Starting phenix.real_space_refine on Thu Feb 15 13:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whv_32512/02_2024/7whv_32512_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Be 1 3.05 5 C 7953 2.51 5 N 2033 2.21 5 O 2278 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 467": "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 PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 916": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1167": "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 TYR 1292": "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 PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B PHE 163": "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: 12331 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 9249 Classifications: {'peptide': 1158} Link IDs: {'PTRANS': 39, 'TRANS': 1118} Chain breaks: 3 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {' MG': 1, '6PL': 2, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.15, per 1000 atoms: 0.58 Number of scatterers: 12331 At special positions: 0 Unit cell: (150.87, 97.37, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2278 8.00 N 2033 7.00 C 7953 6.00 Be 1 4.00 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=2.01 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 C 1 " - " ASN B 240 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 11 sheets defined 38.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 240 through 273 removed outlier: 3.682A pdb=" N ALA A 244 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix removed outlier: 3.809A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 544 through 575 removed outlier: 4.272A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.523A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 616 through 633 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 709 through 724 Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.546A pdb=" N MET A 771 " --> pdb=" O CYS A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 922 through 935 removed outlier: 3.690A pdb=" N ALA A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 951 removed outlier: 3.614A pdb=" N ALA A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 980 Processing helix chain 'A' and resid 993 through 1002 Processing helix chain 'A' and resid 1036 through 1047 removed outlier: 3.582A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A1047 " --> pdb=" O GLU A1043 " (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 1075 through 1079 removed outlier: 3.778A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1075 through 1079' Processing helix chain 'A' and resid 1084 through 1096 removed outlier: 3.691A pdb=" N LYS A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1120 Processing helix chain 'A' and resid 1132 through 1140 removed outlier: 4.668A pdb=" N ALA A1136 " --> pdb=" O ASN A1133 " (cutoff:3.500A) 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 1173 removed outlier: 3.814A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1204 Proline residue: A1189 - end of helix removed outlier: 4.359A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A1201 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1203 " --> pdb=" O ALA A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1231 through 1238 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: 3.806A 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 1329 removed outlier: 3.698A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1358 removed outlier: 3.551A pdb=" N SER A1345 " --> pdb=" O PHE A1341 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1349 " --> pdb=" O SER A1345 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A1350 " --> pdb=" O CYS A1346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1362 No H-bonds generated for 'chain 'A' and resid 1360 through 1362' Processing helix chain 'A' and resid 1368 through 1371 No H-bonds generated for 'chain 'A' and resid 1368 through 1371' Processing helix chain 'A' and resid 1376 through 1403 removed outlier: 3.841A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.500A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1417 Processing helix chain 'B' and resid 72 through 98 Proline residue: B 77 - end of helix 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 232 through 236 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 398 Processing sheet with id= A, first strand: chain 'A' and resid 168 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 278 through 280 Processing sheet with id= C, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.528A pdb=" N ASP A 418 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 430 through 434 Processing sheet with id= E, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.161A pdb=" N LYS A 984 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 666 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TRP A 986 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A1100 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A1099 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU A1011 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A1071 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A1013 " --> pdb=" O VAL A1071 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 682 through 684 Processing sheet with id= G, first strand: chain 'A' and resid 781 through 784 Processing sheet with id= H, first strand: chain 'A' and resid 813 through 818 removed outlier: 6.920A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 818 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 835 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 852 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE A 839 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 850 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL A 676 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1145 through 1147 removed outlier: 6.537A pdb=" N TYR A1161 " --> pdb=" O GLY A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.219A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 141 through 145 438 hydrogen bonds defined for protein. 1224 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: 4.07 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2113 1.31 - 1.44: 3404 1.44 - 1.56: 6999 1.56 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 12613 Sorted by residual: bond pdb=" BE BEF A1602 " pdb=" F3 BEF A1602 " ideal model delta sigma weight residual 1.476 1.757 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" BE BEF A1602 " pdb=" F2 BEF A1602 " ideal model delta sigma weight residual 1.476 1.754 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" BE BEF A1602 " pdb=" F1 BEF A1602 " ideal model delta sigma weight residual 1.476 1.745 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.326 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CG1 ILE A1321 " pdb=" CD1 ILE A1321 " ideal model delta sigma weight residual 1.513 1.362 0.151 3.90e-02 6.57e+02 1.51e+01 ... (remaining 12608 not shown) Histogram of bond angle deviations from ideal: 93.91 - 102.40: 44 102.40 - 110.90: 4211 110.90 - 119.40: 6475 119.40 - 127.90: 6229 127.90 - 136.40: 130 Bond angle restraints: 17089 Sorted by residual: angle pdb=" N ILE A 706 " pdb=" CA ILE A 706 " pdb=" C ILE A 706 " ideal model delta sigma weight residual 112.29 105.60 6.69 9.40e-01 1.13e+00 5.07e+01 angle pdb=" C TYR B 229 " pdb=" N PRO B 230 " pdb=" CA PRO B 230 " ideal model delta sigma weight residual 119.84 111.34 8.50 1.25e+00 6.40e-01 4.63e+01 angle pdb=" CA TRP A 398 " pdb=" CB TRP A 398 " pdb=" CG TRP A 398 " ideal model delta sigma weight residual 113.60 126.23 -12.63 1.90e+00 2.77e-01 4.42e+01 angle pdb=" C ASN B 279 " pdb=" N TYR B 280 " pdb=" CA TYR B 280 " ideal model delta sigma weight residual 126.86 135.51 -8.65 1.57e+00 4.06e-01 3.03e+01 angle pdb=" N ILE B 403 " pdb=" CA ILE B 403 " pdb=" C ILE B 403 " ideal model delta sigma weight residual 111.91 107.33 4.58 8.90e-01 1.26e+00 2.65e+01 ... (remaining 17084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 7298 22.58 - 45.16: 221 45.16 - 67.74: 25 67.74 - 90.32: 6 90.32 - 112.90: 4 Dihedral angle restraints: 7554 sinusoidal: 3116 harmonic: 4438 Sorted by residual: dihedral pdb=" CA ASN B 240 " pdb=" C ASN B 240 " pdb=" N ASP B 241 " pdb=" CA ASP B 241 " ideal model delta harmonic sigma weight residual -180.00 -145.93 -34.07 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CA ASN B 279 " pdb=" C ASN B 279 " pdb=" N TYR B 280 " pdb=" CA TYR B 280 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA PHE A1365 " pdb=" C PHE A1365 " pdb=" N PHE A1366 " pdb=" CA PHE A1366 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1662 0.116 - 0.231: 213 0.231 - 0.346: 10 0.346 - 0.462: 4 0.462 - 0.577: 2 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CG LEU A1126 " pdb=" CB LEU A1126 " pdb=" CD1 LEU A1126 " pdb=" CD2 LEU A1126 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CB ILE B 359 " pdb=" CA ILE B 359 " pdb=" CG1 ILE B 359 " pdb=" CG2 ILE B 359 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 1888 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.050 2.00e-02 2.50e+03 4.04e-02 4.08e+01 pdb=" CG TRP B 142 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 398 " -0.079 2.00e-02 2.50e+03 3.87e-02 3.75e+01 pdb=" CG TRP A 398 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 398 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 398 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP A 398 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 398 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 398 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 398 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 398 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 398 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C PHE B 398 " -0.099 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.033 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 318 2.66 - 3.22: 11720 3.22 - 3.78: 21344 3.78 - 4.34: 29242 4.34 - 4.90: 46495 Nonbonded interactions: 109119 Sorted by model distance: nonbonded pdb=" OD1 ASP A 667 " pdb="MG MG A1601 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP A 667 " pdb=" F1 BEF A1602 " model vdw 2.123 2.390 nonbonded pdb=" OD1 ASP A1130 " pdb=" F1 BEF A1602 " model vdw 2.141 2.390 nonbonded pdb=" O THR A 669 " pdb=" F1 BEF A1602 " model vdw 2.175 2.390 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.246 2.440 ... (remaining 109114 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: 7.140 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 36.900 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.016 0.281 12613 Z= 1.037 Angle : 1.294 12.629 17089 Z= 0.702 Chirality : 0.079 0.577 1891 Planarity : 0.009 0.061 2159 Dihedral : 12.087 112.895 4700 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.02 % Favored : 92.91 % Rotamer: Outliers : 0.60 % Allowed : 3.25 % Favored : 96.15 % 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: -3.98 (0.17), residues: 1510 helix: -3.44 (0.13), residues: 601 sheet: -2.01 (0.30), residues: 192 loop : -1.94 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.007 TRP B 142 HIS 0.013 0.005 HIS B 186 PHE 0.060 0.006 PHE B 243 TYR 0.046 0.006 TYR B 297 ARG 0.018 0.002 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 269 time to evaluate : 1.412 Fit side-chains REVERT: A 464 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7598 (mtm180) REVERT: A 599 PHE cc_start: 0.7186 (t80) cc_final: 0.6929 (t80) REVERT: A 674 GLN cc_start: 0.8053 (tt0) cc_final: 0.7789 (tt0) REVERT: A 685 ASN cc_start: 0.7522 (t160) cc_final: 0.7244 (t0) REVERT: A 715 GLU cc_start: 0.7173 (tp30) cc_final: 0.6972 (tp30) REVERT: A 765 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6516 (mmp80) REVERT: A 782 VAL cc_start: 0.7695 (t) cc_final: 0.7416 (m) REVERT: A 824 ILE cc_start: 0.8091 (mt) cc_final: 0.7761 (mp) REVERT: A 827 MET cc_start: 0.7069 (mtp) cc_final: 0.6835 (mtp) REVERT: A 835 GLU cc_start: 0.7539 (tt0) cc_final: 0.7314 (tt0) REVERT: A 837 LEU cc_start: 0.8227 (mt) cc_final: 0.8008 (mp) REVERT: A 840 LEU cc_start: 0.8587 (mt) cc_final: 0.8354 (mt) REVERT: A 847 LYS cc_start: 0.7603 (mttp) cc_final: 0.7351 (mtpm) REVERT: A 853 VAL cc_start: 0.8101 (m) cc_final: 0.7720 (p) REVERT: A 854 LYS cc_start: 0.7406 (tttt) cc_final: 0.7066 (ttpp) REVERT: A 898 LEU cc_start: 0.8011 (tp) cc_final: 0.7748 (tp) REVERT: A 973 ASP cc_start: 0.7238 (m-30) cc_final: 0.6958 (m-30) REVERT: A 1222 MET cc_start: 0.8115 (mtp) cc_final: 0.7798 (mtp) REVERT: B 54 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7399 (mmtm) REVERT: B 134 LYS cc_start: 0.7948 (mttt) cc_final: 0.7700 (mttt) REVERT: B 215 ASN cc_start: 0.8368 (p0) cc_final: 0.8116 (p0) REVERT: B 290 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6809 (mm-30) REVERT: B 315 MET cc_start: 0.8712 (mmm) cc_final: 0.8277 (mmm) outliers start: 8 outliers final: 3 residues processed: 277 average time/residue: 1.1525 time to fit residues: 348.6632 Evaluate side-chains 166 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 410 HIS A 411 ASN A 437 ASN A 443 ASN A 477 ASN A 497 ASN A 556 ASN ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 939 ASN A1004 ASN A1061 HIS A1067 ASN A1176 HIS A1266 ASN A1295 ASN A1307 HIS A1330 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 155 GLN B 255 ASN B 256 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12613 Z= 0.268 Angle : 0.689 11.426 17089 Z= 0.363 Chirality : 0.047 0.352 1891 Planarity : 0.005 0.050 2159 Dihedral : 9.348 66.248 1822 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 3.47 % Allowed : 9.59 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 1510 helix: -1.61 (0.17), residues: 611 sheet: -1.56 (0.33), residues: 183 loop : -1.39 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 142 HIS 0.004 0.001 HIS A1176 PHE 0.022 0.002 PHE A 206 TYR 0.022 0.002 TYR A 923 ARG 0.007 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 1.364 Fit side-chains REVERT: A 455 THR cc_start: 0.7561 (p) cc_final: 0.7345 (m) REVERT: A 561 PHE cc_start: 0.7889 (t80) cc_final: 0.7683 (t80) REVERT: A 674 GLN cc_start: 0.8131 (tt0) cc_final: 0.7829 (tt0) REVERT: A 685 ASN cc_start: 0.7166 (t0) cc_final: 0.6948 (t0) REVERT: A 715 GLU cc_start: 0.7246 (tp30) cc_final: 0.6831 (tp30) REVERT: A 768 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 824 ILE cc_start: 0.7912 (mt) cc_final: 0.7616 (mp) REVERT: A 827 MET cc_start: 0.7271 (mtp) cc_final: 0.6931 (mtp) REVERT: A 847 LYS cc_start: 0.7509 (mttp) cc_final: 0.7248 (mtpm) REVERT: A 913 ILE cc_start: 0.7710 (mm) cc_final: 0.7238 (tp) REVERT: A 916 ARG cc_start: 0.6532 (ptm-80) cc_final: 0.6176 (mtm180) REVERT: A 1187 MET cc_start: 0.7647 (ttp) cc_final: 0.7313 (tmt) REVERT: A 1215 TYR cc_start: 0.8573 (m-80) cc_final: 0.8290 (m-80) REVERT: B 54 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7399 (mmtm) REVERT: B 80 LEU cc_start: 0.7713 (mt) cc_final: 0.7394 (tp) REVERT: B 96 GLN cc_start: 0.7225 (mp-120) cc_final: 0.6630 (tt0) REVERT: B 215 ASN cc_start: 0.8341 (p0) cc_final: 0.8028 (p0) REVERT: B 307 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6443 (p0) REVERT: B 315 MET cc_start: 0.8697 (mmm) cc_final: 0.8172 (mmm) outliers start: 46 outliers final: 18 residues processed: 221 average time/residue: 1.1220 time to fit residues: 272.4460 Evaluate side-chains 177 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 556 ASN A 610 GLN B 60 GLN B 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12613 Z= 0.244 Angle : 0.630 11.735 17089 Z= 0.327 Chirality : 0.046 0.362 1891 Planarity : 0.004 0.046 2159 Dihedral : 8.216 54.595 1822 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.31 % Allowed : 11.63 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.53 (0.21), residues: 1510 helix: -0.64 (0.20), residues: 613 sheet: -1.24 (0.34), residues: 185 loop : -1.18 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 142 HIS 0.006 0.001 HIS A 769 PHE 0.020 0.002 PHE A1198 TYR 0.033 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 1.483 Fit side-chains REVERT: A 189 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6738 (tmt) REVERT: A 561 PHE cc_start: 0.7860 (t80) cc_final: 0.7647 (t80) REVERT: A 642 LYS cc_start: 0.8181 (tttt) cc_final: 0.7870 (ttpt) REVERT: A 674 GLN cc_start: 0.8139 (tt0) cc_final: 0.7827 (tt0) REVERT: A 685 ASN cc_start: 0.7249 (t0) cc_final: 0.7038 (t0) REVERT: A 768 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6587 (mt-10) REVERT: A 792 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7716 (pp) REVERT: A 824 ILE cc_start: 0.7823 (mt) cc_final: 0.7615 (mp) REVERT: A 827 MET cc_start: 0.7279 (mtp) cc_final: 0.7006 (mtp) REVERT: A 847 LYS cc_start: 0.7474 (mttp) cc_final: 0.7211 (mtpm) REVERT: A 898 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7287 (mm) REVERT: A 913 ILE cc_start: 0.7824 (mm) cc_final: 0.7510 (tp) REVERT: A 1215 TYR cc_start: 0.8593 (m-80) cc_final: 0.8323 (m-80) REVERT: B 54 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7351 (mmtm) REVERT: B 80 LEU cc_start: 0.7632 (mt) cc_final: 0.7357 (tp) REVERT: B 96 GLN cc_start: 0.7263 (mp-120) cc_final: 0.6692 (tt0) REVERT: B 292 MET cc_start: 0.7519 (tpp) cc_final: 0.6745 (ttm) REVERT: B 307 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6610 (p0) REVERT: B 315 MET cc_start: 0.8856 (mmm) cc_final: 0.8373 (mmm) REVERT: B 333 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7336 (p0) outliers start: 57 outliers final: 25 residues processed: 210 average time/residue: 1.1473 time to fit residues: 265.2305 Evaluate side-chains 181 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.0000 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN A 534 ASN A1416 GLN B 197 GLN B 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12613 Z= 0.194 Angle : 0.584 11.799 17089 Z= 0.301 Chirality : 0.044 0.364 1891 Planarity : 0.003 0.048 2159 Dihedral : 7.674 54.076 1822 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.38 % Allowed : 13.22 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1510 helix: -0.11 (0.21), residues: 612 sheet: -1.16 (0.35), residues: 195 loop : -1.06 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 314 HIS 0.005 0.001 HIS A 769 PHE 0.017 0.002 PHE A1198 TYR 0.026 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 167 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 642 LYS cc_start: 0.8179 (tttt) cc_final: 0.7895 (ttpt) REVERT: A 674 GLN cc_start: 0.8116 (tt0) cc_final: 0.7823 (tt0) REVERT: A 685 ASN cc_start: 0.7302 (t0) cc_final: 0.7095 (t0) REVERT: A 768 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6636 (mt-10) REVERT: A 792 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (pp) REVERT: A 827 MET cc_start: 0.7294 (mtp) cc_final: 0.7011 (mtp) REVERT: A 835 GLU cc_start: 0.7670 (tt0) cc_final: 0.7366 (tp30) REVERT: A 847 LYS cc_start: 0.7382 (mttp) cc_final: 0.7147 (mtpm) REVERT: A 898 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7247 (mm) REVERT: A 1215 TYR cc_start: 0.8574 (m-80) cc_final: 0.8357 (m-80) REVERT: A 1416 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: B 54 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7354 (mmtm) REVERT: B 80 LEU cc_start: 0.7652 (mt) cc_final: 0.7361 (tp) REVERT: B 96 GLN cc_start: 0.7160 (mp-120) cc_final: 0.6605 (tt0) REVERT: B 307 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6762 (p0) REVERT: B 315 MET cc_start: 0.8848 (mmm) cc_final: 0.8493 (mmm) outliers start: 58 outliers final: 26 residues processed: 207 average time/residue: 1.0891 time to fit residues: 248.7797 Evaluate side-chains 175 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 36 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A 675 ASN B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12613 Z= 0.189 Angle : 0.572 11.736 17089 Z= 0.296 Chirality : 0.044 0.366 1891 Planarity : 0.003 0.053 2159 Dihedral : 7.488 57.654 1821 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.93 % Allowed : 14.73 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.85 (0.22), residues: 1510 helix: 0.15 (0.21), residues: 605 sheet: -1.02 (0.35), residues: 205 loop : -0.97 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 314 HIS 0.005 0.001 HIS A1417 PHE 0.017 0.002 PHE A1198 TYR 0.027 0.002 TYR A 172 ARG 0.007 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 1.488 Fit side-chains REVERT: A 642 LYS cc_start: 0.8165 (tttt) cc_final: 0.7886 (ttpt) REVERT: A 674 GLN cc_start: 0.8122 (tt0) cc_final: 0.7839 (tt0) REVERT: A 685 ASN cc_start: 0.7290 (t0) cc_final: 0.7035 (t0) REVERT: A 706 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6621 (mp) REVERT: A 768 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6836 (mt-10) REVERT: A 792 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7652 (pp) REVERT: A 827 MET cc_start: 0.7260 (mtp) cc_final: 0.6984 (mtp) REVERT: A 835 GLU cc_start: 0.7724 (tt0) cc_final: 0.7175 (tp30) REVERT: A 847 LYS cc_start: 0.7500 (mttp) cc_final: 0.7252 (mtpm) REVERT: A 898 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7244 (mm) REVERT: A 916 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5672 (mtm180) REVERT: A 1087 ARG cc_start: 0.6215 (mtt180) cc_final: 0.5999 (mtm-85) REVERT: A 1215 TYR cc_start: 0.8581 (m-80) cc_final: 0.8357 (m-80) REVERT: B 54 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7427 (tptt) REVERT: B 80 LEU cc_start: 0.7647 (mt) cc_final: 0.7361 (tp) REVERT: B 96 GLN cc_start: 0.7166 (mp-120) cc_final: 0.6619 (tt0) REVERT: B 292 MET cc_start: 0.7516 (tpp) cc_final: 0.6747 (ttm) REVERT: B 307 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6860 (p0) REVERT: B 315 MET cc_start: 0.8855 (mmm) cc_final: 0.8513 (mmm) outliers start: 52 outliers final: 28 residues processed: 187 average time/residue: 1.1138 time to fit residues: 229.2872 Evaluate side-chains 172 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12613 Z= 0.281 Angle : 0.622 11.697 17089 Z= 0.322 Chirality : 0.046 0.349 1891 Planarity : 0.004 0.055 2159 Dihedral : 7.719 59.424 1821 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.98 % Allowed : 14.50 % Favored : 80.51 % 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: -0.77 (0.22), residues: 1510 helix: 0.17 (0.21), residues: 606 sheet: -0.93 (0.35), residues: 205 loop : -0.89 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.004 0.001 HIS B 347 PHE 0.022 0.002 PHE A1198 TYR 0.031 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 145 time to evaluate : 1.398 Fit side-chains REVERT: A 674 GLN cc_start: 0.8193 (tt0) cc_final: 0.7935 (tt0) REVERT: A 685 ASN cc_start: 0.7321 (t0) cc_final: 0.7107 (t0) REVERT: A 706 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 768 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6848 (mt-10) REVERT: A 792 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7650 (pp) REVERT: A 827 MET cc_start: 0.7189 (mtp) cc_final: 0.6945 (mtp) REVERT: A 847 LYS cc_start: 0.7540 (mttp) cc_final: 0.7300 (mtpm) REVERT: A 898 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7261 (mm) REVERT: A 916 ARG cc_start: 0.6437 (ttm170) cc_final: 0.5705 (mtm180) REVERT: A 1087 ARG cc_start: 0.6218 (mtt180) cc_final: 0.6010 (mtm-85) REVERT: A 1215 TYR cc_start: 0.8615 (m-80) cc_final: 0.8350 (m-80) REVERT: B 54 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7437 (tptt) REVERT: B 80 LEU cc_start: 0.7688 (mt) cc_final: 0.7376 (tp) REVERT: B 96 GLN cc_start: 0.7243 (mp-120) cc_final: 0.6705 (tt0) REVERT: B 292 MET cc_start: 0.7526 (tpp) cc_final: 0.6731 (ttm) REVERT: B 307 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7049 (p0) REVERT: B 315 MET cc_start: 0.8860 (mmm) cc_final: 0.8485 (mmm) outliers start: 66 outliers final: 42 residues processed: 192 average time/residue: 1.1071 time to fit residues: 235.4069 Evaluate side-chains 188 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12613 Z= 0.275 Angle : 0.621 11.752 17089 Z= 0.320 Chirality : 0.045 0.356 1891 Planarity : 0.004 0.055 2159 Dihedral : 7.706 56.234 1821 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.91 % Allowed : 15.11 % Favored : 79.98 % 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: -0.81 (0.22), residues: 1510 helix: 0.16 (0.21), residues: 612 sheet: -0.80 (0.36), residues: 197 loop : -1.00 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 314 HIS 0.003 0.001 HIS A 899 PHE 0.022 0.002 PHE A1198 TYR 0.034 0.002 TYR A 172 ARG 0.007 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 674 GLN cc_start: 0.8165 (tt0) cc_final: 0.7899 (tt0) REVERT: A 706 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6517 (mp) REVERT: A 768 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 792 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7645 (pp) REVERT: A 827 MET cc_start: 0.7224 (mtp) cc_final: 0.6995 (mtp) REVERT: A 835 GLU cc_start: 0.7700 (tt0) cc_final: 0.7348 (mt-10) REVERT: A 847 LYS cc_start: 0.7535 (mttp) cc_final: 0.7289 (mtpm) REVERT: A 898 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7352 (mm) REVERT: A 1036 LEU cc_start: 0.5683 (pt) cc_final: 0.5213 (pp) REVERT: A 1215 TYR cc_start: 0.8600 (m-80) cc_final: 0.8326 (m-80) REVERT: B 54 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7433 (tptt) REVERT: B 80 LEU cc_start: 0.7733 (mt) cc_final: 0.7432 (tp) REVERT: B 96 GLN cc_start: 0.7294 (mp-120) cc_final: 0.6723 (tt0) REVERT: B 292 MET cc_start: 0.7560 (tpp) cc_final: 0.6759 (ttm) REVERT: B 307 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7058 (p0) REVERT: B 315 MET cc_start: 0.8866 (mmm) cc_final: 0.8468 (mmm) outliers start: 65 outliers final: 39 residues processed: 195 average time/residue: 1.0790 time to fit residues: 232.2713 Evaluate side-chains 185 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.0570 chunk 132 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 ASN B 155 GLN B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12613 Z= 0.208 Angle : 0.584 11.770 17089 Z= 0.302 Chirality : 0.044 0.370 1891 Planarity : 0.003 0.055 2159 Dihedral : 7.460 56.482 1821 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.00 % Allowed : 16.09 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1510 helix: 0.28 (0.21), residues: 608 sheet: -0.78 (0.36), residues: 197 loop : -1.01 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1352 HIS 0.003 0.001 HIS B 347 PHE 0.019 0.002 PHE A1198 TYR 0.031 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 674 GLN cc_start: 0.8134 (tt0) cc_final: 0.7846 (tt0) REVERT: A 706 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6465 (mt) REVERT: A 768 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 792 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7636 (pp) REVERT: A 827 MET cc_start: 0.7281 (mtp) cc_final: 0.7047 (mtp) REVERT: A 835 GLU cc_start: 0.7705 (tt0) cc_final: 0.7077 (tp30) REVERT: A 847 LYS cc_start: 0.7500 (mttp) cc_final: 0.7236 (mtpm) REVERT: A 898 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7341 (mm) REVERT: A 1036 LEU cc_start: 0.5321 (pt) cc_final: 0.4944 (pp) REVERT: A 1215 TYR cc_start: 0.8598 (m-80) cc_final: 0.8355 (m-80) REVERT: B 54 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7411 (tptt) REVERT: B 80 LEU cc_start: 0.7705 (mt) cc_final: 0.7384 (tp) REVERT: B 96 GLN cc_start: 0.7226 (mp-120) cc_final: 0.6685 (tt0) REVERT: B 315 MET cc_start: 0.8871 (mmm) cc_final: 0.8495 (mmm) outliers start: 53 outliers final: 33 residues processed: 185 average time/residue: 1.1806 time to fit residues: 240.0433 Evaluate side-chains 178 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12613 Z= 0.249 Angle : 0.610 11.844 17089 Z= 0.315 Chirality : 0.045 0.362 1891 Planarity : 0.004 0.059 2159 Dihedral : 7.515 57.051 1821 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.55 % Allowed : 17.07 % Favored : 79.38 % 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: -0.75 (0.22), residues: 1510 helix: 0.24 (0.21), residues: 608 sheet: -0.73 (0.36), residues: 197 loop : -1.01 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 314 HIS 0.003 0.001 HIS B 347 PHE 0.021 0.002 PHE A1198 TYR 0.035 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 674 GLN cc_start: 0.8166 (tt0) cc_final: 0.7899 (tt0) REVERT: A 706 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6431 (mp) REVERT: A 768 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A 792 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7644 (pp) REVERT: A 827 MET cc_start: 0.7239 (mtp) cc_final: 0.7032 (mtp) REVERT: A 847 LYS cc_start: 0.7532 (mttp) cc_final: 0.7259 (mtpm) REVERT: A 898 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7358 (mm) REVERT: A 1036 LEU cc_start: 0.5466 (pt) cc_final: 0.5098 (pp) REVERT: A 1215 TYR cc_start: 0.8599 (m-80) cc_final: 0.8354 (m-80) REVERT: B 54 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7421 (tptt) REVERT: B 80 LEU cc_start: 0.7723 (mt) cc_final: 0.7417 (tp) REVERT: B 96 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: B 292 MET cc_start: 0.7506 (tpp) cc_final: 0.6847 (ttm) REVERT: B 315 MET cc_start: 0.8871 (mmm) cc_final: 0.8483 (mmm) REVERT: B 388 MET cc_start: 0.5806 (mmp) cc_final: 0.5502 (mmt) outliers start: 47 outliers final: 34 residues processed: 180 average time/residue: 1.2039 time to fit residues: 239.5935 Evaluate side-chains 178 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 150 optimal weight: 0.0370 chunk 138 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12613 Z= 0.225 Angle : 0.602 11.847 17089 Z= 0.311 Chirality : 0.044 0.369 1891 Planarity : 0.004 0.062 2159 Dihedral : 7.440 57.978 1821 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.25 % Allowed : 17.67 % Favored : 79.08 % 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: -0.73 (0.22), residues: 1510 helix: 0.29 (0.21), residues: 607 sheet: -0.77 (0.35), residues: 203 loop : -1.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1352 HIS 0.003 0.001 HIS A 899 PHE 0.019 0.002 PHE A1198 TYR 0.031 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 603 TRP cc_start: 0.7318 (m100) cc_final: 0.7095 (m-10) REVERT: A 674 GLN cc_start: 0.8139 (tt0) cc_final: 0.7864 (tt0) REVERT: A 706 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6415 (mp) REVERT: A 768 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 792 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7639 (pp) REVERT: A 827 MET cc_start: 0.7200 (mtp) cc_final: 0.6986 (mtp) REVERT: A 835 GLU cc_start: 0.7669 (tt0) cc_final: 0.7254 (mt-10) REVERT: A 847 LYS cc_start: 0.7519 (mttp) cc_final: 0.7250 (mtpm) REVERT: A 898 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 1036 LEU cc_start: 0.5395 (pt) cc_final: 0.5078 (pp) REVERT: A 1215 TYR cc_start: 0.8602 (m-80) cc_final: 0.8366 (m-80) REVERT: B 54 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7387 (tptt) REVERT: B 80 LEU cc_start: 0.7777 (mt) cc_final: 0.7433 (tp) REVERT: B 96 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: B 292 MET cc_start: 0.7504 (tpp) cc_final: 0.6831 (ttm) REVERT: B 315 MET cc_start: 0.8871 (mmm) cc_final: 0.8493 (mmm) REVERT: B 388 MET cc_start: 0.5792 (mmp) cc_final: 0.5485 (mmt) outliers start: 43 outliers final: 35 residues processed: 173 average time/residue: 1.1253 time to fit residues: 215.0702 Evaluate side-chains 175 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 ASN B 155 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129116 restraints weight = 14991.795| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.53 r_work: 0.3393 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12613 Z= 0.304 Angle : 0.647 11.722 17089 Z= 0.334 Chirality : 0.046 0.354 1891 Planarity : 0.004 0.060 2159 Dihedral : 7.685 58.650 1821 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.40 % Allowed : 17.52 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1510 helix: 0.22 (0.21), residues: 610 sheet: -0.79 (0.35), residues: 205 loop : -1.00 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.004 0.001 HIS A 899 PHE 0.023 0.002 PHE A1198 TYR 0.034 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.14 seconds wall clock time: 85 minutes 17.05 seconds (5117.05 seconds total)