Starting phenix.real_space_refine on Wed Apr 30 20:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j3w_35967/04_2025/8j3w_35967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j3w_35967/04_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_35967/04_2025/8j3w_35967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j3w_35967/04_2025/8j3w_35967.map" model { file = "/net/cci-nas-00/data/ceres_data/8j3w_35967/04_2025/8j3w_35967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j3w_35967/04_2025/8j3w_35967_neut.cif" } resolution = 3.07 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= 0.029 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.45, per 1000 atoms: 0.66 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: 3.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.18 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: 3.99 Time building geometry restraints manager: 3.42 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.950 Find NCS groups from input model: 0.110 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- 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 (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: -1.89 (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 TRP 0.020 0.002 TRP A1147 HIS 0.017 0.002 HIS A 213 PHE 0.019 0.002 PHE A 352 TYR 0.018 0.002 TYR A 917 ARG 0.006 0.001 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.15925 ( 636) hydrogen bonds : angle 7.92184 ( 1854) covalent geometry : bond 0.00366 ( 9948) covalent geometry : angle 0.67900 (13479) *********************** 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 : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7423 (tt0) cc_final: 0.6672 (pt0) REVERT: A 288 MET cc_start: 0.8040 (mtt) cc_final: 0.7806 (mtp) 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 409 MET cc_start: 0.6203 (ppp) cc_final: 0.5847 (mpp) 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: 0.2264 time to fit residues: 47.3970 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS A 903 HIS ** 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 = 0.4680 r_free = 0.4680 target = 0.244131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.188216 restraints weight = 11230.041| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.89 r_work: 0.3686 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9948 Z= 0.194 Angle : 0.651 6.798 13479 Z= 0.346 Chirality : 0.043 0.152 1561 Planarity : 0.006 0.068 1676 Dihedral : 5.332 36.251 1318 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 4.80 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.93 (0.23), residues: 1212 helix: -0.40 (0.18), residues: 786 sheet: -0.80 (0.56), residues: 74 loop : -0.67 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.011 0.002 HIS A 934 PHE 0.026 0.002 PHE A 352 TYR 0.022 0.002 TYR A 157 ARG 0.006 0.001 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.05976 ( 636) hydrogen bonds : angle 6.00833 ( 1854) covalent geometry : bond 0.00426 ( 9948) covalent geometry : angle 0.65078 (13479) *********************** 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 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.016 Fit side-chains REVERT: A 102 GLU cc_start: 0.8109 (tt0) cc_final: 0.7322 (tt0) REVERT: A 291 TRP cc_start: 0.7993 (m-10) cc_final: 0.6874 (m-90) REVERT: A 296 SER cc_start: 0.8491 (t) cc_final: 0.8288 (p) REVERT: A 301 ASN cc_start: 0.8088 (m110) cc_final: 0.7536 (m110) REVERT: A 363 LEU cc_start: 0.7987 (mm) cc_final: 0.7686 (mm) REVERT: A 374 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: A 409 MET cc_start: 0.6625 (ppp) cc_final: 0.6013 (mpp) REVERT: A 1089 PHE cc_start: 0.8655 (m-80) cc_final: 0.8409 (m-80) outliers start: 9 outliers final: 4 residues processed: 137 average time/residue: 0.2080 time to fit residues: 42.4046 Evaluate side-chains 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.246348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190951 restraints weight = 11355.097| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 3.15 r_work: 0.3695 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2003 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= 0.157 Angle : 0.566 7.355 13479 Z= 0.301 Chirality : 0.041 0.151 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.981 31.067 1318 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 7.44 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.34 (0.24), residues: 1212 helix: 0.03 (0.18), residues: 795 sheet: -0.57 (0.57), residues: 76 loop : -0.39 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.010 0.001 HIS A 934 PHE 0.020 0.002 PHE A 352 TYR 0.017 0.002 TYR A 157 ARG 0.004 0.000 ARG A 922 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 636) hydrogen bonds : angle 5.51124 ( 1854) covalent geometry : bond 0.00341 ( 9948) covalent geometry : angle 0.56621 (13479) *********************** 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 155 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.996 Fit side-chains REVERT: A 102 GLU cc_start: 0.8193 (tt0) cc_final: 0.7477 (tt0) REVERT: A 291 TRP cc_start: 0.7910 (m-10) cc_final: 0.6958 (m-10) REVERT: A 301 ASN cc_start: 0.8116 (m110) cc_final: 0.7526 (m110) REVERT: A 374 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: A 409 MET cc_start: 0.6633 (ppp) cc_final: 0.6230 (mpp) REVERT: A 744 MET cc_start: 0.7733 (tpp) cc_final: 0.7464 (mpp) REVERT: A 1112 ASP cc_start: 0.8456 (m-30) cc_final: 0.8126 (m-30) outliers start: 16 outliers final: 8 residues processed: 147 average time/residue: 0.2063 time to fit residues: 44.8501 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 967 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A 924 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 = 0.4670 r_free = 0.4670 target = 0.242993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.187130 restraints weight = 11268.539| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 3.15 r_work: 0.3648 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9948 Z= 0.221 Angle : 0.594 6.923 13479 Z= 0.314 Chirality : 0.043 0.175 1561 Planarity : 0.005 0.065 1676 Dihedral : 4.878 28.925 1318 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 8.66 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.27 (0.24), residues: 1212 helix: 0.10 (0.18), residues: 797 sheet: -0.26 (0.64), residues: 66 loop : -0.46 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 947 HIS 0.008 0.001 HIS A 153 PHE 0.025 0.002 PHE A 352 TYR 0.016 0.002 TYR A 92 ARG 0.007 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.05316 ( 636) hydrogen bonds : angle 5.45761 ( 1854) covalent geometry : bond 0.00504 ( 9948) covalent geometry : angle 0.59381 (13479) *********************** 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: 23 poor density : 126 time to evaluate : 1.105 Fit side-chains REVERT: A 102 GLU cc_start: 0.8195 (tt0) cc_final: 0.7007 (pt0) REVERT: A 247 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6853 (mm) REVERT: A 291 TRP cc_start: 0.8101 (m-10) cc_final: 0.7005 (m-90) REVERT: A 301 ASN cc_start: 0.8127 (m110) cc_final: 0.7502 (m110) REVERT: A 374 GLU cc_start: 0.7961 (tt0) cc_final: 0.7370 (mt-10) REVERT: A 409 MET cc_start: 0.6683 (ppp) cc_final: 0.6310 (mpp) REVERT: A 744 MET cc_start: 0.7651 (tpp) cc_final: 0.7341 (mpp) REVERT: A 1071 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5192 (t) REVERT: A 1112 ASP cc_start: 0.8380 (m-30) cc_final: 0.6962 (t0) outliers start: 23 outliers final: 14 residues processed: 141 average time/residue: 0.2114 time to fit residues: 44.3522 Evaluate side-chains 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 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 489 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 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 105 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.245941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.190670 restraints weight = 11301.877| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.37 r_work: 0.3686 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9948 Z= 0.162 Angle : 0.549 8.227 13479 Z= 0.288 Chirality : 0.040 0.145 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.656 27.269 1318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.88 % Allowed : 9.60 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1212 helix: 0.32 (0.18), residues: 799 sheet: -0.12 (0.61), residues: 73 loop : -0.25 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.021 0.002 PHE A 352 TYR 0.014 0.001 TYR A 92 ARG 0.003 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 636) hydrogen bonds : angle 5.22870 ( 1854) covalent geometry : bond 0.00355 ( 9948) covalent geometry : angle 0.54879 (13479) *********************** 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 146 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.115 Fit side-chains REVERT: A 102 GLU cc_start: 0.8089 (tt0) cc_final: 0.7135 (pt0) REVERT: A 109 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: A 247 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6936 (mm) REVERT: A 291 TRP cc_start: 0.8022 (m-10) cc_final: 0.7369 (m-10) REVERT: A 301 ASN cc_start: 0.8114 (m110) cc_final: 0.7486 (m110) REVERT: A 374 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 409 MET cc_start: 0.6735 (ppp) cc_final: 0.6398 (mpp) REVERT: A 492 ASN cc_start: 0.5343 (OUTLIER) cc_final: 0.4817 (t0) REVERT: A 744 MET cc_start: 0.7798 (tpp) cc_final: 0.7424 (mpp) REVERT: A 1112 ASP cc_start: 0.8379 (m-30) cc_final: 0.6954 (t0) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.1836 time to fit residues: 38.2161 Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 489 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 811 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 26 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 0.0170 chunk 54 optimal weight: 5.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- 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 = 0.4680 r_free = 0.4680 target = 0.244310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188971 restraints weight = 11353.214| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.28 r_work: 0.3655 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9948 Z= 0.198 Angle : 0.596 16.487 13479 Z= 0.309 Chirality : 0.042 0.163 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.647 29.700 1318 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.73 % Allowed : 10.45 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1212 helix: 0.37 (0.18), residues: 799 sheet: 0.02 (0.61), residues: 73 loop : -0.32 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.023 0.002 PHE A 352 TYR 0.016 0.002 TYR A 92 ARG 0.004 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 636) hydrogen bonds : angle 5.22168 ( 1854) covalent geometry : bond 0.00448 ( 9948) covalent geometry : angle 0.59639 (13479) *********************** 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 154 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.756 Fit side-chains REVERT: A 102 GLU cc_start: 0.8077 (tt0) cc_final: 0.7163 (pt0) REVERT: A 184 MET cc_start: 0.8201 (ttm) cc_final: 0.7995 (ttt) REVERT: A 247 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 291 TRP cc_start: 0.8054 (m-10) cc_final: 0.6916 (m-90) REVERT: A 301 ASN cc_start: 0.8117 (m110) cc_final: 0.7439 (m-40) REVERT: A 374 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: A 409 MET cc_start: 0.6750 (ppp) cc_final: 0.6478 (mpp) REVERT: A 492 ASN cc_start: 0.5416 (OUTLIER) cc_final: 0.4922 (t0) REVERT: A 1112 ASP cc_start: 0.8403 (m-30) cc_final: 0.6993 (t0) outliers start: 29 outliers final: 19 residues processed: 144 average time/residue: 0.2200 time to fit residues: 46.1317 Evaluate side-chains 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 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 811 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 967 SER Chi-restraints excluded: chain A residue 969 ILE 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 48 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.243845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188092 restraints weight = 11386.271| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.20 r_work: 0.3653 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9948 Z= 0.208 Angle : 0.597 13.561 13479 Z= 0.311 Chirality : 0.043 0.199 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.640 29.492 1318 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.73 % Allowed : 11.30 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.12 (0.24), residues: 1212 helix: 0.37 (0.18), residues: 801 sheet: 0.12 (0.62), residues: 73 loop : -0.32 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.024 0.002 PHE A 352 TYR 0.017 0.002 TYR A 92 ARG 0.005 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 636) hydrogen bonds : angle 5.23142 ( 1854) covalent geometry : bond 0.00472 ( 9948) covalent geometry : angle 0.59716 (13479) *********************** 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: 29 poor density : 121 time to evaluate : 1.094 Fit side-chains REVERT: A 102 GLU cc_start: 0.8071 (tt0) cc_final: 0.7176 (pt0) REVERT: A 109 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: A 247 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6958 (mm) REVERT: A 291 TRP cc_start: 0.7995 (m-10) cc_final: 0.6983 (m-90) REVERT: A 301 ASN cc_start: 0.8111 (m110) cc_final: 0.7416 (m-40) REVERT: A 319 MET cc_start: 0.7242 (mmt) cc_final: 0.6966 (mmm) REVERT: A 374 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 409 MET cc_start: 0.6745 (ppp) cc_final: 0.6482 (mpp) REVERT: A 492 ASN cc_start: 0.5312 (OUTLIER) cc_final: 0.4857 (t0) REVERT: A 815 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7582 (mtm110) REVERT: A 911 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7814 (tt) REVERT: A 1112 ASP cc_start: 0.8466 (m-30) cc_final: 0.7078 (t0) outliers start: 29 outliers final: 21 residues processed: 139 average time/residue: 0.1898 time to fit residues: 39.5463 Evaluate side-chains 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 233 ILE 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 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 811 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 911 LEU Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 ILE 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 81 optimal weight: 0.6980 chunk 120 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 GLN A1216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.241574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.184591 restraints weight = 11389.303| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.22 r_work: 0.3609 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 9948 Z= 0.285 Angle : 0.667 18.596 13479 Z= 0.344 Chirality : 0.045 0.250 1561 Planarity : 0.005 0.065 1676 Dihedral : 4.770 30.649 1318 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.54 % Allowed : 11.77 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.06 (0.24), residues: 1212 helix: 0.20 (0.18), residues: 802 sheet: 0.13 (0.62), residues: 73 loop : -0.32 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 947 HIS 0.010 0.002 HIS A 153 PHE 0.030 0.002 PHE A 352 TYR 0.019 0.002 TYR A 92 ARG 0.007 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.05448 ( 636) hydrogen bonds : angle 5.37811 ( 1854) covalent geometry : bond 0.00661 ( 9948) covalent geometry : angle 0.66746 (13479) *********************** 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 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.980 Fit side-chains REVERT: A 102 GLU cc_start: 0.8090 (tt0) cc_final: 0.7015 (pt0) REVERT: A 109 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 247 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6931 (mm) REVERT: A 291 TRP cc_start: 0.8043 (m-10) cc_final: 0.7067 (m-90) REVERT: A 301 ASN cc_start: 0.8150 (m110) cc_final: 0.7441 (m-40) REVERT: A 319 MET cc_start: 0.7384 (mmt) cc_final: 0.7104 (mmm) REVERT: A 374 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: A 409 MET cc_start: 0.6785 (ppp) cc_final: 0.6481 (mpp) REVERT: A 492 ASN cc_start: 0.5229 (OUTLIER) cc_final: 0.4718 (t0) REVERT: A 815 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7581 (mtm110) REVERT: A 911 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7880 (tt) REVERT: A 1047 ASN cc_start: 0.6249 (t0) cc_final: 0.5943 (t0) REVERT: A 1112 ASP cc_start: 0.8453 (m-30) cc_final: 0.7098 (t0) outliers start: 27 outliers final: 20 residues processed: 138 average time/residue: 0.1802 time to fit residues: 37.2435 Evaluate side-chains 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 233 ILE 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 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 811 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 911 LEU Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 ILE 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 84 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.246057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.190833 restraints weight = 11303.315| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.41 r_work: 0.3700 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9948 Z= 0.151 Angle : 0.573 15.931 13479 Z= 0.296 Chirality : 0.041 0.209 1561 Planarity : 0.005 0.067 1676 Dihedral : 4.576 28.612 1318 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.07 % Allowed : 12.62 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.28 (0.24), residues: 1212 helix: 0.46 (0.18), residues: 803 sheet: 0.22 (0.61), residues: 73 loop : -0.18 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 947 HIS 0.010 0.001 HIS A 934 PHE 0.025 0.001 PHE A 112 TYR 0.017 0.002 TYR A 92 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 636) hydrogen bonds : angle 5.12836 ( 1854) covalent geometry : bond 0.00328 ( 9948) covalent geometry : angle 0.57314 (13479) *********************** 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 143 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.138 Fit side-chains REVERT: A 102 GLU cc_start: 0.8018 (tt0) cc_final: 0.7247 (pt0) REVERT: A 109 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: A 247 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6989 (mm) REVERT: A 291 TRP cc_start: 0.7963 (m-10) cc_final: 0.6970 (m-90) REVERT: A 301 ASN cc_start: 0.8080 (m110) cc_final: 0.7384 (m-40) REVERT: A 374 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: A 409 MET cc_start: 0.6741 (ppp) cc_final: 0.6490 (mpp) REVERT: A 492 ASN cc_start: 0.5233 (OUTLIER) cc_final: 0.4812 (t0) REVERT: A 815 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7547 (mtm110) REVERT: A 1112 ASP cc_start: 0.8442 (m-30) cc_final: 0.7055 (t0) outliers start: 22 outliers final: 14 residues processed: 135 average time/residue: 0.1926 time to fit residues: 38.8765 Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 230 TRP 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 489 LEU Chi-restraints excluded: chain A residue 492 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4703 r_free = 0.4703 target = 0.247135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192497 restraints weight = 11376.165| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.46 r_work: 0.3716 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9948 Z= 0.147 Angle : 0.563 13.705 13479 Z= 0.290 Chirality : 0.041 0.235 1561 Planarity : 0.005 0.066 1676 Dihedral : 4.445 27.960 1318 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.41 % Allowed : 13.28 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.51 (0.24), residues: 1212 helix: 0.62 (0.18), residues: 803 sheet: 0.81 (0.67), residues: 61 loop : -0.13 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 947 HIS 0.009 0.001 HIS A 710 PHE 0.019 0.001 PHE A 352 TYR 0.015 0.001 TYR A1050 ARG 0.004 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 636) hydrogen bonds : angle 4.97410 ( 1854) covalent geometry : bond 0.00321 ( 9948) covalent geometry : angle 0.56278 (13479) ********************** 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 141 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7997 (tt0) cc_final: 0.7275 (pt0) REVERT: A 109 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: A 247 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7084 (mm) REVERT: A 291 TRP cc_start: 0.7957 (m-10) cc_final: 0.7020 (m-90) REVERT: A 301 ASN cc_start: 0.8034 (m110) cc_final: 0.7337 (m-40) REVERT: A 374 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: A 409 MET cc_start: 0.6816 (ppp) cc_final: 0.6466 (mpp) REVERT: A 492 ASN cc_start: 0.5168 (OUTLIER) cc_final: 0.4918 (t0) REVERT: A 1047 ASN cc_start: 0.6406 (t0) cc_final: 0.6047 (t0) REVERT: A 1112 ASP cc_start: 0.8356 (m-30) cc_final: 0.7044 (t0) outliers start: 15 outliers final: 9 residues processed: 136 average time/residue: 0.1957 time to fit residues: 39.3277 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 : 1.002 ------------------------------------------------------------------------------- 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 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 374 GLU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 869 VAL 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 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.246538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190836 restraints weight = 11294.570| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.59 r_work: 0.3708 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9948 Z= 0.158 Angle : 0.565 13.506 13479 Z= 0.291 Chirality : 0.041 0.244 1561 Planarity : 0.004 0.065 1676 Dihedral : 4.420 27.755 1318 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.41 % Allowed : 13.94 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.57 (0.24), residues: 1212 helix: 0.67 (0.18), residues: 803 sheet: 0.88 (0.67), residues: 61 loop : -0.11 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.020 0.002 PHE A 352 TYR 0.015 0.001 TYR A 92 ARG 0.009 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 636) hydrogen bonds : angle 4.95431 ( 1854) covalent geometry : bond 0.00351 ( 9948) covalent geometry : angle 0.56534 (13479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6285.82 seconds wall clock time: 110 minutes 16.00 seconds (6616.00 seconds total)