Starting phenix.real_space_refine on Fri Aug 22 19:57:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg4_33807/08_2025/7yg4_33807.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 40 5.16 5 C 4779 2.51 5 N 1270 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6432 Classifications: {'peptide': 819} Link IDs: {'PTRANS': 27, 'TRANS': 791} Chain breaks: 7 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 539 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "E" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 539 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Time building chain proxies: 1.85, per 1000 atoms: 0.25 Number of scatterers: 7510 At special positions: 0 Unit cell: (91.8, 113.05, 142.8, 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 40 16.00 O 1421 8.00 N 1270 7.00 C 4779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 397.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 397 through 413 Proline residue: A 408 - end of helix removed outlier: 3.882A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 452 through 458 removed outlier: 3.799A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 4.240A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.688A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.893A pdb=" N LEU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.636A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.864A pdb=" N ALA A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.606A pdb=" N LEU A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 575 removed outlier: 3.516A pdb=" N THR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 removed outlier: 4.740A pdb=" N ARG A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 681 through 689 removed outlier: 4.095A pdb=" N LEU A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.833A pdb=" N VAL A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 708 " --> pdb=" O THR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.523A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 724 " --> pdb=" O PHE A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 737 removed outlier: 3.596A pdb=" N ASN A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.608A pdb=" N PHE A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.571A pdb=" N THR A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.747A pdb=" N ALA A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.602A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.622A pdb=" N ASN A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 882 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.716A pdb=" N LEU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 893 " --> pdb=" O GLN A 889 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 929 through 941 removed outlier: 3.614A pdb=" N LEU A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 941 " --> pdb=" O LEU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.649A pdb=" N LEU A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 984 removed outlier: 3.590A pdb=" N ILE A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.799A pdb=" N ARG A 988 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1021 removed outlier: 3.860A pdb=" N ARG A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1044 removed outlier: 3.524A pdb=" N LEU A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1074 removed outlier: 3.658A pdb=" N ILE A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A1074 " --> pdb=" O THR A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1089 through 1103 Processing helix chain 'A' and resid 1109 through 1120 Processing helix chain 'A' and resid 1138 through 1154 removed outlier: 4.067A pdb=" N VAL A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A1154 " --> pdb=" O HIS A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.591A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A1167 " --> pdb=" O ARG A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1188 removed outlier: 4.136A pdb=" N ALA A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1210 removed outlier: 3.534A pdb=" N ALA A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A1210 " --> pdb=" O ASP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 removed outlier: 3.585A pdb=" N SER A1234 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 3.590A pdb=" N ALA A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A1248 " --> pdb=" O HIS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1269 removed outlier: 3.798A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1292 Processing helix chain 'B' and resid 172 through 237 removed outlier: 4.310A pdb=" N LYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 237 removed outlier: 3.997A pdb=" N SER E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2473 1.34 - 1.46: 1120 1.46 - 1.58: 3958 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7613 Sorted by residual: bond pdb=" CB MET E 218 " pdb=" CG MET E 218 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ILE B 222 " pdb=" CG2 ILE B 222 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB ARG B 233 " pdb=" CG ARG B 233 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CB GLN B 226 " pdb=" CG GLN B 226 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CG1 ILE A 855 " pdb=" CD1 ILE A 855 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 ... (remaining 7608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 10175 2.26 - 4.52: 101 4.52 - 6.79: 14 6.79 - 9.05: 3 9.05 - 11.31: 1 Bond angle restraints: 10294 Sorted by residual: angle pdb=" CA LEU E 229 " pdb=" CB LEU E 229 " pdb=" CG LEU E 229 " ideal model delta sigma weight residual 116.30 127.61 -11.31 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C PRO A 668 " pdb=" N TYR A 669 " pdb=" CA TYR A 669 " ideal model delta sigma weight residual 120.09 123.97 -3.88 1.25e+00 6.40e-01 9.65e+00 angle pdb=" N GLN B 210 " pdb=" CA GLN B 210 " pdb=" CB GLN B 210 " ideal model delta sigma weight residual 110.28 114.70 -4.42 1.55e+00 4.16e-01 8.13e+00 angle pdb=" N GLU B 216 " pdb=" CA GLU B 216 " pdb=" CB GLU B 216 " ideal model delta sigma weight residual 110.28 114.65 -4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C VAL B 215 " pdb=" N GLU B 216 " pdb=" CA GLU B 216 " ideal model delta sigma weight residual 120.31 116.04 4.27 1.52e+00 4.33e-01 7.90e+00 ... (remaining 10289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4136 18.00 - 35.99: 427 35.99 - 53.99: 81 53.99 - 71.98: 23 71.98 - 89.98: 13 Dihedral angle restraints: 4680 sinusoidal: 1898 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU E 196 " pdb=" C GLU E 196 " pdb=" N LEU E 197 " pdb=" CA LEU E 197 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A1258 " pdb=" CG GLU A1258 " pdb=" CD GLU A1258 " pdb=" OE1 GLU A1258 " ideal model delta sinusoidal sigma weight residual 0.00 89.98 -89.98 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CG ARG A 396 " pdb=" CD ARG A 396 " pdb=" NE ARG A 396 " pdb=" CZ ARG A 396 " ideal model delta sinusoidal sigma weight residual -90.00 -134.46 44.46 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 945 0.039 - 0.079: 251 0.079 - 0.118: 43 0.118 - 0.158: 8 0.158 - 0.197: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA GLU E 196 " pdb=" N GLU E 196 " pdb=" C GLU E 196 " pdb=" CB GLU E 196 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE A 691 " pdb=" N ILE A 691 " pdb=" C ILE A 691 " pdb=" CB ILE A 691 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA GLN B 210 " pdb=" N GLN B 210 " pdb=" C GLN B 210 " pdb=" CB GLN B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1246 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1105 " 0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A1106 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A1106 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1106 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 691 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO A 692 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 692 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 692 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 216 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" CD GLU B 216 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU B 216 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 216 " -0.013 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 119 2.70 - 3.25: 7578 3.25 - 3.80: 11361 3.80 - 4.35: 14990 4.35 - 4.90: 24770 Nonbonded interactions: 58818 Sorted by model distance: nonbonded pdb=" NZ LYS B 198 " pdb=" OG SER E 194 " model vdw 2.147 3.120 nonbonded pdb=" O ILE A 511 " pdb=" OH TYR A 675 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG B 233 " pdb=" OE1 GLN E 228 " model vdw 2.262 3.120 nonbonded pdb=" O LEU A1122 " pdb=" NH2 ARG A1144 " model vdw 2.268 3.120 nonbonded pdb=" O GLU A 883 " pdb=" NE2 GLN A 889 " model vdw 2.324 3.120 ... (remaining 58813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.003 0.050 7613 Z= 0.148 Angle : 0.584 11.309 10294 Z= 0.307 Chirality : 0.037 0.197 1249 Planarity : 0.005 0.090 1296 Dihedral : 15.981 89.976 2858 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.28), residues: 933 helix: 0.85 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1163 TYR 0.010 0.001 TYR B 193 PHE 0.011 0.001 PHE A 775 TRP 0.004 0.001 TRP A 760 HIS 0.006 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7613) covalent geometry : angle 0.58422 (10294) hydrogen bonds : bond 0.20887 ( 509) hydrogen bonds : angle 6.20494 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.262 Fit side-chains REVERT: A 524 ARG cc_start: 0.5525 (mpp-170) cc_final: 0.5169 (mpp-170) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0684 time to fit residues: 8.3679 Evaluate side-chains 74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 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 779 GLN A1088 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115265 restraints weight = 11640.664| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.55 r_work: 0.3448 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7613 Z= 0.158 Angle : 0.585 13.544 10294 Z= 0.296 Chirality : 0.037 0.139 1249 Planarity : 0.005 0.064 1296 Dihedral : 3.815 15.145 999 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.59 % Allowed : 7.52 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.27), residues: 933 helix: 1.17 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 935 TYR 0.013 0.001 TYR B 193 PHE 0.010 0.001 PHE A 775 TRP 0.010 0.001 TRP A1091 HIS 0.004 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7613) covalent geometry : angle 0.58527 (10294) hydrogen bonds : bond 0.05873 ( 509) hydrogen bonds : angle 4.16610 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 524 ARG cc_start: 0.5422 (mpp-170) cc_final: 0.5039 (mpp-170) REVERT: A 725 TYR cc_start: 0.6970 (t80) cc_final: 0.6657 (t80) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.0642 time to fit residues: 7.9051 Evaluate side-chains 79 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.153179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.115597 restraints weight = 11623.059| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.41 r_work: 0.3457 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7613 Z= 0.134 Angle : 0.529 10.402 10294 Z= 0.266 Chirality : 0.036 0.149 1249 Planarity : 0.004 0.056 1296 Dihedral : 3.678 14.412 999 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.29 % Allowed : 10.46 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.28), residues: 933 helix: 1.51 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.010 0.001 TYR A 560 PHE 0.010 0.001 PHE A1071 TRP 0.006 0.001 TRP A1091 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7613) covalent geometry : angle 0.52890 (10294) hydrogen bonds : bond 0.05011 ( 509) hydrogen bonds : angle 3.85742 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8623 (m) cc_final: 0.8306 (p) REVERT: A 524 ARG cc_start: 0.5388 (mpp-170) cc_final: 0.5065 (mpp-170) outliers start: 11 outliers final: 5 residues processed: 96 average time/residue: 0.0809 time to fit residues: 10.7555 Evaluate side-chains 82 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115378 restraints weight = 11917.021| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.43 r_work: 0.3452 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7613 Z= 0.132 Angle : 0.529 13.528 10294 Z= 0.264 Chirality : 0.036 0.143 1249 Planarity : 0.005 0.089 1296 Dihedral : 3.640 14.458 999 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.88 % Allowed : 11.28 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.28), residues: 933 helix: 1.58 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 233 TYR 0.011 0.001 TYR A 560 PHE 0.010 0.001 PHE A1071 TRP 0.006 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7613) covalent geometry : angle 0.52876 (10294) hydrogen bonds : bond 0.04721 ( 509) hydrogen bonds : angle 3.75566 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8621 (m) cc_final: 0.8326 (p) REVERT: A 524 ARG cc_start: 0.5512 (mpp-170) cc_final: 0.5157 (mpp-170) REVERT: A 1001 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7721 (p) REVERT: B 228 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7198 (tm-30) outliers start: 16 outliers final: 9 residues processed: 93 average time/residue: 0.0623 time to fit residues: 8.3704 Evaluate side-chains 87 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115937 restraints weight = 11803.222| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.42 r_work: 0.3452 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7613 Z= 0.119 Angle : 0.505 12.277 10294 Z= 0.254 Chirality : 0.035 0.143 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.546 14.104 999 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.65 % Allowed : 12.69 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.28), residues: 933 helix: 1.72 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.010 0.001 TYR A 560 PHE 0.010 0.001 PHE A1109 TRP 0.006 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7613) covalent geometry : angle 0.50511 (10294) hydrogen bonds : bond 0.04423 ( 509) hydrogen bonds : angle 3.64806 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8657 (m) cc_final: 0.8361 (p) REVERT: A 524 ARG cc_start: 0.5502 (mpp-170) cc_final: 0.5159 (mpp-170) REVERT: A 711 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 1001 THR cc_start: 0.8109 (m) cc_final: 0.7800 (p) REVERT: B 210 GLN cc_start: 0.7109 (mp-120) cc_final: 0.6902 (mp10) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.0756 time to fit residues: 9.8558 Evaluate side-chains 90 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 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 779 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.154102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116384 restraints weight = 11729.457| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.42 r_work: 0.3464 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7613 Z= 0.122 Angle : 0.514 12.438 10294 Z= 0.257 Chirality : 0.035 0.131 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.491 13.260 999 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.88 % Allowed : 13.51 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.28), residues: 933 helix: 1.80 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 233 TYR 0.010 0.001 TYR A 560 PHE 0.008 0.001 PHE A1071 TRP 0.005 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7613) covalent geometry : angle 0.51410 (10294) hydrogen bonds : bond 0.04350 ( 509) hydrogen bonds : angle 3.61273 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 THR cc_start: 0.8608 (m) cc_final: 0.8319 (p) REVERT: A 524 ARG cc_start: 0.5499 (mpp-170) cc_final: 0.5166 (mpp-170) REVERT: A 711 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 993 MET cc_start: 0.3260 (mmt) cc_final: 0.1486 (mmt) REVERT: A 1001 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 1176 MET cc_start: 0.6835 (mmp) cc_final: 0.6494 (mmm) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.0775 time to fit residues: 10.3276 Evaluate side-chains 93 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116541 restraints weight = 11791.044| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.37 r_work: 0.3467 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7613 Z= 0.122 Angle : 0.515 12.744 10294 Z= 0.256 Chirality : 0.035 0.131 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.461 13.668 999 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.23 % Allowed : 14.10 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.28), residues: 933 helix: 1.87 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.010 0.001 TYR A 560 PHE 0.011 0.001 PHE A1109 TRP 0.005 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7613) covalent geometry : angle 0.51452 (10294) hydrogen bonds : bond 0.04334 ( 509) hydrogen bonds : angle 3.58069 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8636 (m) cc_final: 0.8362 (p) REVERT: A 524 ARG cc_start: 0.5551 (mpp-170) cc_final: 0.5211 (mpp-170) REVERT: A 711 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 993 MET cc_start: 0.3242 (mmt) cc_final: 0.1487 (mmt) REVERT: A 1001 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 1176 MET cc_start: 0.6875 (mmp) cc_final: 0.6565 (mmm) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.0816 time to fit residues: 10.8416 Evaluate side-chains 94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.153669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116279 restraints weight = 11696.840| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.36 r_work: 0.3475 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7613 Z= 0.132 Angle : 0.538 13.236 10294 Z= 0.271 Chirality : 0.036 0.188 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.469 13.490 999 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.12 % Allowed : 14.57 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.28), residues: 933 helix: 1.81 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.011 0.001 TYR A 560 PHE 0.007 0.001 PHE A1071 TRP 0.005 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7613) covalent geometry : angle 0.53760 (10294) hydrogen bonds : bond 0.04448 ( 509) hydrogen bonds : angle 3.63861 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.298 Fit side-chains REVERT: A 475 THR cc_start: 0.8642 (m) cc_final: 0.8364 (p) REVERT: A 524 ARG cc_start: 0.5539 (mpp-170) cc_final: 0.5166 (mpp-170) REVERT: A 711 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 993 MET cc_start: 0.3192 (mmt) cc_final: 0.1434 (mmt) REVERT: A 1001 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7839 (p) REVERT: E 216 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6393 (pt0) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.0772 time to fit residues: 10.7972 Evaluate side-chains 94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.153958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116540 restraints weight = 11656.571| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.35 r_work: 0.3478 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7613 Z= 0.124 Angle : 0.540 13.535 10294 Z= 0.275 Chirality : 0.036 0.193 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.449 13.142 999 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.88 % Allowed : 14.69 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.28), residues: 933 helix: 1.83 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.010 0.001 TYR A 560 PHE 0.007 0.001 PHE A1109 TRP 0.005 0.001 TRP A1091 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7613) covalent geometry : angle 0.54038 (10294) hydrogen bonds : bond 0.04357 ( 509) hydrogen bonds : angle 3.64642 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.275 Fit side-chains REVERT: A 475 THR cc_start: 0.8646 (m) cc_final: 0.8377 (p) REVERT: A 524 ARG cc_start: 0.5555 (mpp-170) cc_final: 0.5167 (mpp-170) REVERT: A 711 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 993 MET cc_start: 0.3181 (mmt) cc_final: 0.1452 (mmt) REVERT: A 1001 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7846 (p) REVERT: E 216 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6405 (pt0) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.0874 time to fit residues: 11.3663 Evaluate side-chains 91 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.0050 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.154863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117270 restraints weight = 11676.374| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.40 r_work: 0.3478 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7613 Z= 0.123 Angle : 0.559 13.657 10294 Z= 0.283 Chirality : 0.036 0.179 1249 Planarity : 0.004 0.050 1296 Dihedral : 3.426 12.843 999 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.12 % Allowed : 14.69 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.28), residues: 933 helix: 1.83 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.009 0.001 TYR A 560 PHE 0.008 0.001 PHE A1109 TRP 0.005 0.001 TRP A1091 HIS 0.007 0.001 HIS A1175 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7613) covalent geometry : angle 0.55852 (10294) hydrogen bonds : bond 0.04248 ( 509) hydrogen bonds : angle 3.65572 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 THR cc_start: 0.8625 (m) cc_final: 0.8358 (p) REVERT: A 524 ARG cc_start: 0.5509 (mpp-170) cc_final: 0.5123 (mpp-170) REVERT: A 711 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 993 MET cc_start: 0.3110 (mmt) cc_final: 0.1431 (mmt) REVERT: A 1001 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7868 (p) outliers start: 18 outliers final: 13 residues processed: 89 average time/residue: 0.0836 time to fit residues: 10.5110 Evaluate side-chains 93 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.153388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115753 restraints weight = 11734.765| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.40 r_work: 0.3453 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7613 Z= 0.145 Angle : 0.572 13.519 10294 Z= 0.290 Chirality : 0.037 0.191 1249 Planarity : 0.004 0.049 1296 Dihedral : 3.503 13.056 999 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 14.45 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.28), residues: 933 helix: 1.69 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.013 0.001 TYR A 560 PHE 0.008 0.001 PHE A1071 TRP 0.005 0.001 TRP A1091 HIS 0.004 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7613) covalent geometry : angle 0.57173 (10294) hydrogen bonds : bond 0.04681 ( 509) hydrogen bonds : angle 3.71518 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.78 seconds wall clock time: 31 minutes 3.77 seconds (1863.77 seconds total)