Starting phenix.real_space_refine on Wed Apr 30 20:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d43_46548/04_2025/9d43_46548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d43_46548/04_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_46548/04_2025/9d43_46548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d43_46548/04_2025/9d43_46548.map" model { file = "/net/cci-nas-00/data/ceres_data/9d43_46548/04_2025/9d43_46548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d43_46548/04_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-5669/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: 10.15, per 1000 atoms: 1.04 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: 2.37 Conformation dependent library (CDL) restraints added in 2.4 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: 1.08 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: 3.25 Time building geometry restraints manager: 2.83 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.660 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- 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 : 1.073 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: 0.2070 time to fit residues: 15.0945 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 : 1.177 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.032861 restraints weight = 71262.162| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 5.57 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 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 = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- 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 : 1.170 Fit side-chains REVERT: A 598 ASN cc_start: 0.9444 (OUTLIER) cc_final: 0.9068 (p0) REVERT: A 627 MET cc_start: 0.8718 (ptm) cc_final: 0.7993 (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: 0.7363 (m) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.1868 time to fit residues: 13.9641 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 : 1.178 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 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: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.049233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.034339 restraints weight = 65057.193| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 5.33 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1698 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= 0.110 Angle : 0.506 8.623 13496 Z= 0.253 Chirality : 0.037 0.170 1525 Planarity : 0.003 0.037 1701 Dihedral : 3.776 17.226 1287 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.81 % Allowed : 13.21 % Favored : 85.97 % 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 0.006 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 618) hydrogen bonds : angle 4.25067 ( 1828) covalent geometry : bond 0.00245 ( 9965) covalent geometry : angle 0.50575 (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 : 1.084 Fit side-chains REVERT: A 404 TYR cc_start: 0.8165 (p90) cc_final: 0.7823 (p90) REVERT: A 627 MET cc_start: 0.8782 (ptm) cc_final: 0.8124 (ppp) REVERT: A 1001 CYS cc_start: 0.8156 (m) cc_final: 0.7348 (m) outliers start: 9 outliers final: 3 residues processed: 45 average time/residue: 0.1738 time to fit residues: 13.0796 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 : 1.066 ------------------------------------------------------------------------------- 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 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.033104 restraints weight = 94932.441| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 6.26 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9965 Z= 0.144 Angle : 0.529 8.760 13496 Z= 0.260 Chirality : 0.038 0.155 1525 Planarity : 0.003 0.039 1701 Dihedral : 3.757 17.726 1287 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: 2.37 (0.25), residues: 1186 helix: 2.42 (0.18), residues: 863 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 288 PHE 0.008 0.001 PHE A 570 TYR 0.018 0.001 TYR A 301 ARG 0.005 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 618) hydrogen bonds : angle 4.17916 ( 1828) covalent geometry : bond 0.00339 ( 9965) covalent geometry : angle 0.52905 (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 51 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 1.215 Fit side-chains REVERT: A 627 MET cc_start: 0.8892 (ptm) cc_final: 0.8316 (ppp) REVERT: A 1001 CYS cc_start: 0.8093 (m) cc_final: 0.7421 (m) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.1738 time to fit residues: 14.2663 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 : 1.125 ------------------------------------------------------------------------------- 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 418 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 652 HIS 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: 0.0670 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.049705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.034507 restraints weight = 86473.562| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 6.01 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2181 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= 0.098 Angle : 0.493 8.715 13496 Z= 0.242 Chirality : 0.037 0.144 1525 Planarity : 0.003 0.037 1701 Dihedral : 3.693 18.290 1287 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.00 % Allowed : 13.85 % Favored : 85.16 % 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: 2.43 (0.25), residues: 1186 helix: 2.48 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 807 HIS 0.002 0.000 HIS A 288 PHE 0.009 0.001 PHE A 570 TYR 0.018 0.001 TYR A 301 ARG 0.005 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 618) hydrogen bonds : angle 4.02106 ( 1828) covalent geometry : bond 0.00216 ( 9965) covalent geometry : angle 0.49302 (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 : 1.144 Fit side-chains REVERT: A 627 MET cc_start: 0.8865 (ptm) cc_final: 0.8543 (ppp) REVERT: A 1001 CYS cc_start: 0.8149 (m) cc_final: 0.7309 (m) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1968 time to fit residues: 15.6577 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 : 1.712 ------------------------------------------------------------------------------- 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 418 VAL 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: 1.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.048544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.034010 restraints weight = 56033.381| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 4.92 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9965 Z= 0.141 Angle : 0.517 8.605 13496 Z= 0.253 Chirality : 0.037 0.135 1525 Planarity : 0.003 0.037 1701 Dihedral : 3.700 17.533 1287 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.54 % Allowed : 13.57 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.26), residues: 1186 helix: 2.50 (0.18), residues: 866 sheet: None (None), residues: 0 loop : -0.84 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 288 PHE 0.009 0.001 PHE A 570 TYR 0.017 0.001 TYR A 301 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 618) hydrogen bonds : angle 4.06939 ( 1828) covalent geometry : bond 0.00336 ( 9965) covalent geometry : angle 0.51718 (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 54 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 1.181 Fit side-chains REVERT: A 627 MET cc_start: 0.8852 (ptm) cc_final: 0.8226 (ppp) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.2086 time to fit residues: 18.6062 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 : 1.315 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 12 optimal weight: 0.0980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.050138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.035459 restraints weight = 61781.617| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 5.22 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 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 = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2446 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 : 0.487 9.083 13496 Z= 0.239 Chirality : 0.036 0.125 1525 Planarity : 0.003 0.036 1701 Dihedral : 3.647 17.341 1287 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 2.48 (0.25), residues: 1186 helix: 2.49 (0.18), residues: 870 sheet: None (None), residues: 0 loop : -0.88 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 807 HIS 0.001 0.000 HIS A 288 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 0.02819 ( 618) hydrogen bonds : angle 3.92682 ( 1828) covalent geometry : bond 0.00191 ( 9965) covalent geometry : angle 0.48735 (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 55 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 1.079 Fit side-chains REVERT: A 452 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7528 (mtp180) REVERT: A 627 MET cc_start: 0.8817 (ptm) cc_final: 0.7928 (ppp) REVERT: A 837 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7850 (t0) REVERT: A 1001 CYS cc_start: 0.8121 (m) cc_final: 0.7495 (m) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1989 time to fit residues: 16.3974 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 : 1.346 ------------------------------------------------------------------------------- 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8945 > 50: distance: 14 - 18: 22.523 distance: 18 - 19: 35.746 distance: 19 - 20: 11.990 distance: 19 - 22: 25.132 distance: 20 - 21: 15.921 distance: 20 - 24: 21.552 distance: 22 - 23: 39.934 distance: 24 - 25: 36.802 distance: 25 - 26: 48.683 distance: 25 - 28: 40.971 distance: 26 - 27: 57.788 distance: 26 - 34: 11.374 distance: 28 - 29: 23.102 distance: 29 - 30: 51.085 distance: 29 - 31: 32.341 distance: 30 - 32: 31.250 distance: 31 - 33: 32.899 distance: 32 - 33: 29.029 distance: 34 - 35: 40.739 distance: 35 - 36: 15.117 distance: 35 - 38: 46.418 distance: 36 - 37: 42.282 distance: 36 - 42: 5.965 distance: 38 - 39: 28.207 distance: 39 - 40: 16.533 distance: 40 - 41: 34.247 distance: 42 - 43: 16.344 distance: 43 - 44: 8.747 distance: 43 - 46: 37.905 distance: 44 - 45: 54.869 distance: 44 - 50: 42.061 distance: 46 - 47: 41.386 distance: 47 - 48: 15.570 distance: 47 - 49: 23.431 distance: 50 - 51: 32.226 distance: 51 - 52: 36.070 distance: 51 - 54: 33.724 distance: 52 - 53: 31.810 distance: 52 - 58: 38.003 distance: 54 - 55: 15.051 distance: 55 - 56: 35.042 distance: 55 - 57: 51.969 distance: 58 - 59: 29.559 distance: 59 - 60: 17.912 distance: 59 - 62: 33.187 distance: 60 - 61: 5.310 distance: 60 - 66: 28.966 distance: 62 - 63: 41.128 distance: 63 - 64: 7.944 distance: 64 - 65: 16.031 distance: 66 - 67: 12.061 distance: 67 - 68: 47.670 distance: 67 - 70: 24.561 distance: 68 - 69: 55.113 distance: 70 - 71: 15.898 distance: 71 - 72: 21.865 distance: 71 - 73: 35.799 distance: 75 - 76: 14.166 distance: 75 - 78: 40.149 distance: 76 - 77: 15.920 distance: 76 - 82: 43.809 distance: 79 - 80: 54.964 distance: 80 - 81: 25.410 distance: 83 - 86: 7.180 distance: 84 - 85: 18.377 distance: 84 - 90: 40.226 distance: 86 - 87: 26.123 distance: 87 - 88: 14.736 distance: 87 - 89: 38.694 distance: 90 - 96: 49.814 distance: 91 - 92: 55.030 distance: 91 - 94: 49.743 distance: 92 - 93: 41.411 distance: 92 - 97: 22.309 distance: 94 - 95: 13.770 distance: 95 - 96: 22.736