Starting phenix.real_space_refine on Fri Nov 15 23:27:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_35967_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_35967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_35967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_35967_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/11_2024/8j3w_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-5513/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: 5.75, per 1000 atoms: 0.59 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: 2.92 Conformation dependent library (CDL) restraints added in 1.2 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: 1.06 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: 3.55 Time building geometry restraints manager: 3.19 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: 1.190 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.260 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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= 0.233 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 *********************** 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 : 0.975 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: 0.1974 time to fit residues: 40.6349 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 : 1.103 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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= 0.277 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 *********************** 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 : 1.113 Fit side-chains REVERT: A 102 GLU cc_start: 0.7705 (tt0) cc_final: 0.6919 (tt0) REVERT: A 291 TRP cc_start: 0.7928 (m-10) cc_final: 0.6841 (m-90) REVERT: A 301 ASN cc_start: 0.7828 (m110) cc_final: 0.7335 (m110) REVERT: A 363 LEU cc_start: 0.7875 (mm) cc_final: 0.7605 (mm) outliers start: 9 outliers final: 4 residues processed: 137 average time/residue: 0.2012 time to fit residues: 40.8003 Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9948 Z= 0.223 Angle : 0.574 7.764 13479 Z= 0.305 Chirality : 0.041 0.149 1561 Planarity : 0.005 0.064 1676 Dihedral : 5.002 32.005 1318 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.22 % Allowed : 7.72 % 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: -0.35 (0.24), residues: 1212 helix: 0.03 (0.18), residues: 793 sheet: -0.56 (0.56), residues: 76 loop : -0.42 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 *********************** 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 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.082 Fit side-chains REVERT: A 102 GLU cc_start: 0.7755 (tt0) cc_final: 0.7001 (tt0) REVERT: A 291 TRP cc_start: 0.7889 (m-10) cc_final: 0.6932 (m-10) REVERT: A 301 ASN cc_start: 0.7825 (m110) cc_final: 0.7313 (m110) REVERT: A 435 VAL cc_start: 0.2840 (OUTLIER) cc_final: 0.2551 (t) REVERT: A 1112 ASP cc_start: 0.8140 (m-30) cc_final: 0.7890 (m-30) REVERT: A 1156 LYS cc_start: 0.6941 (tptt) cc_final: 0.6725 (tptt) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.2016 time to fit residues: 42.3197 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 435 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 869 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9948 Z= 0.235 Angle : 0.562 8.390 13479 Z= 0.297 Chirality : 0.041 0.170 1561 Planarity : 0.005 0.062 1676 Dihedral : 4.830 27.677 1318 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 8.95 % Favored : 89.27 % 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: 0.24 (0.18), residues: 797 sheet: -0.61 (0.60), residues: 65 loop : -0.38 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 947 HIS 0.009 0.001 HIS A 934 PHE 0.021 0.002 PHE A 352 TYR 0.015 0.002 TYR A1016 ARG 0.005 0.000 ARG A1189 *********************** 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 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.979 Fit side-chains REVERT: A 102 GLU cc_start: 0.7711 (tt0) cc_final: 0.6923 (pt0) REVERT: A 247 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6967 (mm) REVERT: A 291 TRP cc_start: 0.8022 (m-10) cc_final: 0.6962 (m-90) REVERT: A 301 ASN cc_start: 0.7849 (m110) cc_final: 0.7328 (m110) REVERT: A 435 VAL cc_start: 0.2476 (OUTLIER) cc_final: 0.1895 (t) REVERT: A 1071 VAL cc_start: 0.5846 (OUTLIER) cc_final: 0.5522 (t) REVERT: A 1112 ASP cc_start: 0.8010 (m-30) cc_final: 0.6730 (t0) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.2027 time to fit residues: 41.7746 Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 435 VAL 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 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 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9948 Z= 0.260 Angle : 0.572 11.194 13479 Z= 0.299 Chirality : 0.041 0.153 1561 Planarity : 0.005 0.062 1676 Dihedral : 4.714 28.923 1318 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.45 % Allowed : 8.85 % Favored : 88.70 % 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: -0.01 (0.24), residues: 1212 helix: 0.31 (0.18), residues: 799 sheet: -0.29 (0.59), residues: 66 loop : -0.37 (0.35), residues: 347 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 0.022 0.002 PHE A 352 TYR 0.015 0.002 TYR A 92 ARG 0.003 0.000 ARG A 951 *********************** 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: 26 poor density : 120 time to evaluate : 1.062 Fit side-chains REVERT: A 102 GLU cc_start: 0.7673 (tt0) cc_final: 0.6946 (pt0) REVERT: A 247 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 291 TRP cc_start: 0.7992 (m-10) cc_final: 0.6916 (m-90) REVERT: A 301 ASN cc_start: 0.7847 (m110) cc_final: 0.7277 (m-40) REVERT: A 435 VAL cc_start: 0.2400 (OUTLIER) cc_final: 0.2090 (t) REVERT: A 492 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5144 (t0) REVERT: A 1112 ASP cc_start: 0.8029 (m-30) cc_final: 0.6752 (t0) outliers start: 26 outliers final: 16 residues processed: 137 average time/residue: 0.1951 time to fit residues: 39.7225 Evaluate side-chains 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 435 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9948 Z= 0.276 Angle : 0.590 13.577 13479 Z= 0.305 Chirality : 0.042 0.193 1561 Planarity : 0.005 0.063 1676 Dihedral : 4.669 28.369 1318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 10.08 % Favored : 87.19 % 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: 0.41 (0.18), residues: 798 sheet: -0.08 (0.61), residues: 66 loop : -0.36 (0.35), 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 0.022 0.002 PHE A 352 TYR 0.015 0.002 TYR A 92 ARG 0.004 0.000 ARG A 951 *********************** 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 : 1.100 Fit side-chains REVERT: A 40 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: A 102 GLU cc_start: 0.7653 (tt0) cc_final: 0.6961 (pt0) REVERT: A 109 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6662 (tt0) REVERT: A 184 MET cc_start: 0.7519 (ttm) cc_final: 0.7306 (ttt) REVERT: A 247 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7096 (mm) REVERT: A 291 TRP cc_start: 0.7999 (m-10) cc_final: 0.6872 (m-90) REVERT: A 301 ASN cc_start: 0.7854 (m110) cc_final: 0.7266 (m-40) REVERT: A 492 ASN cc_start: 0.5770 (OUTLIER) cc_final: 0.5265 (t0) REVERT: A 922 ARG cc_start: 0.6493 (tmm160) cc_final: 0.6256 (tmm160) REVERT: A 1112 ASP cc_start: 0.8040 (m-30) cc_final: 0.6847 (t0) REVERT: A 1147 TRP cc_start: 0.7399 (m100) cc_final: 0.7107 (m100) outliers start: 29 outliers final: 18 residues processed: 145 average time/residue: 0.2151 time to fit residues: 45.9844 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 : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 40 GLU 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 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 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 967 SER 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 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9948 Z= 0.212 Angle : 0.563 14.400 13479 Z= 0.291 Chirality : 0.040 0.157 1561 Planarity : 0.004 0.063 1676 Dihedral : 4.586 27.040 1318 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.35 % Allowed : 11.11 % Favored : 86.53 % 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: 0.35 (0.24), residues: 1212 helix: 0.56 (0.18), residues: 800 sheet: -0.02 (0.60), residues: 73 loop : -0.21 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.018 0.001 PHE A 352 TYR 0.014 0.001 TYR A 92 ARG 0.003 0.000 ARG A1189 *********************** 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 157 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.052 Fit side-chains REVERT: A 102 GLU cc_start: 0.7593 (tt0) cc_final: 0.6977 (pt0) REVERT: A 109 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: A 247 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7184 (mm) REVERT: A 291 TRP cc_start: 0.7865 (m-10) cc_final: 0.6909 (m-90) REVERT: A 301 ASN cc_start: 0.7814 (m110) cc_final: 0.7236 (m-40) REVERT: A 492 ASN cc_start: 0.5683 (OUTLIER) cc_final: 0.5356 (t0) REVERT: A 1112 ASP cc_start: 0.8046 (m-30) cc_final: 0.6832 (t0) REVERT: A 1147 TRP cc_start: 0.7418 (m100) cc_final: 0.7127 (m100) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.2031 time to fit residues: 43.8066 Evaluate side-chains 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 373 ILE 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 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 1166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9948 Z= 0.249 Angle : 0.588 15.753 13479 Z= 0.301 Chirality : 0.041 0.163 1561 Planarity : 0.005 0.063 1676 Dihedral : 4.563 28.359 1318 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.54 % Allowed : 11.39 % 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 (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: 0.39 (0.24), residues: 1212 helix: 0.60 (0.18), residues: 800 sheet: 0.06 (0.62), residues: 73 loop : -0.23 (0.36), residues: 339 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 0.014 0.002 TYR A 92 ARG 0.004 0.000 ARG A 951 *********************** 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 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.153 Fit side-chains REVERT: A 40 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6939 (pt0) REVERT: A 102 GLU cc_start: 0.7617 (tt0) cc_final: 0.6998 (pt0) REVERT: A 109 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: A 247 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7192 (mm) REVERT: A 291 TRP cc_start: 0.7892 (m-10) cc_final: 0.6936 (m-90) REVERT: A 301 ASN cc_start: 0.7820 (m110) cc_final: 0.7220 (m-40) REVERT: A 492 ASN cc_start: 0.5706 (OUTLIER) cc_final: 0.5385 (t0) REVERT: A 1112 ASP cc_start: 0.8060 (m-30) cc_final: 0.6845 (t0) REVERT: A 1147 TRP cc_start: 0.7432 (m100) cc_final: 0.7152 (m100) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.1981 time to fit residues: 41.5538 Evaluate side-chains 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 40 GLU 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 292 GLU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 373 ILE 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 1166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9948 Z= 0.237 Angle : 0.596 15.362 13479 Z= 0.303 Chirality : 0.041 0.159 1561 Planarity : 0.005 0.062 1676 Dihedral : 4.533 28.636 1318 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.45 % Allowed : 12.34 % 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 (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: 0.47 (0.24), residues: 1212 helix: 0.64 (0.18), residues: 802 sheet: 0.12 (0.62), residues: 73 loop : -0.16 (0.36), residues: 337 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 0.001 PHE A 352 TYR 0.015 0.002 TYR A 92 ARG 0.008 0.000 ARG A 815 *********************** 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 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.195 Fit side-chains REVERT: A 40 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6964 (pt0) REVERT: A 102 GLU cc_start: 0.7607 (tt0) cc_final: 0.7008 (pt0) REVERT: A 109 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: A 247 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (mm) REVERT: A 291 TRP cc_start: 0.7894 (m-10) cc_final: 0.6973 (m-90) REVERT: A 301 ASN cc_start: 0.7834 (m110) cc_final: 0.7258 (m-40) REVERT: A 492 ASN cc_start: 0.5740 (OUTLIER) cc_final: 0.5265 (t0) REVERT: A 815 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7429 (mtm110) REVERT: A 1112 ASP cc_start: 0.8083 (m-30) cc_final: 0.6837 (t0) outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 0.2056 time to fit residues: 41.7056 Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 40 GLU 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 326 SER Chi-restraints excluded: chain A residue 373 ILE 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 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 54 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 710 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9948 Z= 0.232 Angle : 0.594 12.439 13479 Z= 0.302 Chirality : 0.041 0.216 1561 Planarity : 0.004 0.063 1676 Dihedral : 4.492 28.555 1318 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.07 % Allowed : 12.81 % 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 (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: 0.67 (0.18), residues: 802 sheet: 0.16 (0.63), residues: 73 loop : -0.14 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.020 0.001 PHE A 352 TYR 0.014 0.001 TYR A 92 ARG 0.007 0.000 ARG A 815 ********************** 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 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.047 Fit side-chains REVERT: A 40 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6962 (pt0) REVERT: A 102 GLU cc_start: 0.7573 (tt0) cc_final: 0.7022 (pt0) REVERT: A 109 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6725 (tt0) REVERT: A 247 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7353 (mm) REVERT: A 291 TRP cc_start: 0.7890 (m-10) cc_final: 0.6965 (m-90) REVERT: A 301 ASN cc_start: 0.7816 (m110) cc_final: 0.7234 (m-40) REVERT: A 492 ASN cc_start: 0.5739 (OUTLIER) cc_final: 0.5459 (t0) REVERT: A 1112 ASP cc_start: 0.8038 (m-30) cc_final: 0.6858 (t0) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.1927 time to fit residues: 38.4932 Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 40 GLU 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 326 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 759 LEU 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 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.246631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191741 restraints weight = 11107.874| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 3.40 r_work: 0.3703 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9948 Z= 0.240 Angle : 0.586 10.000 13479 Z= 0.300 Chirality : 0.041 0.186 1561 Planarity : 0.004 0.063 1676 Dihedral : 4.451 28.465 1318 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 (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: 0.52 (0.24), residues: 1212 helix: 0.66 (0.18), residues: 803 sheet: 0.23 (0.63), residues: 73 loop : -0.11 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.022 0.002 PHE A 112 TYR 0.014 0.002 TYR A 92 ARG 0.009 0.000 ARG A 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.96 seconds wall clock time: 42 minutes 27.54 seconds (2547.54 seconds total)