Starting phenix.real_space_refine on Tue May 13 07:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.map" model { file = "/net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d43_46548/05_2025/9d43_46548.cif" } resolution = 3.39 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= 0.001 sd= 0.018 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 56 5.16 5 C 6290 2.51 5 N 1599 2.21 5 O 1809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9754 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9754 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1189, 9742 Classifications: {'peptide': 1189} Link IDs: {'PTRANS': 44, 'TRANS': 1144} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1189, 9742 Classifications: {'peptide': 1189} Link IDs: {'PTRANS': 44, 'TRANS': 1144} Chain breaks: 2 bond proxies already assigned to first conformer: 9937 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 614 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR A 614 " occ=0.52 Time building chain proxies: 9.26, per 1000 atoms: 0.95 Number of scatterers: 9754 At special positions: 0 Unit cell: (85.49, 113.3, 112.27, 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 56 16.00 O 1809 8.00 N 1599 7.00 C 6290 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: 2.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 4.055A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.527A pdb=" N GLN A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 102 through 121 removed outlier: 3.580A pdb=" N LYS A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.011A pdb=" N LYS A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.577A pdb=" N GLN A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.758A pdb=" N ASN A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 182 through 195 Proline residue: A 188 - end of helix removed outlier: 3.673A pdb=" N VAL A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.765A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.503A pdb=" N LYS A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 235 removed outlier: 3.653A pdb=" N ILE A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.868A pdb=" N THR A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.834A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.507A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.539A pdb=" N GLN A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 304 " --> pdb=" O HIS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.560A pdb=" N LEU A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.814A pdb=" N THR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.882A pdb=" N PHE A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 464 Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.869A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 removed outlier: 3.701A pdb=" N ALA A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 552 removed outlier: 4.330A pdb=" N GLU A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 575 removed outlier: 4.069A pdb=" N ALA A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 Processing helix chain 'A' and resid 603 through 627 removed outlier: 3.855A pdb=" N ALA A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 627 " --> pdb=" O MET A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 634 through 645 Processing helix chain 'A' and resid 649 through 668 removed outlier: 3.720A pdb=" N GLU A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.531A pdb=" N ILE A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Proline residue: A 683 - end of helix Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.515A pdb=" N GLU A 714 " --> pdb=" O VAL A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 751 removed outlier: 3.565A pdb=" N LYS A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 770 through 785 Proline residue: A 782 - end of helix Processing helix chain 'A' and resid 787 through 802 removed outlier: 3.871A pdb=" N HIS A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 removed outlier: 4.124A pdb=" N GLY A 809 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 814 through 823 removed outlier: 3.769A pdb=" N ILE A 823 " --> pdb=" O LYS A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 879 removed outlier: 4.055A pdb=" N GLY A 879 " --> pdb=" O ILE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 886 through 897 removed outlier: 4.394A pdb=" N ASP A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 934 through 960 Proline residue: A 940 - end of helix Proline residue: A 944 - end of helix removed outlier: 3.786A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1003 Processing helix chain 'A' and resid 1018 through 1029 removed outlier: 3.752A pdb=" N GLU A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 Proline residue: A1036 - end of helix removed outlier: 3.535A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1064 Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1071 through 1081 removed outlier: 3.615A pdb=" N ASP A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 Processing helix chain 'A' and resid 1099 through 1118 removed outlier: 3.654A pdb=" N LYS A1116 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1130 removed outlier: 3.932A pdb=" N ARG A1122 " --> pdb=" O TYR A1118 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A1123 " --> pdb=" O PRO A1119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1143 removed outlier: 3.669A pdb=" N SER A1143 " --> pdb=" O ARG A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1166 removed outlier: 3.690A pdb=" N GLN A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A1152 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1153 " --> pdb=" O THR A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1198 618 hydrogen bonds defined for protein. 1828 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: 2.89 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3111 1.35 - 1.47: 2299 1.47 - 1.58: 4466 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 9965 Sorted by residual: bond pdb=" N MET A 627 " pdb=" CA MET A 627 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.16e+00 bond pdb=" C MET A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.336 1.352 -0.016 9.80e-03 1.04e+04 2.81e+00 bond pdb=" CA MET A 627 " pdb=" C MET A 627 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.26e-02 6.30e+03 8.52e-01 bond pdb=" CB MET A 967 " pdb=" CG MET A 967 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.81e-01 bond pdb=" CG ARG A 555 " pdb=" CD ARG A 555 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.70e-01 ... (remaining 9960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13385 2.25 - 4.51: 85 4.51 - 6.76: 23 6.76 - 9.02: 2 9.02 - 11.27: 1 Bond angle restraints: 13496 Sorted by residual: angle pdb=" CB MET A 967 " pdb=" CG MET A 967 " pdb=" SD MET A 967 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA LYS A 20 " pdb=" CB LYS A 20 " pdb=" CG LYS A 20 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" N TRP A 253 " pdb=" CA TRP A 253 " pdb=" C TRP A 253 " ideal model delta sigma weight residual 109.81 116.56 -6.75 2.21e+00 2.05e-01 9.33e+00 angle pdb=" CA MET A 627 " pdb=" C MET A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 118.44 122.99 -4.55 1.59e+00 3.96e-01 8.19e+00 angle pdb=" C LYS A1199 " pdb=" N ASN A1200 " pdb=" CA ASN A1200 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.15e+00 ... (remaining 13491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5289 17.75 - 35.51: 604 35.51 - 53.26: 131 53.26 - 71.02: 24 71.02 - 88.77: 6 Dihedral angle restraints: 6054 sinusoidal: 2508 harmonic: 3546 Sorted by residual: dihedral pdb=" CA ARG A 26 " pdb=" C ARG A 26 " pdb=" N GLN A 27 " pdb=" CA GLN A 27 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" N ASN A 904 " pdb=" CA ASN A 904 " pdb=" CB ASN A 904 " pdb=" CG ASN A 904 " ideal model delta sinusoidal sigma weight residual -60.00 -119.74 59.74 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " pdb=" CE MET A 91 " ideal model delta sinusoidal sigma weight residual -180.00 -122.15 -57.85 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 6051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1311 0.054 - 0.107: 207 0.107 - 0.161: 5 0.161 - 0.214: 0 0.214 - 0.268: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CA MET A 627 " pdb=" N MET A 627 " pdb=" C MET A 627 " pdb=" CB MET A 627 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 767 " pdb=" CA ILE A 767 " pdb=" CG1 ILE A 767 " pdb=" CG2 ILE A 767 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA SER A 888 " pdb=" N SER A 888 " pdb=" C SER A 888 " pdb=" CB SER A 888 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1522 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 26 " -0.099 9.50e-02 1.11e+02 4.48e-02 1.58e+00 pdb=" NE ARG A 26 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 26 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 26 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 26 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 646 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO A 647 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 647 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 647 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 900 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 901 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " -0.016 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 929 2.74 - 3.28: 10104 3.28 - 3.82: 16720 3.82 - 4.36: 17936 4.36 - 4.90: 31167 Nonbonded interactions: 76856 Sorted by model distance: nonbonded pdb=" O VAL A 36 " pdb=" OG SER A 42 " model vdw 2.206 3.040 nonbonded pdb=" O ALA A 416 " pdb=" OH TYR A 420 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" OE1 GLU A 92 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 335 " pdb=" OD2 ASP A 435 " model vdw 2.266 3.040 nonbonded pdb=" O TRP A 121 " pdb=" NH2 ARG A 182 " model vdw 2.267 3.120 ... (remaining 76851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 0.680 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.060 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.002 0.032 9965 Z= 0.092 Angle : 0.483 11.272 13496 Z= 0.237 Chirality : 0.037 0.268 1525 Planarity : 0.003 0.045 1701 Dihedral : 15.655 88.770 3742 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.09 % Allowed : 13.21 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1186 helix: 2.12 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.001 HIS A 288 PHE 0.012 0.001 PHE A 206 TYR 0.017 0.001 TYR A 404 ARG 0.010 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.19958 ( 618) hydrogen bonds : angle 6.00234 ( 1828) covalent geometry : bond 0.00189 ( 9965) covalent geometry : angle 0.48255 (13496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.157 Fit side-chains REVERT: A 775 MET cc_start: 0.8766 (tmm) cc_final: 0.8477 (tmm) REVERT: A 1001 CYS cc_start: 0.8028 (m) cc_final: 0.7238 (m) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.2032 time to fit residues: 14.9099 Evaluate side-chains 40 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.032867 restraints weight = 71262.161| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 5.56 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9965 Z= 0.221 Angle : 0.606 8.487 13496 Z= 0.305 Chirality : 0.040 0.182 1525 Planarity : 0.004 0.038 1701 Dihedral : 4.004 32.081 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.72 % Allowed : 12.85 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.20 (0.26), residues: 1186 helix: 2.24 (0.18), residues: 863 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 747 HIS 0.005 0.002 HIS A 288 PHE 0.010 0.001 PHE A 445 TYR 0.016 0.002 TYR A 404 ARG 0.006 0.001 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 618) hydrogen bonds : angle 4.58471 ( 1828) covalent geometry : bond 0.00520 ( 9965) covalent geometry : angle 0.60557 (13496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 1.108 Fit side-chains REVERT: A 598 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9066 (p0) REVERT: A 627 MET cc_start: 0.8718 (ptm) cc_final: 0.7994 (ppp) REVERT: A 847 MET cc_start: 0.8782 (mmm) cc_final: 0.8551 (tpt) REVERT: A 1001 CYS cc_start: 0.8050 (m) cc_final: 0.7362 (m) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.1734 time to fit residues: 13.0752 Evaluate side-chains 43 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1082 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.034497 restraints weight = 65067.476| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 5.31 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9965 Z= 0.109 Angle : 0.504 8.540 13496 Z= 0.252 Chirality : 0.037 0.171 1525 Planarity : 0.003 0.037 1701 Dihedral : 3.769 17.220 1287 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.81 % Allowed : 13.30 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.25), residues: 1186 helix: 2.37 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 807 HIS 0.003 0.001 HIS A 288 PHE 0.010 0.001 PHE A 206 TYR 0.019 0.001 TYR A 301 ARG 0.007 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 618) hydrogen bonds : angle 4.23792 ( 1828) covalent geometry : bond 0.00241 ( 9965) covalent geometry : angle 0.50442 (13496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.128 Fit side-chains REVERT: A 404 TYR cc_start: 0.8165 (p90) cc_final: 0.7864 (p90) REVERT: A 627 MET cc_start: 0.8783 (ptm) cc_final: 0.8128 (ppp) REVERT: A 1001 CYS cc_start: 0.8154 (m) cc_final: 0.7347 (m) outliers start: 9 outliers final: 3 residues processed: 45 average time/residue: 0.1776 time to fit residues: 13.5385 Evaluate side-chains 41 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.032455 restraints weight = 95297.810| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 6.28 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9965 Z= 0.173 Angle : 0.546 8.115 13496 Z= 0.270 Chirality : 0.038 0.154 1525 Planarity : 0.003 0.040 1701 Dihedral : 3.806 18.066 1287 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.18 % Allowed : 13.57 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.26), residues: 1186 helix: 2.41 (0.18), residues: 861 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.004 0.001 HIS A 288 PHE 0.009 0.001 PHE A 445 TYR 0.016 0.001 TYR A 301 ARG 0.005 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 618) hydrogen bonds : angle 4.24916 ( 1828) covalent geometry : bond 0.00410 ( 9965) covalent geometry : angle 0.54637 (13496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 1.128 Fit side-chains REVERT: A 627 MET cc_start: 0.8922 (ptm) cc_final: 0.8398 (ppp) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.1667 time to fit residues: 13.4115 Evaluate side-chains 46 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 GLN A1019 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.033861 restraints weight = 86354.655| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 6.01 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9965 Z= 0.109 Angle : 0.504 9.779 13496 Z= 0.247 Chirality : 0.037 0.148 1525 Planarity : 0.003 0.038 1701 Dihedral : 3.748 18.625 1287 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.00 % Allowed : 13.76 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.25), residues: 1186 helix: 2.45 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.88 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 807 HIS 0.002 0.001 HIS A 652 PHE 0.010 0.001 PHE A 206 TYR 0.018 0.001 TYR A 301 ARG 0.005 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 618) hydrogen bonds : angle 4.07783 ( 1828) covalent geometry : bond 0.00252 ( 9965) covalent geometry : angle 0.50399 (13496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 1.212 Fit side-chains REVERT: A 627 MET cc_start: 0.8862 (ptm) cc_final: 0.7955 (ppp) REVERT: A 1001 CYS cc_start: 0.8171 (m) cc_final: 0.7489 (m) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1759 time to fit residues: 13.8763 Evaluate side-chains 47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.034958 restraints weight = 55740.292| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 4.94 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9965 Z= 0.105 Angle : 0.493 9.172 13496 Z= 0.242 Chirality : 0.037 0.136 1525 Planarity : 0.003 0.037 1701 Dihedral : 3.678 17.456 1287 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.54 % Allowed : 13.67 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1186 helix: 2.47 (0.18), residues: 867 sheet: None (None), residues: 0 loop : -0.85 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 807 HIS 0.002 0.001 HIS A 652 PHE 0.009 0.001 PHE A 206 TYR 0.018 0.001 TYR A 301 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 618) hydrogen bonds : angle 3.98180 ( 1828) covalent geometry : bond 0.00240 ( 9965) covalent geometry : angle 0.49341 (13496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 1.167 Fit side-chains REVERT: A 627 MET cc_start: 0.8849 (ptm) cc_final: 0.8275 (ppp) REVERT: A 1001 CYS cc_start: 0.8143 (m) cc_final: 0.7517 (m) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.1688 time to fit residues: 14.7236 Evaluate side-chains 51 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.035260 restraints weight = 62026.101| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 5.20 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9965 Z= 0.094 Angle : 0.491 9.140 13496 Z= 0.239 Chirality : 0.036 0.129 1525 Planarity : 0.003 0.036 1701 Dihedral : 3.646 17.648 1287 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 13.85 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1186 helix: 2.47 (0.18), residues: 870 sheet: None (None), residues: 0 loop : -0.83 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.002 0.001 HIS A 652 PHE 0.009 0.001 PHE A 206 TYR 0.019 0.001 TYR A 404 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 618) hydrogen bonds : angle 3.93928 ( 1828) covalent geometry : bond 0.00205 ( 9965) covalent geometry : angle 0.49092 (13496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 1.067 Fit side-chains REVERT: A 452 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7535 (mtp180) REVERT: A 627 MET cc_start: 0.8825 (ptm) cc_final: 0.8252 (ppp) REVERT: A 837 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 1001 CYS cc_start: 0.8147 (m) cc_final: 0.7517 (m) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.1842 time to fit residues: 16.0024 Evaluate side-chains 53 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.034439 restraints weight = 71176.483| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 5.55 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9965 Z= 0.112 Angle : 0.501 9.385 13496 Z= 0.243 Chirality : 0.037 0.122 1525 Planarity : 0.003 0.036 1701 Dihedral : 3.645 17.243 1287 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.45 % Allowed : 13.85 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1186 helix: 2.52 (0.18), residues: 870 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.004 0.001 HIS A 652 PHE 0.009 0.001 PHE A 206 TYR 0.017 0.001 TYR A 301 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 618) hydrogen bonds : angle 3.94385 ( 1828) covalent geometry : bond 0.00263 ( 9965) covalent geometry : angle 0.50088 (13496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 1.147 Fit side-chains REVERT: A 404 TYR cc_start: 0.8109 (p90) cc_final: 0.7864 (p90) REVERT: A 452 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7540 (mtp180) REVERT: A 627 MET cc_start: 0.8831 (ptm) cc_final: 0.8263 (ppp) REVERT: A 837 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7788 (t0) REVERT: A 1001 CYS cc_start: 0.8163 (m) cc_final: 0.7540 (m) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.1987 time to fit residues: 16.3331 Evaluate side-chains 53 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.0470 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.0170 chunk 96 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.035107 restraints weight = 78799.644| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 5.84 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9965 Z= 0.092 Angle : 0.486 9.593 13496 Z= 0.237 Chirality : 0.036 0.118 1525 Planarity : 0.003 0.038 1701 Dihedral : 3.603 17.251 1287 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.36 % Allowed : 13.94 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1186 helix: 2.53 (0.18), residues: 871 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE A 206 TYR 0.017 0.001 TYR A 301 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 618) hydrogen bonds : angle 3.87706 ( 1828) covalent geometry : bond 0.00202 ( 9965) covalent geometry : angle 0.48586 (13496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 1.174 Fit side-chains REVERT: A 452 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7522 (mtp180) REVERT: A 627 MET cc_start: 0.8812 (ptm) cc_final: 0.8297 (ppp) REVERT: A 837 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7734 (t0) REVERT: A 1001 CYS cc_start: 0.8171 (m) cc_final: 0.7548 (m) outliers start: 15 outliers final: 12 residues processed: 53 average time/residue: 0.1892 time to fit residues: 16.0152 Evaluate side-chains 52 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.035437 restraints weight = 59900.291| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 5.13 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9965 Z= 0.097 Angle : 0.492 9.371 13496 Z= 0.240 Chirality : 0.036 0.119 1525 Planarity : 0.003 0.038 1701 Dihedral : 3.580 17.009 1287 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.45 % Allowed : 14.12 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.57 (0.25), residues: 1186 helix: 2.57 (0.18), residues: 868 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.003 0.001 HIS A 652 PHE 0.009 0.001 PHE A 206 TYR 0.020 0.001 TYR A 404 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 618) hydrogen bonds : angle 3.87038 ( 1828) covalent geometry : bond 0.00221 ( 9965) covalent geometry : angle 0.49183 (13496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 1.095 Fit side-chains REVERT: A 452 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: A 627 MET cc_start: 0.8804 (ptm) cc_final: 0.8298 (ppp) REVERT: A 837 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7780 (t0) outliers start: 16 outliers final: 13 residues processed: 51 average time/residue: 0.1991 time to fit residues: 16.2570 Evaluate side-chains 52 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.035959 restraints weight = 54496.753| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 4.90 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9965 Z= 0.092 Angle : 0.489 9.155 13496 Z= 0.238 Chirality : 0.036 0.117 1525 Planarity : 0.003 0.038 1701 Dihedral : 3.552 16.868 1287 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.36 % Allowed : 13.94 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.25), residues: 1186 helix: 2.58 (0.18), residues: 867 sheet: None (None), residues: 0 loop : -0.83 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.001 HIS A 652 PHE 0.010 0.001 PHE A 206 TYR 0.017 0.001 TYR A 301 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 618) hydrogen bonds : angle 3.84356 ( 1828) covalent geometry : bond 0.00205 ( 9965) covalent geometry : angle 0.48946 (13496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.31 seconds wall clock time: 67 minutes 15.11 seconds (4035.11 seconds total)