Starting phenix.real_space_refine on Sat Aug 23 05:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967.map" model { file = "/net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j3w_35967/08_2025/8j3w_35967_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.029 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6325 2.51 5 N 1636 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9739 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9726 Classifications: {'peptide': 1218} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'AIN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.19 Number of scatterers: 9739 At special positions: 0 Unit cell: (72.98, 114.8, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1735 8.00 N 1636 7.00 C 6325 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 - 3.00 Amino acid : True - 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: 0.75 Conformation dependent library (CDL) restraints added in 307.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 71.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.650A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.550A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.896A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 122 removed outlier: 3.607A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.872A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 151 through 181 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.645A pdb=" N LEU A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.285A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.065A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.644A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 337 removed outlier: 3.550A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 Processing helix chain 'A' and resid 368 through 392 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.851A pdb=" N CYS A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 4.036A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.983A pdb=" N LEU A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.781A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.073A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.535A pdb=" N SER A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.792A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 632 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.675A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.932A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.502A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.852A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.986A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.081A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 886 Proline residue: A 870 - end of helix removed outlier: 3.651A pdb=" N GLU A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.613A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.643A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 969 removed outlier: 3.529A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1018 removed outlier: 3.503A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.507A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1224 through 1226 No H-bonds generated for 'chain 'A' and resid 1224 through 1226' Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.694A pdb=" N ILE A1239 " --> pdb=" O ASN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.672A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.732A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435 removed outlier: 4.731A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.248A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1065 removed outlier: 6.046A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.594A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1854 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: 1.36 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1547 1.31 - 1.43: 2627 1.43 - 1.56: 5704 1.56 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 9948 Sorted by residual: bond pdb=" C8 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 1.346 1.398 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" CE LYS A1097 " pdb=" NZ LYS A1097 " ideal model delta sigma weight residual 1.489 1.433 0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" C8 AIN A1401 " pdb=" C9 AIN A1401 " ideal model delta sigma weight residual 1.495 1.527 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CB LYS A1097 " pdb=" CG LYS A1097 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C2 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 1.377 1.400 -0.023 2.00e-02 2.50e+03 1.27e+00 ... (remaining 9943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13208 1.96 - 3.92: 249 3.92 - 5.89: 18 5.89 - 7.85: 3 7.85 - 9.81: 1 Bond angle restraints: 13479 Sorted by residual: angle pdb=" N VAL A 889 " pdb=" CA VAL A 889 " pdb=" C VAL A 889 " ideal model delta sigma weight residual 111.45 107.82 3.63 9.30e-01 1.16e+00 1.53e+01 angle pdb=" C TYR A 917 " pdb=" N LYS A 918 " pdb=" CA LYS A 918 " ideal model delta sigma weight residual 122.07 115.69 6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N ILE A 969 " pdb=" CA ILE A 969 " pdb=" C ILE A 969 " ideal model delta sigma weight residual 112.98 108.42 4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" N ASP A 405 " pdb=" CA ASP A 405 " pdb=" C ASP A 405 " ideal model delta sigma weight residual 112.97 109.41 3.56 1.06e+00 8.90e-01 1.13e+01 angle pdb=" C9 AIN A1401 " pdb=" C8 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 110.82 120.63 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 13474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5361 17.31 - 34.62: 475 34.62 - 51.93: 83 51.93 - 69.24: 15 69.24 - 86.55: 11 Dihedral angle restraints: 5945 sinusoidal: 2386 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PHE A 336 " pdb=" C PHE A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PHE A 418 " pdb=" C PHE A 418 " pdb=" N TRP A 419 " pdb=" CA TRP A 419 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1116 0.037 - 0.074: 333 0.074 - 0.110: 91 0.110 - 0.147: 17 0.147 - 0.184: 4 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CG LEU A1104 " pdb=" CB LEU A1104 " pdb=" CD1 LEU A1104 " pdb=" CD2 LEU A1104 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE A 861 " pdb=" N ILE A 861 " pdb=" C ILE A 861 " pdb=" CB ILE A 861 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE A1231 " pdb=" N ILE A1231 " pdb=" C ILE A1231 " pdb=" CB ILE A1231 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 1558 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A 110 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 28 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 29 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 836 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 837 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.028 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 89 2.49 - 3.09: 7656 3.09 - 3.70: 15240 3.70 - 4.30: 23111 4.30 - 4.90: 37605 Nonbonded interactions: 83701 Sorted by model distance: nonbonded pdb=" OG1 THR A 99 " pdb=" OH TYR A 155 " model vdw 1.891 3.040 nonbonded pdb=" OG SER A 570 " pdb=" OH TYR A 596 " model vdw 1.933 3.040 nonbonded pdb=" O THR A 488 " pdb=" OG SER A 491 " model vdw 1.959 3.040 nonbonded pdb=" O ILE A 331 " pdb=" OG1 THR A 335 " model vdw 1.991 3.040 nonbonded pdb=" OE2 GLU A 102 " pdb=" ND1 HIS A 152 " model vdw 2.007 3.120 ... (remaining 83696 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: 1.450 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.056 9948 Z= 0.188 Angle : 0.679 9.810 13479 Z= 0.411 Chirality : 0.039 0.184 1561 Planarity : 0.005 0.075 1676 Dihedral : 13.932 86.553 3639 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.23), residues: 1212 helix: -1.18 (0.17), residues: 788 sheet: -0.75 (0.62), residues: 64 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 398 TYR 0.018 0.002 TYR A 917 PHE 0.019 0.002 PHE A 352 TRP 0.020 0.002 TRP A1147 HIS 0.017 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9948) covalent geometry : angle 0.67900 (13479) hydrogen bonds : bond 0.15925 ( 636) hydrogen bonds : angle 7.92184 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 SER cc_start: 0.8582 (t) cc_final: 0.8264 (p) REVERT: A 301 ASN cc_start: 0.7845 (m110) cc_final: 0.7362 (m110) REVERT: A 893 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0659 time to fit residues: 13.7733 Evaluate side-chains 117 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 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 76 GLN A 710 HIS A 903 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.241491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184579 restraints weight = 11275.818| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.31 r_work: 0.3622 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9948 Z= 0.251 Angle : 0.688 7.493 13479 Z= 0.364 Chirality : 0.045 0.161 1561 Planarity : 0.006 0.071 1676 Dihedral : 5.425 29.986 1318 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.75 % Allowed : 5.84 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.23), residues: 1212 helix: -0.55 (0.17), residues: 790 sheet: -0.87 (0.56), residues: 74 loop : -0.73 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 824 TYR 0.020 0.002 TYR A 157 PHE 0.029 0.002 PHE A 352 TRP 0.021 0.002 TRP A 947 HIS 0.011 0.002 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9948) covalent geometry : angle 0.68795 (13479) hydrogen bonds : bond 0.06054 ( 636) hydrogen bonds : angle 6.08261 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.318 Fit side-chains REVERT: A 102 GLU cc_start: 0.8212 (tt0) cc_final: 0.7493 (tt0) REVERT: A 291 TRP cc_start: 0.8071 (m-10) cc_final: 0.6936 (m-90) REVERT: A 296 SER cc_start: 0.8514 (t) cc_final: 0.8285 (p) REVERT: A 301 ASN cc_start: 0.8098 (m110) cc_final: 0.7521 (m110) REVERT: A 363 LEU cc_start: 0.8002 (mm) cc_final: 0.7693 (mm) REVERT: A 374 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: A 409 MET cc_start: 0.6485 (ppp) cc_final: 0.6044 (mpp) REVERT: A 1025 TRP cc_start: 0.8648 (m-10) cc_final: 0.8376 (m-10) REVERT: A 1089 PHE cc_start: 0.8650 (m-80) cc_final: 0.8438 (m-80) REVERT: A 1111 HIS cc_start: 0.7211 (m170) cc_final: 0.6919 (m-70) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.0903 time to fit residues: 17.7527 Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS A 909 GLN ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.246681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.192216 restraints weight = 11353.294| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.23 r_work: 0.3711 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9948 Z= 0.144 Angle : 0.562 7.588 13479 Z= 0.298 Chirality : 0.040 0.163 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.977 30.504 1318 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.41 % Allowed : 7.44 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.24), residues: 1212 helix: 0.05 (0.18), residues: 795 sheet: -0.15 (0.63), residues: 64 loop : -0.49 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 922 TYR 0.017 0.002 TYR A 157 PHE 0.017 0.001 PHE A 352 TRP 0.018 0.001 TRP A 947 HIS 0.010 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9948) covalent geometry : angle 0.56172 (13479) hydrogen bonds : bond 0.05211 ( 636) hydrogen bonds : angle 5.51776 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.348 Fit side-chains REVERT: A 102 GLU cc_start: 0.8176 (tt0) cc_final: 0.7450 (tt0) REVERT: A 301 ASN cc_start: 0.8077 (m110) cc_final: 0.7492 (m110) REVERT: A 363 LEU cc_start: 0.7971 (mm) cc_final: 0.7620 (mm) REVERT: A 374 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 409 MET cc_start: 0.6558 (ppp) cc_final: 0.6241 (mpp) REVERT: A 744 MET cc_start: 0.7611 (tpp) cc_final: 0.7290 (mpp) REVERT: A 829 ILE cc_start: 0.8262 (mm) cc_final: 0.7828 (mm) REVERT: A 1112 ASP cc_start: 0.8370 (m-30) cc_final: 0.7070 (t0) outliers start: 15 outliers final: 6 residues processed: 153 average time/residue: 0.0906 time to fit residues: 20.4658 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 105 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.246532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.191437 restraints weight = 11329.581| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.24 r_work: 0.3705 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9948 Z= 0.153 Angle : 0.552 8.248 13479 Z= 0.293 Chirality : 0.041 0.170 1561 Planarity : 0.005 0.062 1676 Dihedral : 4.766 29.283 1318 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.88 % Allowed : 8.76 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.24), residues: 1212 helix: 0.24 (0.18), residues: 800 sheet: -0.37 (0.61), residues: 72 loop : -0.28 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1189 TYR 0.022 0.002 TYR A1016 PHE 0.019 0.002 PHE A 352 TRP 0.018 0.001 TRP A 947 HIS 0.009 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9948) covalent geometry : angle 0.55213 (13479) hydrogen bonds : bond 0.05008 ( 636) hydrogen bonds : angle 5.31428 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.367 Fit side-chains REVERT: A 102 GLU cc_start: 0.8159 (tt0) cc_final: 0.6977 (pt0) REVERT: A 247 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6875 (mm) REVERT: A 301 ASN cc_start: 0.8081 (m110) cc_final: 0.7465 (m110) REVERT: A 374 GLU cc_start: 0.7965 (tt0) cc_final: 0.7394 (mt-10) REVERT: A 409 MET cc_start: 0.6654 (ppp) cc_final: 0.6382 (mpp) REVERT: A 744 MET cc_start: 0.7676 (tpp) cc_final: 0.7244 (mpp) REVERT: A 1071 VAL cc_start: 0.5656 (OUTLIER) cc_final: 0.5005 (t) REVERT: A 1112 ASP cc_start: 0.8392 (m-30) cc_final: 0.7114 (t0) outliers start: 20 outliers final: 13 residues processed: 141 average time/residue: 0.0929 time to fit residues: 19.2012 Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.247051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.192705 restraints weight = 11442.684| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.22 r_work: 0.3705 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9948 Z= 0.149 Angle : 0.555 8.688 13479 Z= 0.289 Chirality : 0.040 0.145 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.612 26.964 1318 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.98 % Allowed : 9.98 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1212 helix: 0.43 (0.18), residues: 802 sheet: -0.08 (0.60), residues: 73 loop : -0.24 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1189 TYR 0.014 0.001 TYR A1016 PHE 0.018 0.001 PHE A 352 TRP 0.018 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9948) covalent geometry : angle 0.55534 (13479) hydrogen bonds : bond 0.04859 ( 636) hydrogen bonds : angle 5.15269 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.413 Fit side-chains REVERT: A 102 GLU cc_start: 0.8097 (tt0) cc_final: 0.7146 (pt0) REVERT: A 247 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6958 (mm) REVERT: A 291 TRP cc_start: 0.7955 (m-10) cc_final: 0.6746 (m-10) REVERT: A 301 ASN cc_start: 0.8098 (m110) cc_final: 0.7453 (m-40) REVERT: A 374 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 409 MET cc_start: 0.6691 (ppp) cc_final: 0.6487 (mpp) REVERT: A 492 ASN cc_start: 0.5410 (OUTLIER) cc_final: 0.5079 (t0) REVERT: A 744 MET cc_start: 0.7677 (tpp) cc_final: 0.7356 (mpp) REVERT: A 1112 ASP cc_start: 0.8388 (m-30) cc_final: 0.7113 (t0) REVERT: A 1147 TRP cc_start: 0.7412 (m100) cc_final: 0.6979 (m100) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.0949 time to fit residues: 20.2210 Evaluate side-chains 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 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 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.244893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.190197 restraints weight = 11278.723| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.34 r_work: 0.3670 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9948 Z= 0.183 Angle : 0.587 9.821 13479 Z= 0.302 Chirality : 0.042 0.159 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.595 27.562 1318 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.35 % Allowed : 10.73 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.24), residues: 1212 helix: 0.46 (0.18), residues: 802 sheet: 0.05 (0.61), residues: 73 loop : -0.23 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.013 0.002 TYR A1016 PHE 0.021 0.002 PHE A 352 TRP 0.020 0.002 TRP A 64 HIS 0.007 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9948) covalent geometry : angle 0.58668 (13479) hydrogen bonds : bond 0.04943 ( 636) hydrogen bonds : angle 5.15674 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8107 (tt0) cc_final: 0.7031 (pt0) REVERT: A 109 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: A 247 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6934 (mm) REVERT: A 301 ASN cc_start: 0.8109 (m110) cc_final: 0.7439 (m-40) REVERT: A 374 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: A 409 MET cc_start: 0.6772 (ppp) cc_final: 0.6526 (mpp) REVERT: A 492 ASN cc_start: 0.5351 (OUTLIER) cc_final: 0.5096 (t0) REVERT: A 744 MET cc_start: 0.7795 (tpp) cc_final: 0.7361 (mpp) REVERT: A 815 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7535 (mtm110) REVERT: A 1112 ASP cc_start: 0.8341 (m-30) cc_final: 0.7108 (t0) REVERT: A 1147 TRP cc_start: 0.7412 (m100) cc_final: 0.7008 (m100) REVERT: A 1245 MET cc_start: 0.6850 (ppp) cc_final: 0.6516 (ppp) outliers start: 25 outliers final: 16 residues processed: 140 average time/residue: 0.0861 time to fit residues: 18.1610 Evaluate side-chains 140 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 0.0770 chunk 41 optimal weight: 8.9990 chunk 18 optimal weight: 0.0670 chunk 112 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.248955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.194655 restraints weight = 11277.363| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.89 r_work: 0.3767 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9948 Z= 0.126 Angle : 0.542 9.131 13479 Z= 0.279 Chirality : 0.040 0.168 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.466 27.285 1318 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 12.34 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.24), residues: 1212 helix: 0.70 (0.18), residues: 803 sheet: 0.23 (0.63), residues: 73 loop : -0.08 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 922 TYR 0.011 0.001 TYR A1292 PHE 0.013 0.001 PHE A 352 TRP 0.020 0.001 TRP A1025 HIS 0.008 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9948) covalent geometry : angle 0.54195 (13479) hydrogen bonds : bond 0.04566 ( 636) hydrogen bonds : angle 4.94334 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7978 (tt0) cc_final: 0.7164 (pt0) REVERT: A 109 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: A 247 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7082 (mm) REVERT: A 301 ASN cc_start: 0.8088 (m110) cc_final: 0.7422 (m-40) REVERT: A 374 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 1112 ASP cc_start: 0.8337 (m-30) cc_final: 0.7044 (t0) REVERT: A 1147 TRP cc_start: 0.7381 (m100) cc_final: 0.6941 (m100) REVERT: A 1245 MET cc_start: 0.6731 (ppp) cc_final: 0.6424 (ppp) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.0853 time to fit residues: 18.5635 Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.0770 chunk 95 optimal weight: 0.0060 chunk 114 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 710 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.249156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.194771 restraints weight = 11262.885| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.14 r_work: 0.3763 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9948 Z= 0.133 Angle : 0.559 9.966 13479 Z= 0.284 Chirality : 0.040 0.189 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.430 28.708 1318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.04 % Allowed : 13.37 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1212 helix: 0.79 (0.18), residues: 802 sheet: 0.17 (0.62), residues: 73 loop : 0.01 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 922 TYR 0.012 0.001 TYR A1016 PHE 0.016 0.001 PHE A 352 TRP 0.018 0.001 TRP A1025 HIS 0.008 0.001 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9948) covalent geometry : angle 0.55917 (13479) hydrogen bonds : bond 0.04576 ( 636) hydrogen bonds : angle 4.87499 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.367 Fit side-chains REVERT: A 102 GLU cc_start: 0.7992 (tt0) cc_final: 0.7140 (pt0) REVERT: A 109 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: A 247 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7143 (mm) REVERT: A 270 ASP cc_start: 0.8285 (m-30) cc_final: 0.8067 (m-30) REVERT: A 291 TRP cc_start: 0.7903 (m-10) cc_final: 0.7069 (m-10) REVERT: A 301 ASN cc_start: 0.8071 (m110) cc_final: 0.7416 (m-40) REVERT: A 374 GLU cc_start: 0.7952 (tt0) cc_final: 0.7414 (mt-10) REVERT: A 744 MET cc_start: 0.7697 (tpp) cc_final: 0.7278 (mpp) REVERT: A 1112 ASP cc_start: 0.8320 (m-30) cc_final: 0.7005 (t0) REVERT: A 1147 TRP cc_start: 0.7405 (m100) cc_final: 0.6998 (m100) REVERT: A 1169 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6400 (tm-30) REVERT: A 1245 MET cc_start: 0.6595 (ppp) cc_final: 0.6278 (ppp) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.0890 time to fit residues: 17.5913 Evaluate side-chains 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.248272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193807 restraints weight = 11227.067| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 3.07 r_work: 0.3740 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9948 Z= 0.146 Angle : 0.574 10.655 13479 Z= 0.291 Chirality : 0.041 0.177 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.463 29.542 1318 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.69 % Allowed : 13.28 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1212 helix: 0.79 (0.18), residues: 802 sheet: 0.13 (0.61), residues: 73 loop : 0.01 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 436 TYR 0.012 0.001 TYR A1016 PHE 0.018 0.001 PHE A 352 TRP 0.023 0.002 TRP A1025 HIS 0.008 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9948) covalent geometry : angle 0.57412 (13479) hydrogen bonds : bond 0.04630 ( 636) hydrogen bonds : angle 4.87270 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.349 Fit side-chains REVERT: A 102 GLU cc_start: 0.7987 (tt0) cc_final: 0.7015 (pt0) REVERT: A 109 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: A 247 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 270 ASP cc_start: 0.8289 (m-30) cc_final: 0.8067 (m-30) REVERT: A 291 TRP cc_start: 0.7893 (m-10) cc_final: 0.7121 (m-10) REVERT: A 301 ASN cc_start: 0.8065 (m110) cc_final: 0.7399 (m-40) REVERT: A 374 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 744 MET cc_start: 0.7791 (tpp) cc_final: 0.7271 (mpp) REVERT: A 1112 ASP cc_start: 0.8325 (m-30) cc_final: 0.6996 (t0) REVERT: A 1147 TRP cc_start: 0.7414 (m100) cc_final: 0.7041 (m100) REVERT: A 1169 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6413 (tm-30) REVERT: A 1245 MET cc_start: 0.6535 (ppp) cc_final: 0.6169 (ppp) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.0883 time to fit residues: 17.7038 Evaluate side-chains 136 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 0.0070 chunk 94 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.248895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.195509 restraints weight = 11225.018| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.01 r_work: 0.3762 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9948 Z= 0.134 Angle : 0.564 11.142 13479 Z= 0.284 Chirality : 0.041 0.184 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.409 28.591 1318 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.60 % Allowed : 13.18 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1212 helix: 0.85 (0.18), residues: 802 sheet: 0.15 (0.62), residues: 73 loop : 0.05 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 922 TYR 0.012 0.001 TYR A1016 PHE 0.016 0.001 PHE A 352 TRP 0.022 0.001 TRP A1025 HIS 0.008 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9948) covalent geometry : angle 0.56393 (13479) hydrogen bonds : bond 0.04515 ( 636) hydrogen bonds : angle 4.82350 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.372 Fit side-chains REVERT: A 102 GLU cc_start: 0.7949 (tt0) cc_final: 0.7013 (pt0) REVERT: A 109 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: A 247 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7193 (mm) REVERT: A 270 ASP cc_start: 0.8277 (m-30) cc_final: 0.8061 (m-30) REVERT: A 301 ASN cc_start: 0.8071 (m110) cc_final: 0.7423 (m110) REVERT: A 374 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: A 744 MET cc_start: 0.7813 (tpp) cc_final: 0.7254 (mpp) REVERT: A 1047 ASN cc_start: 0.6596 (t0) cc_final: 0.6293 (t0) REVERT: A 1112 ASP cc_start: 0.8210 (m-30) cc_final: 0.7263 (t0) REVERT: A 1147 TRP cc_start: 0.7441 (m100) cc_final: 0.7100 (m100) REVERT: A 1169 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 1245 MET cc_start: 0.6437 (ppp) cc_final: 0.6106 (ppp) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.0844 time to fit residues: 17.2154 Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 98 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 117 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.249101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.195660 restraints weight = 11177.767| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.26 r_work: 0.3759 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.137 Angle : 0.577 11.229 13479 Z= 0.288 Chirality : 0.041 0.223 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.371 28.384 1318 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.69 % Allowed : 13.18 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1212 helix: 0.89 (0.18), residues: 802 sheet: 0.29 (0.62), residues: 73 loop : 0.09 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 922 TYR 0.013 0.001 TYR A 764 PHE 0.017 0.001 PHE A 352 TRP 0.026 0.002 TRP A1025 HIS 0.008 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9948) covalent geometry : angle 0.57658 (13479) hydrogen bonds : bond 0.04508 ( 636) hydrogen bonds : angle 4.79427 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.55 seconds wall clock time: 52 minutes 30.16 seconds (3150.16 seconds total)