Starting phenix.real_space_refine on Fri Jul 19 21:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/07_2024/8pmd_17759_neut.cif" } resolution = 2.95 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 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5651 2.51 5 N 1497 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1186": "OE1" <-> "OE2" Residue "A GLU 1209": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8844 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8778 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 31, 'TRANS': 1097} Chain breaks: 5 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 6.33, per 1000 atoms: 0.72 Number of scatterers: 8844 At special positions: 0 Unit cell: (89.1, 79.2, 148.5, 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 52 16.00 P 6 15.00 Mg 2 11.99 O 1636 8.00 N 1497 7.00 C 5651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 68.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.690A pdb=" N LEU A 50 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 100 removed outlier: 4.312A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 4.260A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 185 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 194 through 214 removed outlier: 4.949A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 237 removed outlier: 4.304A pdb=" N GLY A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 287 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 296 through 344 removed outlier: 3.904A pdb=" N ASN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.533A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.719A pdb=" N ALA A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.568A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 748 Processing helix chain 'A' and resid 751 through 781 removed outlier: 4.402A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.670A pdb=" N GLY A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 841 removed outlier: 3.788A pdb=" N PHE A 811 " --> pdb=" O CYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.505A pdb=" N PHE A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 873 removed outlier: 4.211A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 871 " --> pdb=" O GLN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 895 Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.625A pdb=" N SER A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 946 removed outlier: 3.846A pdb=" N LEU A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 928 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 955 through 968 removed outlier: 3.994A pdb=" N PHE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1010 removed outlier: 4.416A pdb=" N LYS A 972 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1028 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.145A pdb=" N GLY A1032 " --> pdb=" O THR A1029 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A1033 " --> pdb=" O ALA A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1029 through 1033' Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 3.615A pdb=" N ALA A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1127 removed outlier: 3.556A pdb=" N ILE A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1155 removed outlier: 3.835A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.543A pdb=" N VAL A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 Processing helix chain 'A' and resid 1213 through 1217 Processing helix chain 'A' and resid 1220 through 1234 Processing helix chain 'A' and resid 1256 through 1266 Processing helix chain 'A' and resid 1299 through 1307 removed outlier: 3.597A pdb=" N LYS A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1316 Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.267A pdb=" N VAL A 425 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.267A pdb=" N VAL A 425 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE A 422 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 480 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET A 478 " --> pdb=" O ASN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.169A pdb=" N GLY A 499 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP A 583 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 501 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 580 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 613 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 582 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET A 450 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 627 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 452 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 629 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 454 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1102 through 1103 Processing sheet with id=AA5, first strand: chain 'A' and resid 1083 through 1086 removed outlier: 8.029A pdb=" N PHE A1085 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN A1097 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 6.390A pdb=" N GLY A1157 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP A1243 " --> pdb=" O GLY A1157 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A1159 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A1109 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A1108 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA A1287 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA A1110 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET A1289 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A1112 " --> pdb=" O MET A1289 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1296 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A1290 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL A1294 " --> pdb=" O ALA A1290 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1440 1.32 - 1.44: 2403 1.44 - 1.56: 5073 1.56 - 1.69: 10 1.69 - 1.81: 85 Bond restraints: 9011 Sorted by residual: bond pdb=" C PHE A1111 " pdb=" O PHE A1111 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.22e-02 6.72e+03 1.31e+01 bond pdb=" C LYS A 930 " pdb=" N GLN A 931 " ideal model delta sigma weight residual 1.335 1.297 0.037 1.36e-02 5.41e+03 7.58e+00 bond pdb=" C ALA A 773 " pdb=" N PHE A 774 " ideal model delta sigma weight residual 1.334 1.298 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" N ILE A1273 " pdb=" CA ILE A1273 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.00e+00 bond pdb=" C GLU A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 9006 not shown) Histogram of bond angle deviations from ideal: 98.33 - 106.64: 209 106.64 - 114.96: 5346 114.96 - 123.27: 6354 123.27 - 131.58: 262 131.58 - 139.89: 18 Bond angle restraints: 12189 Sorted by residual: angle pdb=" N LEU A 332 " pdb=" CA LEU A 332 " pdb=" C LEU A 332 " ideal model delta sigma weight residual 111.03 104.70 6.33 1.11e+00 8.12e-01 3.26e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" O ILE A 416 " ideal model delta sigma weight residual 121.23 115.36 5.87 1.07e+00 8.73e-01 3.01e+01 angle pdb=" CA PHE A 70 " pdb=" C PHE A 70 " pdb=" O PHE A 70 " ideal model delta sigma weight residual 120.55 115.55 5.00 1.06e+00 8.90e-01 2.22e+01 angle pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " ideal model delta sigma weight residual 117.63 122.64 -5.01 1.25e+00 6.40e-01 1.61e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 116.10 120.87 -4.77 1.20e+00 6.94e-01 1.58e+01 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4544 17.11 - 34.21: 561 34.21 - 51.32: 224 51.32 - 68.42: 43 68.42 - 85.53: 17 Dihedral angle restraints: 5389 sinusoidal: 2153 harmonic: 3236 Sorted by residual: dihedral pdb=" CA ASP A 404 " pdb=" CB ASP A 404 " pdb=" CG ASP A 404 " pdb=" OD1 ASP A 404 " ideal model delta sinusoidal sigma weight residual -30.00 -89.80 59.80 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG A 575 " pdb=" CD ARG A 575 " pdb=" NE ARG A 575 " pdb=" CZ ARG A 575 " ideal model delta sinusoidal sigma weight residual -90.00 -134.34 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 487 " pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " ideal model delta sinusoidal sigma weight residual 90.00 131.92 -41.92 2 1.50e+01 4.44e-03 9.52e+00 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1095 0.051 - 0.102: 234 0.102 - 0.153: 48 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CG LEU A 827 " pdb=" CB LEU A 827 " pdb=" CD1 LEU A 827 " pdb=" CD2 LEU A 827 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 416 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ILE A 416 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 416 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 417 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 332 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C LEU A 332 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU A 332 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 216 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C GLN A 216 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 216 " -0.018 2.00e-02 2.50e+03 pdb=" N MET A 217 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 7 2.06 - 2.77: 1751 2.77 - 3.48: 13046 3.48 - 4.19: 20598 4.19 - 4.90: 37436 Nonbonded interactions: 72838 Sorted by model distance: nonbonded pdb=" OE2 GLU A1127 " pdb=" CD1 ILE A1158 " model vdw 1.353 3.460 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.962 2.170 nonbonded pdb=" OE1 GLN A1161 " pdb="MG MG A1503 " model vdw 1.981 2.170 nonbonded pdb=" OG SER A1120 " pdb="MG MG A1503 " model vdw 2.018 2.170 nonbonded pdb=" O3G ATP A1502 " pdb="MG MG A1504 " model vdw 2.027 2.170 ... (remaining 72833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.004 0.044 9011 Z= 0.249 Angle : 0.658 6.699 12189 Z= 0.384 Chirality : 0.044 0.255 1382 Planarity : 0.004 0.054 1544 Dihedral : 18.209 85.530 3309 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.21 % Allowed : 28.83 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1117 helix: 1.42 (0.18), residues: 736 sheet: 0.56 (0.54), residues: 77 loop : -0.94 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1071 HIS 0.003 0.001 HIS A 428 PHE 0.018 0.002 PHE A 747 TYR 0.025 0.002 TYR A 337 ARG 0.009 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.858 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 1.0753 time to fit residues: 238.9888 Evaluate side-chains 187 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9011 Z= 0.228 Angle : 0.569 7.794 12189 Z= 0.309 Chirality : 0.042 0.149 1382 Planarity : 0.004 0.052 1544 Dihedral : 8.776 83.041 1285 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 7.07 % Allowed : 25.19 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1117 helix: 1.61 (0.19), residues: 742 sheet: 0.44 (0.53), residues: 77 loop : -0.95 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.024 0.002 PHE A 383 TYR 0.020 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 199 time to evaluate : 0.971 Fit side-chains REVERT: A 80 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 90 PHE cc_start: 0.7441 (m-80) cc_final: 0.7234 (m-80) REVERT: A 181 ARG cc_start: 0.7835 (mpt180) cc_final: 0.7369 (mmm160) REVERT: A 428 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7019 (p90) REVERT: A 573 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 611 ILE cc_start: 0.8890 (mt) cc_final: 0.8654 (tt) REVERT: A 956 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 1238 LYS cc_start: 0.7686 (mtpm) cc_final: 0.7426 (ttmt) REVERT: A 1313 LEU cc_start: 0.8653 (tp) cc_final: 0.8446 (mt) outliers start: 66 outliers final: 31 residues processed: 240 average time/residue: 1.0646 time to fit residues: 274.1203 Evaluate side-chains 227 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9011 Z= 0.201 Angle : 0.540 7.621 12189 Z= 0.292 Chirality : 0.041 0.137 1382 Planarity : 0.004 0.052 1544 Dihedral : 8.570 89.247 1285 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 6.65 % Allowed : 26.26 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1117 helix: 1.73 (0.19), residues: 742 sheet: 0.37 (0.52), residues: 77 loop : -0.94 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.017 0.001 PHE A 70 TYR 0.025 0.001 TYR A 337 ARG 0.004 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8045 (mt) REVERT: A 181 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7354 (mmm160) REVERT: A 254 ILE cc_start: 0.7567 (mm) cc_final: 0.7270 (tp) REVERT: A 428 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7025 (p90) REVERT: A 573 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 611 ILE cc_start: 0.8913 (mt) cc_final: 0.8688 (tt) REVERT: A 956 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: A 1001 ARG cc_start: 0.7491 (tpm170) cc_final: 0.7283 (tpm170) REVERT: A 1313 LEU cc_start: 0.8658 (tp) cc_final: 0.8435 (mt) outliers start: 62 outliers final: 27 residues processed: 241 average time/residue: 1.0544 time to fit residues: 272.4469 Evaluate side-chains 221 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1255 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9011 Z= 0.425 Angle : 0.700 12.469 12189 Z= 0.383 Chirality : 0.049 0.151 1382 Planarity : 0.005 0.053 1544 Dihedral : 8.922 89.731 1283 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 8.68 % Allowed : 25.40 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1117 helix: 0.98 (0.18), residues: 738 sheet: -0.07 (0.50), residues: 77 loop : -1.29 (0.30), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.005 0.001 HIS A 428 PHE 0.030 0.002 PHE A 776 TYR 0.023 0.002 TYR A 337 ARG 0.005 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 209 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8029 (mt) REVERT: A 173 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7802 (mtmm) REVERT: A 268 ASP cc_start: 0.8259 (t0) cc_final: 0.7978 (t70) REVERT: A 321 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7611 (m) REVERT: A 573 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (mp) REVERT: A 956 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: A 989 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: A 1313 LEU cc_start: 0.8736 (tp) cc_final: 0.8536 (mt) outliers start: 81 outliers final: 35 residues processed: 264 average time/residue: 0.9850 time to fit residues: 280.7555 Evaluate side-chains 238 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1009 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9011 Z= 0.213 Angle : 0.578 6.877 12189 Z= 0.313 Chirality : 0.043 0.188 1382 Planarity : 0.004 0.052 1544 Dihedral : 8.345 85.136 1283 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.43 % Allowed : 28.94 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1117 helix: 1.43 (0.18), residues: 744 sheet: 0.09 (0.52), residues: 77 loop : -1.08 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.001 PHE A 774 TYR 0.021 0.002 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 209 time to evaluate : 0.921 Fit side-chains REVERT: A 80 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 269 TYR cc_start: 0.7154 (m-10) cc_final: 0.6790 (m-10) REVERT: A 321 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7681 (m) REVERT: A 496 ASP cc_start: 0.8930 (p0) cc_final: 0.8683 (p0) REVERT: A 830 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7605 (ttp-110) REVERT: A 934 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 956 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 1221 ARG cc_start: 0.7992 (mpt90) cc_final: 0.7635 (mmt180) REVERT: A 1235 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6552 (mtm180) REVERT: A 1313 LEU cc_start: 0.8731 (tp) cc_final: 0.8519 (mt) outliers start: 60 outliers final: 26 residues processed: 242 average time/residue: 1.0383 time to fit residues: 269.9223 Evaluate side-chains 233 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1262 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 361 GLN A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1097 ASN A1300 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9011 Z= 0.174 Angle : 0.548 6.392 12189 Z= 0.296 Chirality : 0.041 0.176 1382 Planarity : 0.003 0.054 1544 Dihedral : 7.918 78.515 1283 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.57 % Allowed : 29.80 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1117 helix: 1.78 (0.19), residues: 741 sheet: 0.41 (0.53), residues: 77 loop : -0.87 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 PHE 0.029 0.001 PHE A 70 TYR 0.020 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7347 (m-80) cc_final: 0.7146 (m-80) REVERT: A 197 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7525 (tm-30) REVERT: A 268 ASP cc_start: 0.8203 (t0) cc_final: 0.7986 (t0) REVERT: A 269 TYR cc_start: 0.7109 (m-10) cc_final: 0.6819 (m-10) REVERT: A 438 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 496 ASP cc_start: 0.8794 (p0) cc_final: 0.8583 (p0) REVERT: A 591 ASN cc_start: 0.7649 (m-40) cc_final: 0.7403 (m110) REVERT: A 830 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7599 (ttp-110) REVERT: A 930 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7454 (mttp) REVERT: A 935 MET cc_start: 0.8434 (tpt) cc_final: 0.8188 (mmm) REVERT: A 956 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: A 1235 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6549 (mtm180) REVERT: A 1313 LEU cc_start: 0.8643 (tp) cc_final: 0.8440 (mt) outliers start: 52 outliers final: 22 residues processed: 234 average time/residue: 1.0546 time to fit residues: 265.4967 Evaluate side-chains 219 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1262 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9011 Z= 0.248 Angle : 0.591 6.541 12189 Z= 0.318 Chirality : 0.043 0.146 1382 Planarity : 0.004 0.055 1544 Dihedral : 8.039 79.518 1283 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.89 % Allowed : 29.37 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1117 helix: 1.61 (0.18), residues: 743 sheet: 0.37 (0.52), residues: 77 loop : -0.98 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 428 PHE 0.025 0.001 PHE A 774 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8220 (t0) cc_final: 0.7983 (t0) REVERT: A 269 TYR cc_start: 0.7192 (m-10) cc_final: 0.6890 (m-10) REVERT: A 321 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7657 (m) REVERT: A 438 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 591 ASN cc_start: 0.7711 (m-40) cc_final: 0.7500 (m110) REVERT: A 830 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7575 (ttp-110) REVERT: A 956 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: A 1171 MET cc_start: 0.7949 (tpp) cc_final: 0.7717 (tpt) REVERT: A 1235 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6559 (mtm180) outliers start: 55 outliers final: 30 residues processed: 228 average time/residue: 1.0081 time to fit residues: 247.2321 Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9011 Z= 0.266 Angle : 0.611 6.735 12189 Z= 0.329 Chirality : 0.044 0.161 1382 Planarity : 0.004 0.054 1544 Dihedral : 8.104 79.908 1283 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.25 % Allowed : 30.01 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1117 helix: 1.53 (0.18), residues: 743 sheet: 0.30 (0.53), residues: 77 loop : -1.04 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 428 PHE 0.029 0.002 PHE A 70 TYR 0.017 0.002 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 0.929 Fit side-chains REVERT: A 268 ASP cc_start: 0.8206 (t0) cc_final: 0.7961 (t0) REVERT: A 269 TYR cc_start: 0.7222 (m-10) cc_final: 0.6879 (m-10) REVERT: A 321 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7666 (m) REVERT: A 438 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 830 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7584 (ttp-110) REVERT: A 956 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: A 989 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6909 (mt0) REVERT: A 1001 ARG cc_start: 0.7572 (tpm170) cc_final: 0.7343 (tpm170) REVERT: A 1171 MET cc_start: 0.7969 (tpp) cc_final: 0.7750 (tpt) REVERT: A 1235 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6594 (mtm180) outliers start: 49 outliers final: 29 residues processed: 226 average time/residue: 1.0682 time to fit residues: 259.2544 Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 372 ASN A 490 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1053 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9011 Z= 0.184 Angle : 0.579 7.231 12189 Z= 0.309 Chirality : 0.042 0.153 1382 Planarity : 0.004 0.055 1544 Dihedral : 7.843 83.943 1283 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.97 % Allowed : 31.73 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1117 helix: 1.78 (0.19), residues: 743 sheet: 0.35 (0.52), residues: 78 loop : -0.88 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1071 HIS 0.004 0.001 HIS A 428 PHE 0.027 0.001 PHE A 774 TYR 0.017 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 0.948 Fit side-chains REVERT: A 268 ASP cc_start: 0.8187 (t0) cc_final: 0.7947 (t0) REVERT: A 269 TYR cc_start: 0.7138 (m-10) cc_final: 0.6838 (m-10) REVERT: A 438 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 496 ASP cc_start: 0.8919 (p0) cc_final: 0.8611 (p0) REVERT: A 830 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7522 (ttp-110) REVERT: A 956 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: A 1079 ASP cc_start: 0.6723 (p0) cc_final: 0.6432 (p0) REVERT: A 1171 MET cc_start: 0.7927 (tpp) cc_final: 0.7617 (tpt) REVERT: A 1235 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6543 (mtm180) REVERT: A 1255 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7087 (mttt) outliers start: 37 outliers final: 17 residues processed: 221 average time/residue: 1.0891 time to fit residues: 258.5498 Evaluate side-chains 210 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1255 LYS Chi-restraints excluded: chain A residue 1262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 0.0000 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9011 Z= 0.177 Angle : 0.577 7.261 12189 Z= 0.306 Chirality : 0.041 0.163 1382 Planarity : 0.004 0.057 1544 Dihedral : 7.644 87.941 1283 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.79 % Allowed : 33.23 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1117 helix: 1.88 (0.19), residues: 741 sheet: 0.43 (0.53), residues: 78 loop : -0.84 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1071 HIS 0.004 0.000 HIS A 428 PHE 0.037 0.001 PHE A 70 TYR 0.017 0.001 TYR A 337 ARG 0.010 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 0.942 Fit side-chains REVERT: A 197 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7514 (tm-30) REVERT: A 268 ASP cc_start: 0.8189 (t0) cc_final: 0.7969 (t0) REVERT: A 269 TYR cc_start: 0.7119 (m-10) cc_final: 0.6825 (m-10) REVERT: A 438 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 496 ASP cc_start: 0.8888 (p0) cc_final: 0.8569 (p0) REVERT: A 830 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7498 (ttp-110) REVERT: A 956 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: A 1079 ASP cc_start: 0.6648 (p0) cc_final: 0.6365 (p0) REVERT: A 1171 MET cc_start: 0.7861 (tpp) cc_final: 0.7604 (tpt) outliers start: 26 outliers final: 17 residues processed: 201 average time/residue: 1.1279 time to fit residues: 242.7669 Evaluate side-chains 202 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.145004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133471 restraints weight = 10698.390| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.14 r_work: 0.3429 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 317 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 321 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9011 Z= 0.275 Angle : 0.633 8.282 12189 Z= 0.339 Chirality : 0.045 0.173 1382 Planarity : 0.004 0.054 1544 Dihedral : 7.933 85.355 1283 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.79 % Allowed : 33.33 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1117 helix: 1.61 (0.18), residues: 743 sheet: 0.46 (0.53), residues: 77 loop : -0.94 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.002 PHE A 774 TYR 0.016 0.001 TYR A 337 ARG 0.011 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4317.01 seconds wall clock time: 75 minutes 44.43 seconds (4544.43 seconds total)