REVERT: A 691 ARG cc_start: 0.6727 (ttp-170) cc_final: 0.6265 (tpp-160) REVERT: A 847 LYS cc_start: 0.6131 (mttt) cc_final: 0.5523 (mttm) REVERT: A 1006 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 1059 LYS cc_start: 0.7453 (ptpp) cc_final: 0.7217 (ptmt) REVERT: A 1196 MET cc_start: 0.8234 (tpp) cc_final: 0.7815 (mmm) outliers start: 43 outliers final: 22 residues processed: 154 average time/residue: 0.2525 time to fit residues: 56.4683 Evaluate side-chains 133 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 98 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12258 Z= 0.211 Angle : 0.596 9.161 16634 Z= 0.305 Chirality : 0.044 0.159 1852 Planarity : 0.003 0.034 2106 Dihedral : 8.687 139.255 1724 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.86 % Allowed : 12.07 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.35 (0.21), residues: 1480 helix: -0.76 (0.21), residues: 569 sheet: -2.30 (0.37), residues: 175 loop : -1.99 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 986 HIS 0.003 0.001 HIS B 347 PHE 0.012 0.002 PHE A1341 TYR 0.026 0.002 TYR A1219 ARG 0.006 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.285 Fit side-chains REVERT: A 223 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 224 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8462 (tm) REVERT: A 519 MET cc_start: 0.3196 (mtt) cc_final: 0.2017 (mmt) REVERT: A 532 MET cc_start: 0.1779 (mtt) cc_final: 0.0145 (mmm) REVERT: A 561 PHE cc_start: 0.7637 (m-80) cc_final: 0.6878 (t80) REVERT: A 691 ARG cc_start: 0.6670 (ttp-170) cc_final: 0.6293 (tpp-160) REVERT: A 964 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6756 (tt0) REVERT: A 1006 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7688 (pp) REVERT: A 1059 LYS cc_start: 0.7481 (ptpp) cc_final: 0.7244 (ptmt) REVERT: A 1196 MET cc_start: 0.8222 (tpp) cc_final: 0.7785 (mmm) REVERT: A 1212 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.7948 (t70) outliers start: 37 outliers final: 28 residues processed: 146 average time/residue: 0.2280 time to fit residues: 49.5960 Evaluate side-chains 137 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12258 Z= 0.207 Angle : 0.589 7.804 16634 Z= 0.302 Chirality : 0.044 0.158 1852 Planarity : 0.003 0.052 2106 Dihedral : 8.550 138.697 1724 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.25 % Allowed : 12.46 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.22), residues: 1480 helix: -0.59 (0.22), residues: 572 sheet: -2.12 (0.38), residues: 173 loop : -1.92 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 986 HIS 0.003 0.001 HIS B 347 PHE 0.012 0.001 PHE A1341 TYR 0.024 0.002 TYR A 903 ARG 0.004 0.000 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.389 Fit side-chains REVERT: A 223 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 224 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8467 (tm) REVERT: A 519 MET cc_start: 0.2826 (mtt) cc_final: 0.1727 (mmt) REVERT: A 532 MET cc_start: 0.2151 (mtt) cc_final: 0.0453 (mmt) REVERT: A 561 PHE cc_start: 0.7618 (m-80) cc_final: 0.6869 (t80) REVERT: A 691 ARG cc_start: 0.6551 (ttp-170) cc_final: 0.6133 (tpp-160) REVERT: A 1006 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 1059 LYS cc_start: 0.7441 (ptpp) cc_final: 0.7135 (ptmt) REVERT: A 1196 MET cc_start: 0.8214 (tpp) cc_final: 0.7755 (mmm) REVERT: A 1212 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7933 (t70) REVERT: B 80 LEU cc_start: 0.7824 (tt) cc_final: 0.6816 (mt) outliers start: 42 outliers final: 33 residues processed: 145 average time/residue: 0.2331 time to fit residues: 50.7551 Evaluate side-chains 144 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12258 Z= 0.265 Angle : 0.611 7.165 16634 Z= 0.312 Chirality : 0.045 0.180 1852 Planarity : 0.004 0.051 2106 Dihedral : 8.516 139.329 1724 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 3.56 % Allowed : 12.23 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.07 (0.22), residues: 1480 helix: -0.58 (0.22), residues: 581 sheet: -2.00 (0.39), residues: 173 loop : -1.84 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 986 HIS 0.005 0.001 HIS A1330 PHE 0.014 0.002 PHE A1341 TYR 0.023 0.002 TYR A 903 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 1.242 Fit side-chains REVERT: A 223 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8148 (t80) REVERT: A 224 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8449 (tm) REVERT: A 519 MET cc_start: 0.2743 (mtt) cc_final: 0.1896 (mmt) REVERT: A 532 MET cc_start: 0.2283 (mtt) cc_final: 0.0540 (mmt) REVERT: A 561 PHE cc_start: 0.7643 (m-80) cc_final: 0.6876 (t80) REVERT: A 691 ARG cc_start: 0.6486 (ttp-170) cc_final: 0.6054 (tpp-160) REVERT: A 1006 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7660 (pp) REVERT: A 1212 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7911 (t70) REVERT: A 1219 TYR cc_start: 0.8106 (t80) cc_final: 0.7531 (t80) REVERT: B 80 LEU cc_start: 0.7869 (tt) cc_final: 0.6847 (mt) REVERT: B 210 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 269 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7899 (t70) REVERT: B 395 PHE cc_start: 0.7133 (m-80) cc_final: 0.6768 (m-10) outliers start: 46 outliers final: 32 residues processed: 153 average time/residue: 0.2439 time to fit residues: 54.7361 Evaluate side-chains 142 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12258 Z= 0.232 Angle : 0.598 7.267 16634 Z= 0.306 Chirality : 0.044 0.171 1852 Planarity : 0.003 0.043 2106 Dihedral : 8.374 138.082 1724 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.41 % Allowed : 12.69 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.97 (0.22), residues: 1480 helix: -0.48 (0.22), residues: 577 sheet: -1.86 (0.40), residues: 173 loop : -1.82 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 986 HIS 0.004 0.001 HIS A1330 PHE 0.014 0.002 PHE A1191 TYR 0.024 0.002 TYR A 903 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 1.308 Fit side-chains REVERT: A 223 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 224 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8470 (tm) REVERT: A 519 MET cc_start: 0.2204 (mtt) cc_final: 0.1743 (mmt) REVERT: A 532 MET cc_start: 0.2339 (mtt) cc_final: 0.0552 (mmt) REVERT: A 561 PHE cc_start: 0.7594 (m-80) cc_final: 0.6841 (t80) REVERT: A 691 ARG cc_start: 0.6477 (ttp-170) cc_final: 0.6048 (tpp-160) REVERT: A 1006 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7686 (pp) REVERT: A 1212 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7906 (t70) REVERT: A 1219 TYR cc_start: 0.8125 (t80) cc_final: 0.7521 (t80) REVERT: B 80 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.6839 (mt) REVERT: B 210 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7565 (p0) REVERT: B 269 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7948 (t0) outliers start: 44 outliers final: 33 residues processed: 146 average time/residue: 0.2372 time to fit residues: 51.6769 Evaluate side-chains 144 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.0970 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 140 optimal weight: 0.0980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12258 Z= 0.191 Angle : 0.580 7.600 16634 Z= 0.296 Chirality : 0.043 0.164 1852 Planarity : 0.003 0.035 2106 Dihedral : 8.217 137.433 1724 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.94 % Allowed : 13.47 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1480 helix: -0.45 (0.22), residues: 586 sheet: -1.66 (0.41), residues: 170 loop : -1.76 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 986 HIS 0.003 0.001 HIS B 347 PHE 0.013 0.001 PHE A1191 TYR 0.023 0.002 TYR A 903 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.451 Fit side-chains REVERT: A 223 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8055 (t80) REVERT: A 224 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8479 (tm) REVERT: A 519 MET cc_start: 0.2204 (mtt) cc_final: 0.1740 (mmt) REVERT: A 532 MET cc_start: 0.2247 (mtt) cc_final: 0.0430 (mmm) REVERT: A 561 PHE cc_start: 0.7553 (m-80) cc_final: 0.6834 (t80) REVERT: A 691 ARG cc_start: 0.6413 (ttp-170) cc_final: 0.6045 (tpp-160) REVERT: A 1006 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7692 (pp) REVERT: A 1212 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7896 (t70) REVERT: A 1219 TYR cc_start: 0.8196 (t80) cc_final: 0.7585 (t80) REVERT: B 80 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.6898 (mt) REVERT: B 210 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7597 (p0) REVERT: B 269 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7906 (t0) outliers start: 38 outliers final: 28 residues processed: 145 average time/residue: 0.2323 time to fit residues: 50.6577 Evaluate side-chains 142 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 0.0970 chunk 117 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN A1416 GLN B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12258 Z= 0.166 Angle : 0.573 10.856 16634 Z= 0.292 Chirality : 0.043 0.158 1852 Planarity : 0.003 0.030 2106 Dihedral : 8.025 136.673 1724 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.71 % Allowed : 13.93 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.70 (0.22), residues: 1480 helix: -0.27 (0.22), residues: 578 sheet: -1.54 (0.42), residues: 164 loop : -1.72 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 986 HIS 0.002 0.001 HIS B 347 PHE 0.011 0.001 PHE A1191 TYR 0.018 0.001 TYR A1040 ARG 0.003 0.000 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.349 Fit side-chains REVERT: A 223 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 224 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8479 (tm) REVERT: A 519 MET cc_start: 0.2058 (mtt) cc_final: 0.1655 (mmt) REVERT: A 532 MET cc_start: 0.2442 (mtt) cc_final: 0.0565 (mmm) REVERT: A 561 PHE cc_start: 0.7321 (m-80) cc_final: 0.6786 (t80) REVERT: A 585 TYR cc_start: 0.8154 (m-80) cc_final: 0.7273 (m-80) REVERT: A 691 ARG cc_start: 0.6296 (ttp-170) cc_final: 0.6036 (tpp-160) REVERT: A 1006 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7603 (pp) REVERT: A 1212 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7927 (t70) REVERT: A 1219 TYR cc_start: 0.8203 (t80) cc_final: 0.7580 (t80) REVERT: B 80 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.6846 (mt) REVERT: B 210 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (p0) REVERT: B 269 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7845 (t70) outliers start: 35 outliers final: 27 residues processed: 143 average time/residue: 0.2236 time to fit residues: 48.5648 Evaluate side-chains 145 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.194255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142241 restraints weight = 14189.551| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.49 r_work: 0.3313 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12258 Z= 0.207 Angle : 0.586 9.307 16634 Z= 0.299 Chirality : 0.044 0.179 1852 Planarity : 0.003 0.035 2106 Dihedral : 7.984 137.908 1724 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.63 % Allowed : 14.32 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.67 (0.22), residues: 1480 helix: -0.27 (0.22), residues: 585 sheet: -1.32 (0.44), residues: 159 loop : -1.74 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 986 HIS 0.004 0.001 HIS B 347 PHE 0.030 0.002 PHE A1402 TYR 0.020 0.002 TYR A 633 ARG 0.003 0.000 ARG B 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.31 seconds wall clock time: 50 minutes 55.66 seconds (3055.66 seconds total)